Pyridine-pyrimidine amides that prevent HGF-induced epithelial scattering by two distinct mechanisms.

PubMed

Siddiqui-Jain, Adam; Hoj, Jacob P; Hargiss, J Blade; Hoj, Taylor H; Payne, Carter J; Ritchie, Collin A; Herron, Steven R; Quinn, Colette; Schuler, Jeffrey T; Hansen, Marc D H

2017-09-01

Stimulation of cultured epithelial cells with scatter factor/hepatocyte growth factor (HGF) results in individual cells detaching and assuming a migratory and invasive phenotype. Epithelial scattering recapitulates cancer progression and studies have implicated HGF signaling as a driver of cancer metastasis. Inhibitors of HGF signaling have been proposed to act as anti-cancer agents. We previously screened a small molecule library for compounds that block HGF-induced epithelial scattering. Most hits identified in this screen exhibit anti-mitotic properties. Here we assess the biological mechanism of a compound that blocks HGF-induced scattering with limited anti-mitotic activity. Analogs of this compound have one of two distinct activities: inhibiting either cell migration or cell proliferation with cell cycle arrest in G2/M. Each activity bears unique structure-activity relationships. The mechanism of action of anti-mitotic compounds is by inhibition of microtubule polymerization; these compounds entropically and enthalpically bind tubulin in the colchicine binding site, generating a conformational change in the tubulin dimer. Copyright © 2017 Elsevier Ltd. All rights reserved.

Pyrrole-Based Antitubulin Agents: Two Distinct Binding Modalities Are Predicted for C-2 Analogues in the Colchicine Site

PubMed Central

2011-01-01

3,5-Dibromo-4-(3,4-dimethoxyphenyl)-1H-pyrrole-2-carboxylic acid ethyl ester is a promising antitubulin lead agent that targets the colchicine site of tubulin. C-2 analogues were synthesized and tested for microtubule depolymerizing and antiproliferative activity. Molecular modeling studies using both GOLD docking and HINT (Hydropathic INTeraction) scoring revealed two distinct binding modes that explain the structure–activity relationships and are in accord with the structural basis of colchicine binding to tubulin. The binding mode of higher activity compounds is buried deeper in the site and overlaps well with rings A and C of colchicine, while the lower activity binding mode shows fewer critical contacts with tubulin. The model distinguishes highly active compounds from those with weaker activities and provides novel insights into the colchicine site and compound design. PMID:22611477

Alkaline earth-based coordination polymers derived from a cyclotriphosphazene-functionalized hexacarboxylate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ling, Yajing; Bai, Dongjie; Feng, Yunlong

Combination of hexakis(4-carboxylatephenoxy)cyclotriphosphazene with alkaline earth ions of increasing ionic radii (Mg{sup 2+}, Ca{sup 2+} and Ba{sup 2+}) under different solvothermal conditions yielded three new coordination polymers, and their crystal structures were determined by single-crystal X-ray diffraction analysis. The magnesium compound displays a three dimensional (3D) network structure constructed from the deprotonated ligand and the secondary building block Mg(COO){sub 4}, which can be rationalized as a (4,6)-connected topological net with the Schläfli symbol of (4{sup 4}·6{sup 2}){sub 3}(4{sup 9}·6{sup 6}){sub 2}. The calcium compound consists of 1D infinite “Ca-O” inorganic chains connected by the deprotonated ligands to from a 3Dmore » framework. The barium compound exhibits a 3D framework in which 1D “Ba-O” inorganic chains are connected together by the deprotonated organic linkers. Due to the semi-rigid nature, the ligand adopts distinctly different conformations in the three compounds. The metal ions’ influence exerted on the final structure of the resulting coordination polymers is also discussed. When the radii of alkaline earth ions increases descending down the group from Mg(II) to Ba(II), the coordination number becomes larger and more versatile: from 6 in the magnesium compound, to 6,7 and 10 in the calcium compound, and to 8 and 9 in the barium compound, thus substantially influencing the resulting final framework structures. Also, the photophysical properties were investigated systematically, revealing that the three compounds are photoluminscent in the solid state at room temperature. This work demonstrates that although the multiplicity of conformation in the hexacarboxylate ligand based on the inorganic scaffold cyclotriphosphazene makes it difficult to predict how this ligand will form extended network, but provides unique opportunities for the formation of diverse inorganic-organic hybrids exhibiting rich structural topologies. - Graphical abstract: Three alkaline earth-based coordination polymers were constructed from a semirigid cyclotriphosphazene-functionalized hexacarboxylate exhibiting different inorganic nodes as well as distinct ligand conformations relying on the metal ions, which presents the first example of such a ligand incorporated into alkaline earth–based coordination polymers. - Highlights: • Three alkaline earth-based coordination polymers were synthesized. • The three compounds exhibit different inorganic nodes and ligand conformations. • The three compounds are photoluminscent in the solid state.« less

DNA interactions of non-chelating tinidazole-based coordination compounds and their structural, redox and cytotoxic properties.

PubMed

Castro-Ramírez, Rodrigo; Ortiz-Pastrana, Naytzé; Caballero, Ana B; Zimmerman, Matthew T; Stadelman, Bradley S; Gaertner, Andrea A E; Brumaghim, Julia L; Korrodi-Gregório, Luís; Pérez-Tomás, Ricardo; Gamez, Patrick; Barba-Behrens, Norah

2018-05-23

Novel tinidazole (tnz) coordination compounds of different geometries were synthesised, whose respective solid-state packing appears to be driven by inter- and intramolecular lone pairπ interactions. The copper(ii) compounds exhibit interesting redox properties originating from both the tnz and the metal ions. These complexes interact with DNA through two distinct ways, namely via electrostatic interactions or/and groove binding, and they can mediate the generation of ROS that damage the biomolecule. Cytotoxic studies revealed an interesting activity of the dinuclear compound [Cu(tnz)2(μ-Cl)Cl]2 7, which is further more efficient towards cancer cells, compared with normal cells.

Modulation of α-synuclein fibrillization by ring-fused 2-pyridones: templation and inhibition involve oligomers with different structure.

PubMed

Horvath, Istvan; Sellstedt, Magnus; Weise, Christoph; Nordvall, Lina-Maria; Krishna Prasad, G; Olofsson, Anders; Larsson, Göran; Almqvist, Fredrik; Wittung-Stafshede, Pernilla

2013-04-15

In a recent study we discovered that a ring-fused 2-pyridone compound triggered fibrillization of a key protein in Parkinson's disease, α-synuclein. To reveal how variations in compound structure affect protein aggregation, we now prepared a number of strategic analogs and tested their effects on α-synuclein amyloid fiber formation in vitro. We find that, in contrast to the earlier templating effect, some analogs inhibit α-synuclein fibrillization. For both templating and inhibiting compounds, the key species formed in the reactions are α-synuclein oligomers that contain compound. Despite similar macroscopic appearance, the templating and inhibiting oligomers are distinctly different in secondary structure content. When the inhibitory oligomers are added in seed amounts, they inhibit fresh α-synuclein aggregation reactions. Our study demonstrates that small chemical changes to the same central fragment can result in opposite effects on protein aggregation. Copyright © 2013 Elsevier Inc. All rights reserved.

Pressure evolution of electrical transport in the 3D topological insulator (Bi,Sb) 2 (Se,Te) 3

DOE PAGES

Jeffries, J. R.; Butch, N. P.; Vohra, Y. K.; ...

2015-03-18

The group V-VI compounds|like Bi 2Se 3, Sb 2Te 3, or Bi 2Te 3|have been widely studied in recent years for their bulk topological properties. The high-Z members of this series form with the same crystal structure, and are therefore amenable to isostructural substitution studies. It is possible to tune the Bi-Sb and Te-Se ratios such that the material exhibits insulating behavior, thus providing an excellent platform for understanding how a topological insulator evolves with applied pressure. We report our observations of the pressure-dependent electrical transport and crystal structure of a pseudobinary (Bi,Sb) 2(Te,Se) 3 compound. Similar to some ofmore » its sister compounds, the (Bi,Sb) 2(Te,Se) 3 pseudobinary compound undergoes multiple, pressure-induced phase transformations that result in metallization, the onset of a close-packed crystal structure, and the development of distinct superconducting phases.« less

Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure.

PubMed

Keskin, O; Bahar, I; Jernigan, R L; Beutler, J A; Shoemaker, R H; Sausville, E A; Covell, D G

2000-04-01

An analysis of the growth inhibitory potency of 122 anticancer agents available from the National Cancer Institute anticancer drug screen is presented. Methods of singular value decomposition (SVD) were applied to determine the matrix of distances between all compounds. These SVD-derived dissimilarity distances were used to cluster compounds that exhibit similar tumor growth inhibitory activity patterns against 60 human cancer cell lines. Cluster analysis divides the 122 standard agents into 25 statistically distinct groups. The first eight groups include structurally diverse compounds with reactive functionalities that act as DNA-damaging agents while the remaining 17 groups include compounds that inhibit nucleic acid biosynthesis and mitosis. Examination of the average activity patterns across the 60 tumor cell lines reveals unique 'fingerprints' associated with each group. A diverse set of structural features are observed for compounds within these groups, with frequent occurrences of strong within-group structural similarities. Clustering of cell types by their response to the 122 anticancer agents divides the 60 cell types into 21 groups. The strongest within-panel groupings were found for the renal, leukemia and ovarian cell panels. These results contribute to the basis for comparisons between log(GI(50)) screening patterns of the 122 anticancer agents and additional tested compounds.

A Study of a Compound Solar Eruption with Two Consecutive Erupting Magnetic Structures

NASA Astrophysics Data System (ADS)

Dhakal, Suman K.; Chintzoglou, Georgios; Zhang, Jie

2018-06-01

We report a study of a compound solar eruption that was associated with two consecutively erupting magnetic structures and correspondingly two distinct peaks, during impulsive phase, of an M-class flare (M8.5). Simultaneous multi-viewpoint observations from SDO, GOES and STEREO-A show that this compound eruption originated from two pre-existing sigmoidal magnetic structures lying along the same polarity inversion line. Observations of the associated pre-existing filaments further show that these magnetic structures are lying one on top of the other, separated by 12 Mm in height, in a so-called “double-decker” configuration. The high-lying magnetic structure became unstable and erupted first, appearing as an expanding hot channel seen at extreme ultraviolet wavelengths. About 12 minutes later, the low-lying structure also started to erupt and moved at an even faster speed compared to the high-lying one. As a result, the two erupting structures interacted and merged with each other, appearing as a single coronal mass ejection in the outer corona. We find that the double-decker configuration is likely caused by the persistent shearing motion and flux cancellation along the source active region’s strong-gradient polarity inversion line. The successive destabilization of these two separate but closely spaced magnetic structures, possibly in the form of magnetic flux ropes, led to a compound solar eruption. The study of the compound eruption provides a unique opportunity to reveal the formation process, initiation, and evolution of complex eruptive structures in solar active regions.

Discovery, SAR, and X-ray Binding Mode Study of BCATm Inhibitors from a Novel DNA-Encoded Library

PubMed Central

2015-01-01

As a potential target for obesity, human BCATm was screened against more than 14 billion DNA encoded compounds of distinct scaffolds followed by off-DNA synthesis and activity confirmation. As a consequence, several series of BCATm inhibitors were discovered. One representative compound (R)-3-((1-(5-bromothiophene-2-carbonyl)pyrrolidin-3-yl)oxy)-N-methyl-2′-(methylsulfonamido)-[1,1′-biphenyl]-4-carboxamide (15e) from a novel compound library synthesized via on-DNA Suzuki–Miyaura cross-coupling showed BCATm inhibitory activity with IC50 = 2.0 μM. A protein crystal structure of 15e revealed that it binds to BCATm within the catalytic site adjacent to the PLP cofactor. The identification of this novel inhibitor series plus the establishment of a BCATm protein structure provided a good starting point for future structure-based discovery of BCATm inhibitors. PMID:26288694

Influence of feedstock chemical composition on product formation and characteristics derived from the hydrothermal carbonization of mixed feedstocks.

PubMed

Lu, Xiaowei; Berge, Nicole D

2014-08-01

As the exploration of the carbonization of mixed feedstocks continues, there is a distinct need to understand how feedstock chemical composition and structural complexity influence the composition of generated products. Laboratory experiments were conducted to evaluate the carbonization of pure compounds, mixtures of the pure compounds, and complex feedstocks comprised of the pure compounds (e.g., paper, wood). Results indicate that feedstock properties do influence carbonization product properties. Carbonization product characteristics were predicted using results from the carbonization of the pure compounds and indicate that recovered solids energy contents are more accurately predicted than solid yields and the carbon mass in each phase, while predictions associated with solids surface functional groups are more difficult to predict using this linear approach. To more accurately predict carbonization products, it may be necessary to account for feedstock structure and/or additional feedstock properties. Copyright © 2014 Elsevier Ltd. All rights reserved.

Preparation and structure of BiCrTeO{sub 6}: A new compound in Bi–Cr–Te–O system. Thermal expansion studies of Cr{sub 2}TeO{sub 6}, Bi{sub 2}TeO{sub 6} and BiCrTeO{sub 6}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vats, Bal Govind; Phatak, Rohan; Krishnan, K.

Graphical abstract: A new compound BiCrTeO{sub 6} in the Bi–Cr–Te–O system was prepared by solid state route and characterized by X-ray diffraction method. The crystal structure of BiCrTeO{sub 6} shows that there is one distinct site for bismuth (Bi) atom (pink color), one chromium rich (Cr/Te = 68/32) (blue/green color), one tellurium rich (Te/Cr = 68/32) sites (green/blue color), and one distinct site for oxygen (O) atom (red color) in the unit cell. All cations in this structure show an octahedral coordination with oxygen atoms at the corners. The thermogram (TG) of the compound in air shows that it ismore » stable up to 1103 K and decomposes thereafter. The thermal expansion behaviour of BiCrTeO{sub 6} was studied using high temperature X-ray diffraction method from room temperature to 923 K under vacuum of 10{sup −8} atmosphere and showed positive thermal expansion with the average volume thermal expansion coefficients of 16.0 × 10{sup −6}/K. - Highlights: • A new compound BiCrTeO{sub 6} in Bi–Cr–Te–O system was prepared and characterized. • The crystal structure of BiCrTeO{sub 6} was determined by Rietveld refinement method. • The structure of BiCrTeO{sub 6} shows an octahedral coordination for all the metal ions. • The thermal expansion behavior of BiCrTeO{sub 6} from room temperature to 923 K showed a positive thermal expansion. • The average volume thermal expansion coefficient for BiCrTeO{sub 6} is 16.0 × 10{sup −6}/K. - Abstract: A new compound BiCrTeO{sub 6} in Bi–Cr–Te–O system was prepared by solid state reaction of Bi{sub 2}O{sub 3}, Cr{sub 2}O{sub 3} and H{sub 6}TeO{sub 6} in oxygen and characterized by X-ray diffraction (XRD) method. It could be indexed on a trigonal lattice, with the space group P-31c, unit cell parameters a = 5.16268(7) Å and c = 9.91861(17) Å. The crystal structure of BiCrTeO{sub 6} was determined by Rietveld refinement method using the powder XRD data. Structure shows that there is one distinct site for bismuth (Bi) atom, one chromium rich (Cr/Te = 68/32), and one tellurium rich (Te/Cr = 68/32) sites, and one distinct site for oxygen (O) atom in the unit cell. All cations in this structure show an octahedral coordination with oxygen atoms at the corners. The thermogravimetric analysis (TGA) of the compound in air shows that it is stable up to 1103 K and decomposes thereafter. The thermal expansion behavior of Cr{sub 2}TeO{sub 6}, Bi{sub 2}TeO{sub 6} and BiCrTeO{sub 6} was studied using High Temperature X-ray diffraction (HTXRD) method from room temperature to 973, 873 and 923 K respectively under vacuum of 10{sup −8} atmospheres. All the compounds showed positive thermal expansion with the average volume thermal expansion coefficients of 14.38 × 10{sup −6}/K, 22.0 × 10{sup −6}/K and 16.0 × 10{sup −6}/K respectively.« less

Binding mode dependent signaling for the detection of Cu2 +: An experimental and theoretical approach with practical applications

NASA Astrophysics Data System (ADS)

Ghosh, Soumen; Khan, Mehebub Ali; Ganguly, Aniruddha; Masum, Abdulla Al; Alam, Md. Akhtarul; Guchhait, Nikhil

2018-02-01

Two amido-schiff bases (3-Hydroxy-naphthalene-2-carboxylic acid pyren-1-ylmethylene-hydrazide and Naphthalene-2-carboxylic acid pyren-1-ylmethylene-hydrazide) have been synthesized having a common structural unit and only differs by a -OH group in the naphthalene ring. Both of them can detect Cu2 + ion selectively in semi-aqueous medium in distinctly different output modes (one detects Cu2 + by naked-eye color change where as the other detects Cu2 + by fluorescence enhancement). The difference in the binding of Cu 2 + with the compounds is the reason for this observation. The detection limit is found to be micromolar region for compound which contains -OH group whereas the compound without -OH group detects copper in nano-molar region. DFT calculations have been performed in order to demonstrate the structure of the compounds and their copper complexes. Practical utility has been explored by successful paper strip response of both the compounds. The biological applications have been evaluated in RAW 264.7.

Extraterrestrial Organic Compounds in Meteorites

NASA Technical Reports Server (NTRS)

Botta, Oliver; Bada, Jeffrey L.; Meyer, Michael (Technical Monitor)

2003-01-01

Many organic compounds or their precursors found in meteorites originated in the interstellar or circumstellar medium and were later incorporated into planetesimals during the formation of the solar system. There they either survived intact or underwent further processing to synthesize secondary products on the meteorite parent body. The most distinct feature of CI and CM carbonaceous chondrites, two types of stony meteorites, is their high carbon content (up to 3% of weight), either in the form of carbonates or of organic compounds. The bulk of the organic carbon consists of an insoluble macromolecular material with a complex structure. Also present is a soluble organic fraction, which has been analyzed by several separation and analytical procedures. Low detection limits can be achieved by derivatization of the organic molecules with reagents that allow for analysis by gas chromatography/mass spectroscopy and high performance liquid chromatography. The CM meteorite Murchison has been found to contain more than 70 extraterrestrial amino acids and several other classes of compounds including carboxylic acids, hydroxy carboxylic acids, sulphonic and phosphonic acids, aliphatic, aromatic and polar hydrocarbons, fullerenes, heterocycles as well as carbonyl compounds, alcohols, amines and amides. The organic matter was found to be enriched in deuterium, and distinct organic compounds show isotopic enrichments of carbon and nitrogen relative to terrestrial matter.

Emergence of a few distinct structures from a single formal structure type during high-throughput screening for stable compounds: The case of RbCuS and RbCuSe

NASA Astrophysics Data System (ADS)

Trimarchi, Giancarlo; Zhang, Xiuwen; DeVries Vermeer, Michael J.; Cantwell, Jacqueline; Poeppelmeier, Kenneth R.; Zunger, Alex

2015-10-01

Theoretical sorting of stable and synthesizable "missing compounds" from those that are unstable is a crucial step in the discovery of previously unknown functional materials. This active research area often involves high-throughput (HT) examination of the total energy of a given compound in a list of candidate formal structure types (FSTs), searching for those with the lowest energy within that list. While it is well appreciated that local relaxation methods based on a fixed list of structure types can lead to inaccurate geometries, this approach is widely used in HT studies because it produces answers faster than global optimization methods (that vary lattice vectors and atomic positions without local restrictions). We find, however, a different failure mode of the HT protocol: specific crystallographic classes of formal structure types each correspond to a series of chemically distinct "daughter structure types" (DSTs) that have the same space group but possess totally different local bonding configurations, including coordination types. Failure to include such DSTs in the fixed list of examined candidate structures used in contemporary high-throughput approaches can lead to qualitative misidentification of the stable bonding pattern, not just quantitative inaccuracies. In this work, we (i) clarify the understanding of the general DST-FST relationship, thus improving current discovery HT approaches, (ii) illustrate this failure mode for RbCuS and RbCuSe (the latter being a yet unreported compound and is predicted here) by developing a synthesis method and accelerated crystal-structure determination, and (iii) apply the genetic-algorithm-based global space-group optimization (GSGO) approach which is not vulnerable to the failure mode of HT searches of fixed lists, demonstrating a correct identification of the stable DST. The broad impact of items (i)-(iii) lies in the demonstrated predictive ability of a more comprehensive search strategy than what is currently used—use HT calculations as the preliminary broad screening followed by unbiased GSGO of the final candidates.

Two structurally distinct inhibitors of glycogen synthase kinase 3 induced centromere positive micronuclei in human lymphoblastoid TK6 cells.

PubMed

Mishima, Masayuki; Tanaka, Kenji; Takeiri, Akira; Harada, Asako; Kubo, Chiyomi; Sone, Sachiko; Nishimura, Yoshikazu; Tachibana, Yukako; Okazaki, Makoto

2008-08-25

Glycogen synthase kinase 3 (GSK3) is an attractive novel pharmacological target. Inhibition of GSK3 is recently regarded as one of the viable approaches to therapy for Alzheimer's disease, cancer, diabetes mellitus, osteoporosis, and bipolar mood disorder. Here, we have investigated the aneugenic potential of two potent and highly specific inhibitors of GSK3 by using an in vitro micronucleus test with human lymphoblastoid TK6 cells. One inhibitor was a newly synthesized maleimide derivative and the other was a previously known aminopyrimidine derivative. Both compounds elicited statistically significant and concentration-dependent increases in micronucleated cells. One hundred micronuclei (MN) of each were analyzed using centromeric DNA staining with fluorescence in situ hybridization. Both the two structurally distinct compounds induced centromere-positive micronuclei (CMN). Calculated from the frequency of MN cells and the percentage of CMN, CMN cell incidence after treatment with the maleimide compound at 1.2 microM, 2.4 microM, and 4.8 microM was 11.6, 27.7, and 56.3 per 1000 cells, respectively; the negative control was 4.5. CMN cell incidence after the treatment with the aminopyrimidine compound at 1.8 microM, 3.6 microM, and 5.4 microM was 6.7, 9.8 and 17.2 per 1000 cells, respectively. Both compounds exhibited concentration-dependent increase in the number of mitotic cells. The frequency of CMN cells correlated well with mitotic cell incidence after treatment with either compound. Furthermore, both inhibitors induced abnormal mitotic cells with asymmetric mitotic spindles and lagging anaphase chromosomes. These results lend further support to the hypothesis that the inhibition of GSK3 activity affects microtubule function and exhibits an aneugenic mode of action.

Effect of divalent Ba cation substitution with Sr on coupled ‘multiglass’ state in the magnetoelectric multiferroic compound Ba3NbFe3Si2O14

PubMed Central

Rathore, Satyapal Singh; Vitta, Satish

2015-01-01

(Ba/Sr)3NbFe3Si2O14 is a magneto-electric multiferroic with an incommensurate antiferromagnetic spiral magnetic structure which induces electric polarization at 26 K. Structural studies show that both the compounds have similar crystal structure down to 6 K. They exhibit a transition, TN at 26 K and 25 K respectively, as indicated by heat capacity and magnetization, into an antiferromagnetic state. Although Ba and Sr are isovalent, they exhibit very different static and dynamic magnetic behaviors. The Ba-compound exhibits a glassy behavior with critical slowing dynamics with a freezing temperature of ~35 K and a critical exponent of 3.9, a value close to the 3-D Ising model above TN, in addition to the invariant transition into an antiferromagnetic state. The Sr-compound however does not exhibit any dispersive behavior except for the invariant transition at TN. The dielectric constant reflects magnetic behavior of the two compounds: the Ba-compound has two distinct dispersive peaks while the Sr-compound has a single dispersive peak. Thus the compounds exhibit coupled ‘multiglass’ behavior. The difference in magnetic properties between the two compounds is found to be due to modifications to super exchange path angle and length as well as anti-site defects which stabilize either ferromagnetic or antiferromagnetic interactions. PMID:25988657

Identification of a Drosophila glucose receptor using Ca2+ imaging of single chemosensory neurons.

PubMed

Miyamoto, Tetsuya; Chen, Yan; Slone, Jesse; Amrein, Hubert

2013-01-01

Evaluation of food compounds by chemosensory cells is essential for animals to make appropriate feeding decisions. In the fruit fly Drosophila melanogaster, structurally diverse chemicals are detected by multimeric receptors composed of members of a large family of Gustatory receptor (Gr) proteins. Putative sugar and bitter receptors are expressed in distinct subsets of Gustatory Receptor Neurons (GRN) of taste sensilla, thereby assigning distinct taste qualities to sugars and bitter tasting compounds, respectively. Here we report a Ca(2+) imaging method that allows association of ligand-mediated responses to a single GRN. We find that different sweet neurons exhibit distinct response profiles when stimulated with various sugars, and likewise, different bitter neurons exhibit distinct response profiles when stimulated with a set of bitter chemicals. These observations suggest that individual neurons within a taste modality are represented by distinct repertoires of sweet and bitter taste receptors, respectively. Furthermore, we employed this novel method to identify glucose as the primary ligand for the sugar receptor Gr61a, which is not only expressed in sweet sensing neurons of classical chemosensory sensilla, but also in two supersensitive neurons of atypical taste sensilla. Thus, single cell Ca(2+) imaging can be employed as a powerful tool to identify ligands for orphan Gr proteins.

Isocoumarin derivatives from the endophytic fungus, Pestalotiopsis sp.

PubMed

Song, Ren-Yu; Wang, Xiao-Bing; Yin, Guo-Ping; Liu, Rui-Huan; Kong, Ling-Yi; Yang, Ming-Hua

2017-10-01

Five new isocoumarin derivatives, pestalactone A-C (1-3) and pestapyrone D-E (4-5), together with two known compounds (6-7) were isolated from the solid cultures of the endophytic fungus Pestalotiopsis sp. obtained from Photinia frasery. Their structures were mainly determined by extensive spectroscopic analysis, Mo 2 (OCOCH 3 ) 4 -induced electronic circular dichroism (ECD), and ECD calculation. Compounds 1 and 2 were rare isocoumarin derivatives and derived from distinctive polyketide pathways. Compound 3 exhibited potent antifungal activity against Candida glabrata (ATCC 90030) with an MIC 50 value of 3.49±0.21μg/mL. Copyright © 2017. Published by Elsevier B.V.

Synthesis and preliminary biological evaluation of potent and selective 2-(3-alkoxy-1-azetidinyl) quinolines as novel PDE10A inhibitors with improved solubility.

PubMed

Rzasa, Robert M; Frohn, Michael J; Andrews, Kristin L; Chmait, Samer; Chen, Ning; Clarine, Jeffrey G; Davis, Carl; Eastwood, Heather A; Horne, Daniel B; Hu, Essa; Jones, Adrie D; Kaller, Matthew R; Kunz, Roxanne K; Miller, Silke; Monenschein, Holger; Nguyen, Thomas; Pickrell, Alexander J; Porter, Amy; Reichelt, Andreas; Zhao, Xiaoning; Treanor, James J S; Allen, Jennifer R

2014-12-01

We report the discovery of a novel series of 2-(3-alkoxy-1-azetidinyl) quinolines as potent and selective PDE10A inhibitors. Structure-activity studies improved the solubility (pH 7.4) and maintained high PDE10A activity compared to initial lead compound 3, with select compounds demonstrating good oral bioavailability. X-ray crystallographic studies revealed two distinct binding modes to the catalytic site of the PDE10A enzyme. An ex vivo receptor occupancy assay in rats demonstrated that this series of compounds covered the target within the striatum.

Protocols for the Design of Kinase-focused Compound Libraries.

PubMed

Jacoby, Edgar; Wroblowski, Berthold; Buyck, Christophe; Neefs, Jean-Marc; Meyer, Christophe; Cummings, Maxwell D; van Vlijmen, Herman

2018-05-01

Protocols for the design of kinase-focused compound libraries are presented. Kinase-focused compound libraries can be differentiated based on the design goal. Depending on whether the library should be a discovery library specific for one particular kinase, a general discovery library for multiple distinct kinase projects, or even phenotypic screening, there exists today a variety of in silico methods to design candidate compound libraries. We address the following scenarios: 1) Datamining of SAR databases and kinase focused vendor catalogues; 2) Predictions and virtual screening; 3) Structure-based design of combinatorial kinase inhibitors; 4) Design of covalent kinase inhibitors; 5) Design of macrocyclic kinase inhibitors; and 6) Design of allosteric kinase inhibitors and activators. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Discovery of Novel Tricyclic Heterocycles as Potent and Selective DPP-4 Inhibitors for the Treatment of Type 2 Diabetes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Wen-Lian; Hao, Jinsong; Domalski, Martin

In our efforts to develop second generation DPP-4 inhibitors, we endeavored to identify distinct structures with long-acting (once weekly) potential. Taking advantage of X-ray cocrystal structures of sitagliptin and other DPP-4 inhibitors, such as alogliptin and linagliptin bound to DPP-4, and aided by molecular modeling, we designed several series of heterocyclic compounds as initial targets. During their synthesis, an unexpected chemical transformation provided a novel tricyclic scaffold that was beyond our original design. Capitalizing on this serendipitous discovery, we have elaborated this scaffold into a very potent and selective DPP-4 inhibitor lead series, as highlighted by compound 17c.

Individual and gender fingerprints in human body odour.

PubMed

Penn, Dustin J; Oberzaucher, Elisabeth; Grammer, Karl; Fischer, Gottfried; Soini, Helena A; Wiesler, Donald; Novotny, Milos V; Dixon, Sarah J; Xu, Yun; Brereton, Richard G

2007-04-22

Individuals are thought to have their own distinctive scent, analogous to a signature or fingerprint. To test this idea, we collected axillary sweat, urine and saliva from 197 adults from a village in the Austrian Alps, taking five sweat samples per subject over 10 weeks using a novel skin sampling device. We analysed samples using stir bar sorptive extraction in connection with thermal desorption gas chromatograph-mass spectrometry (GC-MS), and then we statistically analysed the chromatographic profiles using pattern recognition techniques. We found more volatile compounds in axillary sweat than in urine or saliva, and among these we found 373 peaks that were consistent over time (detected in four out of five samples per individual). Among these candidate compounds, we found individually distinct and reproducible GC-MS fingerprints, a reproducible difference between the sexes, and we identified the chemical structures of 44 individual and 12 gender-specific volatile compounds. These individual compounds provide candidates for major histocompatibility complex and other genetically determined odours. This is the first study on human axillary odour to sample a large number of subjects, and our findings are relevant to understanding the chemical nature of human odour, and efforts to design electronic sensors (e-nose) for biometric fingerprinting and disease diagnoses.

Mechanistic Insights into the Specificity of Human Cytosolic Sulfotransferase 2A1 (hSULT2A1) for Hydroxylated Polychlorinated Biphenyls Through the Use of Fluoro-tagged Probes

PubMed Central

Ekuase, E.J.; van ’t Erve, T.J.; Rahaman, A.; Robertson, L.W.; Duffel, M.W.; Luthe, G.

2015-01-01

Determining the relationships between the structures of substrates and inhibitors and their interactions with drug-metabolizing enzymes is of prime importance in predicting the toxic potential of new and legacy xenobiotics. Traditionally, quantitative structure activity relationship (QSAR) studies are performed with many distinct compounds. Based on the chemical properties of the tested compounds, complex relationships can be established so that models can be developed to predict toxicity of novel compounds. In this study, the use of fluorinated analogues as supplemental QSAR compounds was investigated. Substituting fluorine induces changes in electronic and steric properties of the substrate without substantially changing the chemical backbone of the substrate. In vitro assays were performed using purified human cytosolic sulfotransferase hSULT2A1 as a model enzyme. A mono-hydroxylated polychlorinated biphenyl (4-OH PCB 14) and its four possible mono-fluoro analogues were used as test compounds. Remarkable similarities were found between this approach and previously published QSAR studies for hSULT2A1. Both studies implicate the importance of dipole moment and dihedral angle as being important to PCB structure in respect to being substrates for hSULT2A1. We conclude that mono-fluorinated analogues of a target substrate can be a useful tool to study the structure activity relationships for enzyme specificity. PMID:26165989

Identification and biochemical characterization of small-molecule inhibitors of west nile virus serine protease by a high-throughput screen.

PubMed

Mueller, Niklaus H; Pattabiraman, Nagarajan; Ansarah-Sobrinho, Camilo; Viswanathan, Prasanth; Pierson, Theodore C; Padmanabhan, R

2008-09-01

West Nile virus and dengue virus are mosquito-borne flaviviruses that cause a large number of human infections each year. No vaccines or chemotherapeutics are currently available. These viruses encode a serine protease that is essential for polyprotein processing, a required step in the viral replication cycle. In this study, a high-throughput screening assay for the West Nile virus protease was employed to screen approximately 32,000 small-molecule compounds for identification of inhibitors. Lead inhibitor compounds with three distinct core chemical structures (1 to 3) were identified. In a secondary screening of selected compounds, two compounds, belonging to the 8-hydroxyquinoline family (compounds A and B) and containing core structure 1, were identified as potent inhibitors of the West Nile virus protease, with K(i) values of 3.2 +/- 0.3 microM and 3.4 +/- 0.6 microM, respectively. These compounds inhibited the dengue virus type 2 protease with K(i) values of 28.6 +/- 5.1 microM and 30.2 +/- 8.6 microM, respectively, showing some selectivity in the inhibition of these viral proteases. However, the compounds show no inhibition of cellular serine proteases, trypsin, or factor Xa. Kinetic analysis and molecular docking of compound B onto the known crystal structure of the West Nile virus protease indicate that the inhibitor binds in the substrate-binding cleft. Furthermore, compound B was capable of inhibiting West Nile virus RNA replication in cultured Vero cells (50% effective concentration, 1.4 +/- 0.4 microM; selectivity index, 100), presumably by inhibition of polyprotein processing.

Band Structure Engineering by Substitutional Doping in Solid-State Solutions of [5-Me-PLY(O,O)]2B(1-x)Be(x) Radical Crystals.

PubMed

Bag, Pradip; Itkis, Mikhail E; Stekovic, Dejan; Pal, Sushanta K; Tham, Fook S; Haddon, Robert C

2015-08-12

We report the substitutional doping of solid-state spiro-bis(5-methyl-1,9-oxido-phenalenyl)boron radical ([2]2B) by co-crystallization of this radical with the corresponding spiro-bis(5-methyl-1,9-oxido-phenalenyl)beryllium compound ([2]2Be). The pure compounds crystallize in different space groups ([2]2B, P1̅, Z = 2; [2]2Be, P2₁/c, Z = 4) with distinct packing arrangements, yet we are able to isolate crystals of composition [2]2B(1-x)Be(x), where x = 0-0.59. The phase transition from the P1̅ to the P2₁/c space group occurs at x = 0.1, but the conductivities of the solid solutions are enhanced and the activation energies reduced for values of x = 0-0.25. The molecular packing is driven by the relative concentration of the spin-bearing ([2]2B) and spin-free ([2]2Be) molecules in the crystals, and the extended Hückel theory band structures show that the progressive incorporation of spin-free [2]2Be in the lattice of the [2]2B radical (overall bandwidth, W = 1.4 eV, in the pure compound) leads to very strong narrowing of the bandwidth, which reaches a minimum at [2]2Be (W = 0.3 eV). The results provide a graphic picture of the structural transformations undergone by the lattice, and at certain compositions we are able to identify distinct structures for the [2]2B and [2]2Be molecules in a single crystalline phase.

Karrikin and cyanohydrin smoke signals provide clues to new endogenous plant signaling compounds.

PubMed

Flematti, Gavin R; Waters, Mark T; Scaffidi, Adrian; Merritt, David J; Ghisalberti, Emilio L; Dixon, Kingsley W; Smith, Steven M

2013-01-01

Two new types of signaling compounds have been discovered in wildfire smoke due to their ability to stimulate seed germination. The first discovered were karrikins, which share some structural similarity with the strigolactone class of plant hormones, and both signal through a common F-box protein. However, karrikins and strigolactones operate through otherwise distinct signaling pathways, each distinguished by a specific α/β hydrolase protein. Genetic analysis suggests that plants contain endogenous compounds that signal specifically through the karrikin pathway. The other active compounds discovered in smoke are cyanohydrins that release germination-stimulating cyanide upon hydrolysis. Cyanohydrins occur widely in plants and have a role in defense against other organisms, but an additional role in endogenous cyanide signaling should also now be considered.

Structurally complex Zintl compounds for high temperature thermoelectric power generation

NASA Astrophysics Data System (ADS)

Zevalkink, Alexandra; Pomrehn, Gregory; Gibbs, Zachary; Snyder, Jeffrey

2014-03-01

Zintl phases, characterized by covalently-bonded substructures surrounded by highly electropositive cations, exhibit many of the characteristics desired for thermoelectric applications. Recently, we demonstrated promising thermoelectric performance (zT values between 0.4 and 0.9) in a class of Zintl antimonides that share a common structural motif: anionic moieties resembling infinite chains of linked tetrahedra. These compounds (A5M2 Sb6 and A3 M Sb3 compounds where A = Ca or Sr and M = Al, Ga and In) crystallize as four distinct, but closely related chain-forming structure types. Their large unit cells lead to exceptionally low lattice thermal conductivity due to the containment of heat in low velocity optical phonon modes. Here, we show that chemical substitutions on the A and M sites can be used to control the electronic and thermal transport properties and optimize the thermoelectric figure of merit. Doping with alio-valent elements allows for rational control of the carrier concentration, while isoelectronic substitutions can be used to fine-tune the intrinsic properties. A combination of Density Functional calculations and classical transport models was used to explain the experimentally observed transport properties of these compounds.

Facile construction of structurally diverse thiazolidinedione-derived compounds via divergent stereoselective cascade organocatalysis and their biological exploratory studies.

PubMed

Zhang, Yongqiang; Wang, Shengzheng; Wu, Shanchao; Zhu, Shiping; Dong, Guoqiang; Miao, Zhenyuan; Yao, Jianzhong; Zhang, Wannian; Sheng, Chunquan; Wang, Wei

2013-06-10

In this article, we present a new approach by merging two powerful synthetic tactics, divergent synthesis and cascade organocatalysis, to create a divergent cascade organocatalysis strategy for the facile construction of new "privileged" substructure-based DOS (pDOS) library. As demonstrated, notably 5 distinct molecular architectures are produced facilely from readily available simple synthons thiazolidinedione and its analogues and α,β-unsaturated aldehydes in 1-3 steps with the powerful strategy. The beauty of the chemistry is highlighted by the efficient formation of structurally new and diverse products from structurally close reactants under the similar reaction conditions. Notably, structurally diverse spiro-thiazolidinediones and -rhodanines are produced from organocatalytic enantioselective 3-component Michael-Michael-aldol cascade reactions of respective thiazolidinediones and rhodanines with enals. Nevertheless, under the similar reaction conditions, reactions of isorhodanine via a Michael-cyclization cascade lead to structurally different fused thiopyranoid scaffolds. This strategy significantly minimizes time- and cost-consuming synthetic works. Furthermore, these molecules possess high structural complexity and functional, stereochemical, and skeletal diversity with similarity to natural scaffolds. In the preliminary biological studies of these molecules, compounds 4f, 8a, and 10a exhibit inhibitory activity against the human breast cancer cells, while compounds 8a, 9a, and 9b display good antifungal activities against Candida albicans and Cryptococcus neoformans. Notably, their structures are different from clinically used triazole antifungal drugs. Therefore, they could serve as good lead compounds for the development of new generation of antifungal agents.

The single-crystal structure of the organic superconductor betaCO-(BEDT-TTF)2I3 from a powder grain.

PubMed

Madsen; Burghammer; Fiedler; Müller

1999-08-01

Synchrotron radiation diffraction data have been collected at 200 K on a microscopic single crystal (dimensions 12 x 10 x 2 µm) of the title compound, where BEDT-TTF is bis(ethylenedithio)tetrathiafulvalene, C(10)H(8)S(8). The quality of the diffraction data allowed a full structure refinement and enabled the determination of structural details such as the conformations of the ethylene groups as well as the occupancy of the triiodide sites. The compound was found to be slightly iodine-deficient and better described as beta(CO)-(BEDT-TTF)(2)I(3-x) [x = 0.014 (3)]. One of the ethylene groups of the BEDT-TTF cation is disordered at this temperature and exists in two distinct conformations with occupancies which are identical within the standard uncertainty.

Reducing the Bottleneck in Discovery of Novel Antibiotics.

PubMed

Jones, Marcus B; Nierman, William C; Shan, Yue; Frank, Bryan C; Spoering, Amy; Ling, Losee; Peoples, Aaron; Zullo, Ashley; Lewis, Kim; Nelson, Karen E

2017-04-01

Most antibiotics were discovered by screening soil actinomycetes, but the efficiency of the discovery platform collapsed in the 1960s. By now, more than 3000 antibiotics have been described and most of the current discovery effort is focused on the rediscovery of known compounds, making the approach impractical. The last marketed broad-spectrum antibiotics discovered were daptomycin, linezolid, and fidaxomicin. The current state of the art in the development of new anti-infectives is a non-existent pipeline in the absence of a discovery platform. This is particularly troubling given the emergence of pan-resistant pathogens. The current practice in dealing with the problem of the background of known compounds is to use chemical dereplication of extracts to assess the relative novelty of a compound it contains. Dereplication typically requires scale-up, extraction, and often fractionation before an accurate mass and structure can be produced by MS analysis in combination with 2D NMR. Here, we describe a transcriptome analysis approach using RNA sequencing (RNASeq) to identify promising novel antimicrobial compounds from microbial extracts. Our pipeline permits identification of antimicrobial compounds that produce distinct transcription profiles using unfractionated cell extracts. This efficient pipeline will eliminate the requirement for purification and structure determination of compounds from extracts and will facilitate high-throughput screen of cell extracts for identification of novel compounds.

Vibrational spectroscopy of metal methanesulfonates: M = Na, Cs, Cu, Ag, Cd

NASA Astrophysics Data System (ADS)

Parker, Stewart F.; Zhong, Lisha

2018-04-01

In this work, we have used a combination of vibrational spectroscopy (infrared, Raman and inelastic neutron scattering) and periodic density functional theory to investigate six metal methanesulfonate compounds that exhibit four different modes of complexation of the methanesulfonate ion: ionic, monodentate, bidentate and pentadentate. We found that the transition energies of the modes associated with the methyl group (C-H stretches and deformations, methyl rock and torsion) are essentially independent of the mode of coordination. The SO3 modes in the Raman spectra also show little variation. In the infrared spectra, there is a clear distinction between ionic (i.e. not coordinated) and coordinated forms of the methanesulfonate ion. This is manifested as a splitting of the asymmetric S-O stretch modes of the SO3 moiety. Unfortunately, no further differentiation between the various modes of coordination: unidentate, bidentate etc … is possible with the compounds examined. While it is likely that such a distinction could be made, this will require a much larger dataset of compounds for which both structural and spectroscopic data are available than that available here.

Two structurally distinct chalcone dimers from Helichrysum zivojinii and their activities in cancer cell lines.

PubMed

Aljančić, Ivana S; Vučković, Ivan; Jadranin, Milka; Pešić, Milica; Dorđević, Iris; Podolski-Renić, Ana; Stojković, Sonja; Menković, Nebojša; Vajs, Vlatka E; Milosavljević, Slobodan M

2014-02-01

Dimers tomoroside A (1) and tomoroside B (2) of the co-occuring known chalcone monomer (3), along with the seven known flavonoid glucosides (4-10), were isolated from the aerial parts of Helichrysum zivojinii Černjavski & Soška. The structures of the isolated compounds were elucidated by spectroscopic techniques. Compound 1 inhibited topo IIα and hif-1α expression and stimulated doxorubicin anticancer effect, while 2 increased the expression of hif-1α, probably acting as antioxidant and redox status modulator. Notably, 2 synergized with Tipifarnib showing potential to improve the action of this new chemotherapeutic involved in the modulation of mitogene activated protein (MAP) kinase signaling pathway. Copyright © 2013 Elsevier Ltd. All rights reserved.

Discovery of new antimalarial chemotypes through chemical methodology and library development.

PubMed

Brown, Lauren E; Chih-Chien Cheng, Ken; Wei, Wan-Guo; Yuan, Pingwei; Dai, Peng; Trilles, Richard; Ni, Feng; Yuan, Jing; MacArthur, Ryan; Guha, Rajarshi; Johnson, Ronald L; Su, Xin-zhuan; Dominguez, Melissa M; Snyder, John K; Beeler, Aaron B; Schaus, Scott E; Inglese, James; Porco, John A

2011-04-26

In an effort to expand the stereochemical and structural complexity of chemical libraries used in drug discovery, the Center for Chemical Methodology and Library Development at Boston University has established an infrastructure to translate methodologies accessing diverse chemotypes into arrayed libraries for biological evaluation. In a collaborative effort, the NIH Chemical Genomics Center determined IC(50)'s for Plasmodium falciparum viability for each of 2,070 members of the CMLD-BU compound collection using quantitative high-throughput screening across five parasite lines of distinct geographic origin. Three compound classes displaying either differential or comprehensive antimalarial activity across the lines were identified, and the nascent structure activity relationships (SAR) from this experiment used to initiate optimization of these chemotypes for further development.

Investigations of vibrational spectra and bioactivity of novel anticancer drug N-(6-ferrocenyl-2-naphthoyl)-gamma-amino butyric acid ethyl ester

NASA Astrophysics Data System (ADS)

Sudhi, Geethu; Rajina, S. R.; Praveen, S. G.; Xavier, T. S.; Kenny, Peter T. M.; Jaiswal-Nagar, D.; Binoy, J.

2017-10-01

The bioactivity of compounds is mainly dependent on molecular structure and the present work aims to explore the bonding features responsible for biological activity of novel anticancer drug N-(6-ferrocenyl-2-naphthoyl)-gamma-amino butyric acid ethyl ester (FNGABEE). In the present study, we investigate the molecular structural properties of newly synthesized title compound through experimental and quantum chemical studies. The detailed vibrational analysis has been performed using FT IR and FT Raman spectrum, aided by DFT computed geometry, vibrational spectrum, Eigen vector distribution and PED, at B3LYP/6-311 ++G(d,p) level. The resonance structure of naphthalene, different from that of benzene, revealed by molecular structure has been investigated using Csbnd C and Cdbnd C stretching modes. The proton transfer in amide has been analyzed to obtain spectral distinction between different carbonyl and Csbnd N groups which point to the reactive sites responsible for binding with DNA and bovine serum albumin (BSA). The spectral distinction between eclipsed and staggered form of ferrocene has been analyzed. The molecular docking of FNGABEE with BSA and DNA has been performed to find the strength of binding and the moieties responsible for the interactions. The experimental binding studies of FNGABEE with BSA and DNA has been performed using UV absorption spectroscopy and fluorometric assay, to find the nature and strength of binding.

Single Amino Acid Alteration between Valine and Isoleucine Determines the Distinct Pyrabactin Selectivity by PYL1 and PYL2*

PubMed Central

Yuan, Xiaoqiu; Yin, Ping; Hao, Qi; Yan, Chuangye; Wang, Jiawei; Yan, Nieng

2010-01-01

Abscisic acid (ABA) is one of the most important phytohormones in plant. PYL proteins were identified to be ABA receptors in Arabidopsis thaliana. Despite the remarkably high degree of sequence similarity, PYL1 and PYL2 exhibit distinct responses toward pyrabactin, an ABA agonist. PYL1 inhibits protein phosphatase type 2C upon binding of pyrabactin. In contrast, PYL2 appears relatively insensitive to this compound. The crystal structure of pyrabactin-bound PYL1 revealed that most of the PYL1 residues involved in pyrabactin binding are conserved, hence failing to explain the selectivity of pyrabactin for PYL1 over PYL2. To understand the molecular basis of pyrabactin selectivity, we determined the crystal structure of PYL2 in complex with pyrabactin at 1.64 Å resolution. Structural comparison and biochemical analyses demonstrated that one single amino acid alteration between a corresponding valine and isoleucine determines the distinct pyrabactin selectivity by PYL1 and PYL2. These characterizations provide an important clue to dissecting the redundancy of PYL proteins. PMID:20630864

Organic Matter Composition, Recycling Susceptibility, and the Effectiveness of the Biological Pump – An Evaluation Using NMR Spectra of Marine Plankton

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paytan, Adina

Carbon (C) sequestration through fertilization of phytoplankton with micronutrients and enhancement of the absorption and retention of atmospheric C by ocean biota heavily depends on the efficiency of the “biological pump”. The long-term effectiveness of this strategy depends on a net transfer of C from the upper ocean-atmosphere system to the deep ocean where the C is removed from contact with the atmosphere for an extended period of time. This C removal can be equated to the amount of C fixation by phytoplankton minus the C cycling and regeneration in the euphotic zone. If the regeneration efficiency is increased, thenmore » despite increased C fixation, no net loss (sequestration) of C will result. A reduction in cycling efficiency in the euphotic zone, on the other hand, will increase the effectiveness of the “biological pump” and thus C sequestration. The degree of organic matter biodegradation and recycling depends on the “reactivity” of compounds synthesized by the biota, which in turn, is controlled by the structural characteristic of these compounds. There is considerable evidence that different phytoplankton taxa differ substantially in their biogeochemical characteristics and it is likely that the relative abundance of different compounds synthesized by these distinct taxa, and even within each group at different growth conditions, will differ too. This variability in biosynthesis and thus abundance of a wide range of organic compounds in the water column would lend itself to different susceptibility for biodegradation and regeneration. Knowledge of the distribution of various organic matter structural groups synthesized by distinct taxa, the dependence of the organic matter compound classes on different growth conditions (temperature, light, nutrients) and the selective susceptibility of these compound to regeneration is crucial for estimating the potential for rapid regeneration in the euphotic zone, and thus the effectiveness of the “biological pump”.« less

Identification of Small Molecule Inhibitors of Clostridium perfringens ε-Toxin Cytotoxicity Using a Cell-Based High-Throughput Screen.

PubMed

Lewis, Michelle; Weaver, Charles David; McClain, Mark S

2010-07-01

The Clostridium perfringens epsilon toxin, a select agent, is responsible for a severe, often fatal enterotoxemia characterized by edema in the heart, lungs, kidney, and brain. The toxin is believed to be an oligomeric pore-forming toxin. Currently, there is no effective therapy for countering the cytotoxic activity of the toxin in exposed individuals. Using a robust cell-based high-throughput screening (HTS) assay, we screened a 151,616-compound library for the ability to inhibit ε-toxin-induced cytotoxicity. Survival of MDCK cells exposed to the toxin was assessed by addition of resazurin to detect metabolic activity in surviving cells. The hit rate for this screen was 0.6%. Following a secondary screen of each hit in triplicate and assays to eliminate false positives, we focused on three structurally-distinct compounds: an N-cycloalkylbenzamide, a furo[2,3-b]quinoline, and a 6H-anthra[1,9-cd]isoxazol. None of the three compounds appeared to inhibit toxin binding to cells or the ability of the toxin to form oligomeric complexes. Additional assays demonstrated that two of the inhibitory compounds inhibited ε-toxin-induced permeabilization of MDCK cells to propidium iodide. Furthermore, the two compounds exhibited inhibitory effects on cells pre-treated with toxin. Structural analogs of one of the inhibitors identified through the high-throughput screen were analyzed and provided initial structure-activity data. These compounds should serve as the basis for further structure-activity refinement that may lead to the development of effective anti-ε-toxin therapeutics.

Identification of Small Molecule Inhibitors of Clostridium perfringens ε-Toxin Cytotoxicity Using a Cell-Based High-Throughput Screen

PubMed Central

Lewis, Michelle; Weaver, Charles David; McClain, Mark S.

2010-01-01

The Clostridium perfringens epsilon toxin, a select agent, is responsible for a severe, often fatal enterotoxemia characterized by edema in the heart, lungs, kidney, and brain. The toxin is believed to be an oligomeric pore-forming toxin. Currently, there is no effective therapy for countering the cytotoxic activity of the toxin in exposed individuals. Using a robust cell-based high-throughput screening (HTS) assay, we screened a 151,616-compound library for the ability to inhibit ε-toxin-induced cytotoxicity. Survival of MDCK cells exposed to the toxin was assessed by addition of resazurin to detect metabolic activity in surviving cells. The hit rate for this screen was 0.6%. Following a secondary screen of each hit in triplicate and assays to eliminate false positives, we focused on three structurally-distinct compounds: an N-cycloalkylbenzamide, a furo[2,3-b]quinoline, and a 6H-anthra[1,9-cd]isoxazol. None of the three compounds appeared to inhibit toxin binding to cells or the ability of the toxin to form oligomeric complexes. Additional assays demonstrated that two of the inhibitory compounds inhibited ε-toxin-induced permeabilization of MDCK cells to propidium iodide. Furthermore, the two compounds exhibited inhibitory effects on cells pre-treated with toxin. Structural analogs of one of the inhibitors identified through the high-throughput screen were analyzed and provided initial structure-activity data. These compounds should serve as the basis for further structure-activity refinement that may lead to the development of effective anti-ε-toxin therapeutics. PMID:20721308

Structure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance

PubMed Central

Stogios, Peter J.; Spanogiannopoulos, Peter; Evdokimova, Elena; Egorova, Olga; Shakya, Tushar; Todorovic, Nick; Capretta, Alfredo; Wright, Gerard D.; Savchenko, Alexei

2013-01-01

SYNOPSIS Activity of the aminoglycoside phosphotransferase APH(3’)-Ia leads to resistance to aminoglycoside antibiotics in pathogenic Gram-negative bacteria, and contributes to the clinical obsolescence of this class of antibiotics. One strategy to rescue compromised antibiotics such as aminoglycosides is targeting the enzymes that confer resistance with small molecules. Previously we demonstrated that eukaryotic protein kinase (ePK) inhibitors could inhibit APH enzymes, due to the structural similarity between these two enzyme families. However, limited structural information of enzyme-inhibitor complexes hindered interpretation of the results. As well, cross-reactivity of compounds between APHs and ePKs represents an obstacle to their use as aminoglycoside adjuvants to rescue aminoglycoside antibiotic activity. Here, we structurally and functionally characterize inhibition of APH(3’)-Ia by three diverse chemical scaffolds – anthrapyrazolone, 4-anilinoquinazoline and pyrazolopyrimidine (PP) – and reveal distinctions in the binding mode of anthrapyrazolone and PP compounds to APH(3’)-Ia versus ePKs. Using this observation, we identify PP-derivatives that select against ePKs, attenuate APH(3’)-Ia activity and rescue aminoglycoside antibiotic activity against a resistant E. coli strain. The structures presented here and these inhibition studies provide an important opportunity for structure-based design of compounds to target aminoglycoside phosphotransferases for inhibition, potentially overcoming this form of antibiotic resistance. PMID:23758273

Intrinsic Thermodynamics and Structure Correlation of Benzenesulfonamides with a Pyrimidine Moiety Binding to Carbonic Anhydrases I, II, VII, XII, and XIII

PubMed Central

Kišonaitė, Miglė; Zubrienė, Asta; Čapkauskaitė, Edita; Smirnov, Alexey; Smirnovienė, Joana; Kairys, Visvaldas; Michailovienė, Vilma; Manakova, Elena; Gražulis, Saulius; Matulis, Daumantas

2014-01-01

The early stage of drug discovery is often based on selecting the highest affinity lead compound. To this end the structural and energetic characterization of the binding reaction is important. The binding energetics can be resolved into enthalpic and entropic contributions to the binding Gibbs free energy. Most compound binding reactions are coupled to the absorption or release of protons by the protein or the compound. A distinction between the observed and intrinsic parameters of the binding energetics requires the dissection of the protonation/deprotonation processes. Since only the intrinsic parameters can be correlated with molecular structural perturbations associated with complex formation, it is these parameters that are required for rational drug design. Carbonic anhydrase (CA) isoforms are important therapeutic targets to treat a range of disorders including glaucoma, obesity, epilepsy, and cancer. For effective treatment isoform-specific inhibitors are needed. In this work we investigated the binding and protonation energetics of sixteen [(2-pyrimidinylthio)acetyl]benzenesulfonamide CA inhibitors using isothermal titration calorimetry and fluorescent thermal shift assay. The compounds were built by combining four sulfonamide headgroups with four tailgroups yielding 16 compounds. Their intrinsic binding thermodynamics showed the limitations of the functional group energetic additivity approach used in fragment-based drug design, especially at the level of enthalpies and entropies of binding. Combined with high resolution crystal structural data correlations were drawn between the chemical functional groups on selected inhibitors and intrinsic thermodynamic parameters of CA-inhibitor complex formation. PMID:25493428

Isolation, structure elucidation and antibacterial activity of methyl-4,8-dimethylundecanate from the marine actinobacterium Streptomyces albogriseolus ECR64.

PubMed

Thirumurugan, Durairaj; Vijayakumar, Ramasamy; Vadivalagan, Chithravel; Karthika, Pushparaj; Alam Khan, Md Khurshid

2018-05-25

Around 120 actinobacterial colonies were isolated from various regions of marine East coast region of Tamil Nadu, India. Among them, 33 were morphologically distinct and they were preliminarily screened for their antibacterial activity against Pseudomonas fluorescens, Vibrio cholerae, V. parahaemolyticus, V. alginolyticus, and Aeromonas hydrophila by cross-streak plate technique. Among the isolated, the isolate ECR64 exhibited maximum zone of inhibition against fish pathogenic bacteria. The crude bioactive compounds were extracted from the isolate ECR64 using different organic solvents which exhibited maximum antibacterial activity. Separation and purification of the bioactive compounds were made by column chromatography which yielded 27 fractions and were re-chromatographed to obtain the active compound. Ultra violet (UV), Fourier transform infrared (FT-IR) and nuclear magnetic resonance (NMR) spectral studies were used to predict the structure of the active compound which was identified as methyl-4,8-dimethylundecanate. The potential isolate ECR64 was identified as Streptomyces albogriseolus by phylogenetic, phenotypic and genotypic (16S rRNA gene sequence) analyses. The identified compound methyl-4,8-dimethylundecanate can be used as potential and alternative drug in disease management of aquaculture. Copyright © 2018 Elsevier Ltd. All rights reserved.

Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor

NASA Astrophysics Data System (ADS)

Duan, Rui; Xu, Xianjin; Zou, Xiaoqin

2018-01-01

D3R 2016 Grand Challenge 2 focused on predictions of binding modes and affinities for 102 compounds against the farnesoid X receptor (FXR). In this challenge, two distinct methods, a docking-based method and a template-based method, were employed by our team for the binding mode prediction. For the new template-based method, 3D ligand similarities were calculated for each query compound against the ligands in the co-crystal structures of FXR available in Protein Data Bank. The binding mode was predicted based on the co-crystal protein structure containing the ligand with the best ligand similarity score against the query compound. For the FXR dataset, the template-based method achieved a better performance than the docking-based method on the binding mode prediction. For the binding affinity prediction, an in-house knowledge-based scoring function ITScore2 and MM/PBSA approach were employed. Good performance was achieved for MM/PBSA, whereas the performance of ITScore2 was sensitive to ligand composition, e.g. the percentage of carbon atoms in the compounds. The sensitivity to ligand composition could be a clue for the further improvement of our knowledge-based scoring function.

Characterization and structure elucidation of antibacterial compound of Streptomyces sp. ECR77 isolated from east coast of India.

PubMed

Thirumurugan, D; Vijayakumar, R

2015-05-01

Forty marine actinobacteria were isolated from the sediments of east coast (Bay of Bengal) region of Tamilnadu, India. Morphologically distinct colonies were primarily tested against fish pathogenic bacteria such as Vibrio cholerae, V. parahaemolyticus, V. alginolyticus, Pseudomonas fluorescens and Aeromonas hydrophila by cross-streak plate method. The secondary metabolites produced by the highly potential strain cultured on starch casein broth were extracted separately with various solvents such as alcohol, ethyl acetate, methanol, petroleum ether and chloroform. The antibacterial assay of the bioactive compounds was tested against the fish pathogenic bacteria by well diffusion method. Of the various solvents used, the ethyl acetate extract of the isolate had good antibacterial activity. The potential strain was identified as Streptomyces labedae by phenotypic, 16S rRNA gene sequence and phylogenetic analysis. Purification of the biologically active compounds by column chromatography led to isolation of 27 fractions. The biologically active fraction was re-chromatographed on a silica gel column to obtain a single active compound, namely N-isopentyltridecanamide. The structure of the compounds was elucidated on the basis of ultra violet, Fourier transform infrared and nuclear magnetic resonance spectra.

Discovery of Potent Myeloid Cell Leukemia 1 (Mcl-1) Inhibitors Using Fragment-Based Methods and Structure-Based Design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Friberg, Anders; Vigil, Dominico; Zhao, Bin

2012-12-17

Myeloid cell leukemia 1 (Mcl-1), a member of the Bcl-2 family of proteins, is overexpressed and amplified in various cancers and promotes the aberrant survival of tumor cells that otherwise would undergo apoptosis. Here we describe the discovery of potent and selective Mcl-1 inhibitors using fragment-based methods and structure-based design. NMR-based screening of a large fragment library identified two chemically distinct hit series that bind to different sites on Mcl-1. Members of the two fragment classes were merged together to produce lead compounds that bind to Mcl-1 with a dissociation constant of <100 nM with selectivity for Mcl-1 over Bcl-xLmore » and Bcl-2. Structures of merged compounds when complexed to Mcl-1 were obtained by X-ray crystallography and provide detailed information about the molecular recognition of small-molecule ligands binding Mcl-1. The compounds represent starting points for the discovery of clinically useful Mcl-1 inhibitors for the treatment of a wide variety of cancers.« less

Synthesis and structural characterization of dinuclear Cd2+, Hg2+ and Fe2+ complexes with neutral bi and tetradentate flexible pyrazole-based ligands

NASA Astrophysics Data System (ADS)

Beheshti, Azizolla; Lalegani, Arash; Behvandi, Fatemeh; Safaeiyan, Forough; Sarkarzadeh, Afsoon; Bruno, Giuseppe; Amiri Rudbari, Hadi

2015-02-01

Four new complexes of [Hg2Cl4(bpp)]n (1), [Hg2Cl4(tdmpp)] (2), [Cd2I4(tdmpp)] (3) and [Fe2Cl4(tdmpp)] (4) were prepared by using the neutral N-donor ligands 1,3-bis(3,5-dimethyl-1-pyrazolyl)propane (bpp) and 1,1,3,3-tetrakis(3,5-dimethyl-1-pyrazolyl)propane (tdmpp) with different flexibility and appropriate metal salts of Cd(II), Hg(II) and Fe(II) ions. These compounds were characterized by the infrared spectroscopy, elemental analysis and X-ray crystallography. Flexible ligands and non-covalent Csbnd H⋯Cl hydrogen bonds play a major role in the crystal packing of compounds 1, 2 and 4. In the two-dimensional non-covalent structure of 1, there are two distinctly different coordination modes for the mercury atoms. One mercury atom has pseudo-trigonal bipyramidal geometry and the other adopts a distorted tetrahedral environment. In the dinuclear structures of 2 and 4 the neutral molecules are linked together by the Csbnd H⋯Cl hydrogen bonds, forming an infinite one-dimensional zigzag chain structure. Compounds 2-4 are isostructural with each other.

Patterning of a compound eye on an extinct dipteran wing.

PubMed

Dinwiddie, April; Rachootin, Stan

2011-04-23

We have discovered unexpected similarities between a novel and characteristic wing organ in an extinct biting midge from Baltic amber, Eohelea petrunkevitchi, and the surface of a dipteran's compound eye. Scanning electron microscope images now reveal vestigial mechanoreceptors between the facets of the organ. We interpret Eohelea's wing organ as the blending of these two developmental systems: the formation and patterning of the cuticle in the eye and of the wing. Typically, only females in the genus carry this distinctive, highly organized structure. Two species were studied (E. petrunkevitchi and E. sinuosa), and the structure differs in form between them. We examine Eohelea's wing structures for modes of fabrication, material properties and biological functions, and the effective ecological environment in which these midges lived. We argue that the current view of the wing organ's function in stridulation has been misconstrued since it was described half a century ago.

Structure of the Zinc-Bound Amino-Terminal Domain of the NMDA Receptor NR2B Subunit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karakas, E.; Simorowski, N; Furukawa, H

2009-01-01

N-methyl-D-aspartate (NMDA) receptors belong to the family of ionotropic glutamate receptors (iGluRs) that mediate the majority of fast excitatory synaptic transmission in the mammalian brain. One of the hallmarks for the function of NMDA receptors is that their ion channel activity is allosterically regulated by binding of modulator compounds to the extracellular amino-terminal domain (ATD) distinct from the L-glutamate-binding domain. The molecular basis for the ATD-mediated allosteric regulation has been enigmatic because of a complete lack of structural information on NMDA receptor ATDs. Here, we report the crystal structures of ATD from the NR2B NMDA receptor subunit in the zinc-freemore » and zinc-bound states. The structures reveal the overall clamshell-like architecture distinct from the non-NMDA receptor ATDs and molecular determinants for the zinc-binding site, ion-binding sites, and the architecture of the putative phenylethanolamine-binding site.« less

Eu9Cd4-xCM2+x-y□ySb9: Ca9Mn4Bi9-type structure stuffed with coinage metals (Cu, Ag, and Au) and the challenges with classical valence theory in describing these possible zintl phases.

PubMed

Kazem, Nasrin; Hurtado, Antonio; Klobes, Benedikt; Hermann, Raphaël P; Kauzlarich, Susan M

2015-02-02

The synthesis, crystal structure, magnetic properties, and europium Mössbauer spectroscopy of the new members of the 9-4-9 Zintl family of Eu(9)Cd(4-x)CM(2+x-y)□(y)Sb(9) (CM = coinage metal: Au, Ag, and Cu) are reported. These compounds crystallize in the Ca(9)Mn(4)Bi(9) structure type (9-4-9) with the 4g interstitial site almost half-occupied by coinage metals; these are the first members in the 9-4-9 family where the interstitial positions are occupied by a monovalent metal. All previously known compounds with this structure type include divalent interstitials where these interstitials are typically the same as the transition metals in the anionic framework. Single-crystal magnetic susceptibility data indicate paramagnetic behavior for all three compounds with antiferromagnetic ordering below 10 K (at 100 Oe) that shifts to lower temperature (<7 K) by applying a 3 T magnetic field. (151)Eu Mössbauer spectra were collected on polycrystalline powder samples of Eu(9)Cd(4-x)CM(2+x-y)□(y)Sb(9) at 50 and 6.5 K in order to evaluate the valence of Eu cations. Although the Zintl formalism states that the five crystallographically distinct Eu sites in Eu(9)Cd(4-x)CM(2+x-y)□(y)Sb9 should bear Eu(2+), the Mössbauer spectral isomer shifts are clearly indicative of both 2+ and 3+ valence of the Eu cations with the Cu- and Au-containing compounds showing higher amounts of Eu(3+). This electronic configuration leads to an excess of negative charge in these compounds that contradicts the expected valence-precise requirement of Zintl phases. The spectra obtained at 6.5 K reveal magnetic ordering for both Eu(2+) and Eu(3+). The field dependence of Eu(2+) indicates two distinct magnetic sublattices, with higher and lower fields, and of a small field for Eu(3+). The site symmetry of the five Eu sites is not distinguishable from the Mössbauer data.

Tuning reactivity of diphenylpropynone derivatives with metal-associated amyloid-β species via structural modifications.

PubMed

Liu, Yuzhong; Kochi, Akiko; Pithadia, Amit S; Lee, Sanghyun; Nam, Younwoo; Beck, Michael W; He, Xiaoming; Lee, Dongkuk; Lim, Mi Hee

2013-07-15

A diphenylpropynone derivative, DPP2, has been recently demonstrated to target metal-associated amyloid-β (metal-Aβ) species implicated in Alzheimer's disease (AD). DPP2 was shown to interact with metal-Aβ species and subsequently control Aβ aggregation (reactivity) in vitro; however, its cytotoxicity has limited further biological applications. In order to improve reactivity toward Aβ species and lower cytotoxicity, along with gaining an understanding of a structure-reactivity-cytotoxicity relationship, we designed, prepared, and characterized a series of small molecules (C1/C2, P1/P2, and PA1/PA2) as structurally modified DPP2 analogues. A similar metal binding site to that of DPP2 was contained in these compounds while their structures were varied to afford different interactions and reactivities with metal ions, Aβ species, and metal-Aβ species. Distinct reactivities of our chemical family toward in vitro Aβ aggregation in the absence and presence of metal ions were observed. Among our chemical series, the compound (C2) with a relatively rigid backbone and a dimethylamino group was observed to noticeably regulate both metal-free and metal-mediated Aβ aggregation to different extents. Using our compounds, cell viability was significantly improved, compared to that with DPP2. Lastly, modifications on the DPP framework maintained the structural properties for potential blood-brain barrier (BBB) permeability. Overall, our studies demonstrated that structural variations adjacent to the metal binding site of DPP2 could govern different metal binding properties, interactions with Aβ and metal-Aβ species, reactivity toward metal-free and metal-induced Aβ aggregation, and cytotoxicity of the compounds, establishing a structure-reactivity-cytotoxicity relationship. This information could help gain insight into structural optimization for developing nontoxic chemical reagents toward targeting metal-Aβ species and modulating their reactivity in biological systems.

Formation of ZrO{sub 2} in coating on Mg–3 wt.%Al–1 wt.%Zn alloy via plasma electrolytic oxidation: Phase and structure of zirconia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Kang Min; Kim, Yeon Sung; Yang, Hae Woong

2015-01-15

An investigation of the coating structure formed on Mg–3 wt.%Al–1 wt.%Zn alloy sample subjected to plasma electrolytic oxidation was examined by field-emission transmission electron microscopy. The plasma electrolytic oxidation process was conducted in a phosphoric acid electrolyte containing K{sub 2}ZrF{sub 6} for 600 s. Microstructural observations showed that the coating consisting of MgO, MgF{sub 2}, and ZrO{sub 2} phases was divided into three distinctive parts, the barrier, intermediate, and outer layers. Nanocrystalline MgO and MgF{sub 2} compounds were observed mainly in the barrier layer of ~ 1 μm thick near to the substrate. From the intermediate to outer layers, variousmore » ZrO{sub 2} polymorphs appeared due to the effects of the plasma arcing temperature on the phase transition of ZrO{sub 2} compounds during the plasma electrolytic oxidation process. In the outer layer, MgO compound grew in the form of a dendrite-like structure surrounded by cubic ZrO{sub 2}. - Highlights: • The barrier layer containing MgO and MgF{sub 2} was observed near to the Mg substrate. • In the intermediate layer, m-, t-, and o-ZrO{sub 2} compounds were additionally detected. • The outer layer contained MgO with the dendrite-like structure surrounded by c-ZrO{sub 2}. • The grain sizes of compounds in oxide layer increased from barrier to outer layer.« less

The synthetic diazonamide DZ-2384 has distinct effects on microtubule curvature and dynamics without neurotoxicity

PubMed Central

Wieczorek, Michal; Tcherkezian, Joseph; Bernier, Cynthia; Prota, Andrea E.; Chaaban, Sami; Rolland, Yannève; Godbout, Claude; Hancock, Mark A.; Arezzo, Joseph C.; Ocal, Ozhan; Rocha, Cecilia; Olieric, Natacha; Hall, Anita; Ding, Hui; Bramoullé, Alexandre; Annis, Matthew G.; Zogopoulos, George; Harran, Patrick G.; Wilkie, Thomas M.; Brekken, Rolf A.; Siegel, Peter M.; Steinmetz, Michel O.; Shore, Gordon C.; Brouhard, Gary J.; Roulston, Anne

2017-01-01

Microtubule-targeting agents (MTAs) are widely used anticancer agents, but toxicities such as neuropathy limit their clinical use. MTAs bind to and alter the stability of microtubules, causing cell death in mitosis. We describe DZ-2384, a preclinical compound that exhibits potent antitumor activity in models of multiple cancer types. It has an unusually high safety margin and lacks neurotoxicity in rats at effective plasma concentrations. DZ-2384 binds the vinca domain of tubulin in a distinct way, imparting structurally and functionally different effects on microtubule dynamics compared to other vinca-binding compounds. X-ray crystallography and electron microscopy studies demonstrate that DZ-2384 causes straightening of curved protofilaments, an effect proposed to favor polymerization of tubulin. Both DZ-2384 and the vinca alkaloid vinorelbine inhibit microtubule growth rate; however, DZ-2384 increases the rescue frequency and preserves the microtubule network in nonmitotic cells and in primary neurons. This differential modulation of tubulin results in a potent MTA therapeutic with enhanced safety. PMID:27856798

Origin of polymorphism of the two-dimensional group-IV monochalcogenides

NASA Astrophysics Data System (ADS)

Wu, Minghui; Wei, Su-Huai; Huang, Li

2017-11-01

Unlike other two-dimensional (2D) isovalent materials, the 2D group IV monochalcogenides, M X (M =Si , Ge, Sn, and Pb; X =S , Se, and Te), are found to be either in a black phosphorene-derived distorted NaCl-type (d -NaCl) structure or a recently predicted P m a 2 structure. Both M and X atoms in the d -NaCl structure are threefold coordinated, whereas M and X in the P m a 2 structure are fourfold and twofold coordinated, respectively. Using first-principles total energy and electronic structure calculations and a global structural search technique, we systematically investigated the mechanism underlying the polymorphism of the 2D group-IV monochalcogenides. Our analysis show that the relative stability of the two distinct crystallographic phases depends on the strength of the M -M covalent bond and the electronegativity difference between the constituent elements M and X . For small cations, the covalency plays more important role, whereas for large cations the Coulomb interaction becomes more dominant. Therefore, the Si X and Ge X compounds assume the P m a 2 structure, whereas the M X compounds with heavy cation elements (M =Sn and Pb) tend to adopt the d -NaCl structure.

Distinct local structure of superconducting Ca10M4As8(Fe2As2)5 (M =Pt ,Ir)

NASA Astrophysics Data System (ADS)

Paris, E.; Wakita, T.; Proux, O.; Yokoya, T.; Kudo, K.; Mitsuoka, D.; Kimura, T.; Fujimura, K.; Nishimoto, N.; Ioka, S.; Nohara, M.; Mizokawa, T.; Saini, N. L.

2017-12-01

We have studied the local structure of superconducting Ca10Pt4As8(Fe2As2)5 (Pt10418) and Ca10Ir4As8(Fe2As2)5 (Ir10418) iron arsenides, showing different transition temperatures (Tc=38 and 16 K, respectively), by polarized Fe K -edge extended x-ray absorption fine-structure measurements. Despite the similar average crystal structures, the local structures of the FeAs4 tetrahedra in the two compounds are found to be very different. The FeAs4 in Pt10418 is close to a regular tetrahedron, while it deviates largely in Ir10418. The Fe-Fe correlations in the two compounds are characterized by similar bond-length characteristics; however, the static disorder in Pt10418 is significantly lower than that in Ir10418. The results suggest that the optimized local structure and reduced disorder are the reasons for higher Tc and well-defined electronic states in Pt10418 unlike Ir10418 showing the coexistence of glassy and normal electrons at the Fermi surface, and hence provide direct evidence of the local-structure-driven optimization of the electronic structure and superconductivity in iron arsenides.

Gas chromatography-mass spectrometric studies of O-alkyl O-2-(N,N-dialkylamino) ethyl alkylphosphonites(phosphonates) for chemical weapons convention verification.

PubMed

Saeidian, Hamid; Babri, Mehran; Ramezani, Atefeh; Ashrafi, Davood; Sarabadani, Mansour; Naseri, Mohammad Taghi

2013-01-01

The electron ionization (EI) mass spectra of a series of O-alkyl O-2-(N,N-dialkylaminolethyl alkylphosphonites(phosphonates), which are precursors of nerve agents, were studied for Chemical Weapons Convention (CWC) verification. General El fragmentation pathways were constructed and discussed. Proposed fragment structures were confirmed through analyzing fragment ions of deuterated analogs and density functional theory (DFT) calculations. The observed fragment ions are due to different fragmentation pathways such as hydrogen and McLafferty+1 rearrangements, alkene, amine and alkoxy elimination by alpha- or beta-cleavage process. Fragment ions distinctly allow unequivocal identification of the interested compounds including those of isomeric compounds. The presence and abundance of fragment ions were found to depend on the size and structure of the alkyl group attached to nitrogen, phosphorus and oxygen atoms.

CamMedNP: building the Cameroonian 3D structural natural products database for virtual screening.

PubMed

Ntie-Kang, Fidele; Mbah, James A; Mbaze, Luc Meva'a; Lifongo, Lydia L; Scharfe, Michael; Hanna, Joelle Ngo; Cho-Ngwa, Fidelis; Onguéné, Pascal Amoa; Owono Owono, Luc C; Megnassan, Eugene; Sippl, Wolfgang; Efange, Simon M N

2013-04-16

Computer-aided drug design (CADD) often involves virtual screening (VS) of large compound datasets and the availability of such is vital for drug discovery protocols. We present CamMedNP - a new database beginning with more than 2,500 compounds of natural origin, along with some of their derivatives which were obtained through hemisynthesis. These are pure compounds which have been previously isolated and characterized using modern spectroscopic methods and published by several research teams spread across Cameroon. In the present study, 224 distinct medicinal plant species belonging to 55 plant families from the Cameroonian flora have been considered. About 80 % of these have been previously published and/or referenced in internationally recognized journals. For each compound, the optimized 3D structure, drug-like properties, plant source, collection site and currently known biological activities are given, as well as literature references. We have evaluated the "drug-likeness" of this database using Lipinski's "Rule of Five". A diversity analysis has been carried out in comparison with the ChemBridge diverse database. CamMedNP could be highly useful for database screening and natural product lead generation programs.

2-tert-Butylamino-4-chloro-6-ethylamino-1,3,5-triazine: a structure with Z' = 4 containing two different molecular conformations and two independent chains of hydrogen-bonded R(2)2(8) rings.

PubMed

Quesada, Antonio; Fontecha, Maria A; López, Maria V; Low, John N; Glidewell, Christopher

2008-08-01

The title compound (trivial name terbutylazine), C(9)H(16)ClN(5), (I), crystallizes with Z' = 4 in the space group Pca2(1), and equal numbers of molecules adopt two different conformations for the ethylamine groups. The four independent molecules form two approximately enantiomorphic pairs. Eight independent N-H...N hydrogen bonds link the molecules into two independent chains of R(2)(2)(8) rings, in which the arrangement of the alkylamine substituents in the independent molecules precludes any further crystallographic symmetry. The significance of this study lies in its finding of two distinct molecular conformations within the structure and two distinct ways in which the molecules are organized into hydrogen-bonded chains, and in its comparison of the hydrogen-bonded structure of (I) with those of analogous 1,3,5-triazines and pyrimidines.

Probing the Sulfur-Modified Capping Layer of Gold Nanoparticles Using Surface Enhanced Raman Spectroscopy (SERS) Effects.

PubMed

Prado, Adilson R; Souza, Danilo Oliveira de; Oliveira, Jairo P; Pereira, Rayssa H A; Guimarães, Marco C C; Nogueira, Breno V; Dixini, Pedro V; Ribeiro, Moisés R N; Pontes, Maria J

2017-12-01

Gold nanoparticles (AuNP) exhibit particular plasmonic properties when stimulated by visible light, which makes them a promising tool to many applications in sensor technology and biomedical applications, especially when associated to sulfur-based compounds. Sulfur species form a great variety of self-assembled structures that cap AuNP and this interaction rules the optical and plasmonic properties of the system. Here, we report the behavior of citrate-stabilized gold nanospheres in two distinct sulfur colloidal solutions, namely, thiocyanate and sulfide ionic solutions. Citrate-capped gold nanospheres were characterized using ultraviolet-visible (UV-Vis) absorption, transmission electron microscopy (TEM), energy dispersive spectroscopy (EDS), and atomic force microscopy (AFM). In the presence of sulfur species, we have observed the formation of NP clusters and chain-like structures, giving rise to surface-enhanced effects. Surface-enhanced Raman spectroscopy (SERS) pointed to a modification in citrate vibrational modes, which suggests substitution of citrate by either thiocyanate or sulfide ions with distinct dynamics, as showed by in situ fluorescence. Moreover, we report the emergence of surface-enhanced infrared absorption (SEIRA) effect, which corroborates SERS conclusions. Further, SEIRA shows a great potential as a tool for specification of sulfur compounds in colloidal solutions, which is particularly useful when dealing with sensor technology.

The Role of Structural and Compositional Heterogeneities in the Insulator-to-Metal Transition in Hole-Doped APd3O4 (A = Ca, Sr).

PubMed

Lamontagne, Leo K; Laurita, Geneva; Knight, Michael; Yusuf, Huma; Hu, Jerry; Seshadri, Ram; Page, Katharine

2017-05-01

The cubic semiconducting compounds APd 3 O 4 (A = Ca, Sr) can be hole-doped by Na substitution on the A site and driven toward more conducting states. This process has been followed here by a number of experimental techniques to understand the evolution of electronic properties. While an insulator-to-metal transition is observed in Ca 1-x Na x Pd 3 O 4 for x ≥ 0.15, bulk metallic behavior is not observed for Sr 1-x Na x Pd 3 O 4 up to x = 0.20. Given the very similar crystal and (calculated) electronic structures of the two materials, the distinct behavior is a matter of interest. We present evidence of local disorder in the A = Sr materials through the analysis of the neutron pair distribution function, which is potentially at the heart of the distinct behavior. Solid-state 23 Na nuclear magnetic resonance studies additionally suggest a percolative insulator-to-metal transition mechanism, wherein presumably small regions with a signal resembling metallic NaPd 3 O 4 form almost immediately upon Na substitution, and this signal grows monotonically with substitution. Some signatures of increased local disorder and a propensity for Na clustering are seen in the A = Sr compounds.

The Structural Enzymology of Iterative Aromatic Polyketide Synthases: A Critical Comparison with Fatty Acid Synthases.

PubMed

Tsai, Shiou-Chuan Sheryl

2018-06-20

Polyketides are a large family of structurally complex natural products including compounds with important bioactivities. Polyketides are biosynthesized by polyketide synthases (PKSs), multienzyme complexes derived evolutionarily from fatty acid synthases (FASs). The focus of this review is to critically compare the properties of FASs with iterative aromatic PKSs, including type II PKSs and fungal type I nonreducing PKSs whose chemical logic is distinct from that of modular PKSs. This review focuses on structural and enzymological studies that reveal both similarities and striking differences between FASs and aromatic PKSs. The potential application of FAS and aromatic PKS structures for bioengineering future drugs and biofuels is highlighted.

In vitro digestion of the self-emulsifying lipid excipient Labrasol(®) by gastrointestinal lipases and influence of its colloidal structure on lipolysis rate.

PubMed

Fernandez, Sylvie; Jannin, Vincent; Chevrier, Stéphanie; Chavant, Yann; Demarne, Frédéric; Carrière, Frédéric

2013-12-01

Labrasol(®) is a self-emulsifying excipient used to improve the oral bioavailability of poorly water-soluble drugs. It is a mixture of acylglycerols and PEG esters, these compounds being substrates for digestive lipases. The characterization of Labrasol(®) gastrointestinal lipolysis is essential for understanding its mode of action. Labrasol(®) lipolysis was investigated using either individual enzymes (gastric lipase, pancreatic lipase-related protein 2, pancreatic carboxyl ester hydrolase) or a combination of enzymes under in vitro conditions mimicking first the gastric phase of lipolysis and second the duodenal one. Specific methods for quantifying lipolysis products were established in order to determine which compounds in Labrasol(®) were preferentially hydrolyzed. Gastric lipase showed a preference for di- and triacylglycerols and the main acylglycerols remaining after gastric lipolysis were monoacylglycerols. PEG-8 diesters were also hydrolyzed to a large extent by gastric lipase. Most of the compounds initially present in Labrasol(®) were found to be totally hydrolyzed after the duodenal phase of lipolysis. The rate of Labrasol(®) hydrolysis by individual lipases was found to vary significantly with the dilution of the excipient in water and the resulting colloidal structures (translucent dispersion; opaque emulsion; transparent microemulsion), each lipase displaying a distinct pattern depending on the particle size. The lipases with distinct substrate specificities used in this study were found to be sensitive probes of phase transitions occurring upon Labrasol(®) dilution. In addition to their use for developing in vitro digestion models, these enzymes are interesting tools for the characterization of self-emulsifying lipid-based formulations.

Conformational interpretation of vescalagin and castalagin physicochemical properties.

PubMed

Vivas, Nicolas; Laguerre, Michel; Pianet de Boissel, Isabelle; Vivas de Gaulejac, Nathalie; Nonier, Marie-Françoise

2004-04-07

Vescalagin and castalagin are two diastereoisomers. The variability of their principal physicochemical properties, compared with their small structural differences, suggests important conformational variations. This study shows, experimentally, that vescalagin has a greater effect on polarity, oxidizability in solution, and thermodegradability than castalagin. Conformational analysis by molecular mechanics demonstrated that vescalagin was more hydrophilic and was more reactive to electrophilic reagents than castalagin. Experimental results were thus explained and demonstrated the distinct behaviors of vescalagin and castalagin. These results were attributed to the C1 position of the two compounds because vescalin and castalin have comparable characteristics. Experimental data were confirmed and interpreted by molecular mechanics. This work represents one of the first attempts to correlate conformation and the properties of phenolic compounds. This step constitutes a predictive method for the pharmacology or chemistry of new compounds.

Two Types of 2D Layered Iodoargentates Based on Trimeric [Ag3I7] Secondary Building Units and Hexameric [Ag6I12] Ternary Building Units: Syntheses, Crystal Structures, and Efficient Visible Light Responding Photocatalytic Properties.

PubMed

Lei, Xiao-Wu; Yue, Cheng-Yang; Zhao, Jian-Qiang; Han, Yong-Fang; Yang, Jiang-Tao; Meng, Rong-Rong; Gao, Chuan-Sheng; Ding, Hao; Wang, Chun-Yan; Chen, Wan-Dong; Hong, Mao-Chun

2015-11-16

With mixed transition-metal-complex, alkali-metal, or organic cations as structure-directing agents, a series of novel two-dimensional (2D) layered inorganic-organic hybrid iodoargentates, namely, Kx[TM(2,2-bipy)3]2Ag6I11 (TM = Mn (1), Fe (2), Co (3), Ni (4), Zn (5); x = 0.89-1) and [(Ni(2,2-bipy)3][H-2,2-bipy]Ag3I6 (6), have been solvothermally synthesized and structurally characterized. All the title compounds feature 2D microporous layers composed by [Ag3I7] secondary building units based on AgI4 tetrahedra. Differently, the [Ag3I7] trimers are directly interconnected via corner-sharing to form the 2D [Ag6I11](5-) layer in compounds 1-5, whereas two neighboring [Ag3I7] trimers are initially condensed into a hexameric [Ag6I12] ternary building unit as a new node, which further self-assembles, leading to the 2D [Ag6I10](4-) layer in compound 6. The UV-vis diffuse-reflectance measurements reveal that all the compounds possess proper semiconductor behaviors with tunable band gaps of 1.66-2.75 eV, which lead to highly efficient photocatalytic degradation activities over organic pollutants under visible light irradiation compared to that of N-dotted P25. Interestingly, all the samples feature distinct photodegradative speeds at the same reaction conditions, and compound 1 features the highest photocatalytic activity among the title phases. The luminescence properties, band structures, and thermal stabilities were also studied.

Differential modulation of FXR activity by chlorophacinone and ivermectin analogs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hsu, Chia-Wen

Chemicals that alter normal function of farnesoid X receptor (FXR) have been shown to affect the homeostasis of bile acids, glucose, and lipids. Several structural classes of environmental chemicals and drugs that modulated FXR transactivation were previously identified by quantitative high-throughput screening (qHTS) of the Tox21 10 K chemical collection. In the present study, we validated the FXR antagonist activity of selected structural classes, including avermectin anthelmintics, dihydropyridine calcium channel blockers, 1,3-indandione rodenticides, and pyrethroid pesticides, using in vitro assay and quantitative structural-activity relationship (QSAR) analysis approaches. (Z)-Guggulsterone, chlorophacinone, ivermectin, and their analogs were profiled for their ability to altermore » CDCA-mediated FXR binding using a panel of 154 coregulator motifs and to induce or inhibit transactivation and coactivator recruitment activities of constitutive androstane receptor (CAR), liver X receptor alpha (LXRα), or pregnane X receptor (PXR). Our results showed that chlorophacinone and ivermectin had distinct modes of action (MOA) in modulating FXR-coregulator interactions and compound selectivity against the four aforementioned functionally-relevant nuclear receptors. These findings collectively provide mechanistic insights regarding compound activities against FXR and possible explanations for in vivo toxicological observations of chlorophacinone, ivermectin, and their analogs. - Highlights: • A subset of Tox21 chemicals was investigated for FXR antagonism. • In vitro and computational approaches were used to evaluate FXR antagonists. • Chlorophacinone and ivermectin had distinct patterns in modulating FXR activity.« less

A diversity-oriented synthesis strategy enabling the combinatorial-type variation of macrocyclic peptidomimetic scaffolds.

PubMed

Isidro-Llobet, Albert; Hadje Georgiou, Kathy; Galloway, Warren R J D; Giacomini, Elisa; Hansen, Mette R; Méndez-Abt, Gabriela; Tan, Yaw Sing; Carro, Laura; Sore, Hannah F; Spring, David R

2015-04-21

Macrocyclic peptidomimetics are associated with a broad range of biological activities. However, despite such potentially valuable properties, the macrocyclic peptidomimetic structural class is generally considered as being poorly explored within drug discovery. This has been attributed to the lack of general methods for producing collections of macrocyclic peptidomimetics with high levels of structural, and thus shape, diversity. In particular, there is a lack of scaffold diversity in current macrocyclic peptidomimetic libraries; indeed, the efficient construction of diverse molecular scaffolds presents a formidable general challenge to the synthetic chemist. Herein we describe a new, advanced strategy for the diversity-oriented synthesis (DOS) of macrocyclic peptidomimetics that enables the combinatorial variation of molecular scaffolds (core macrocyclic ring architectures). The generality and robustness of this DOS strategy is demonstrated by the step-efficient synthesis of a structurally diverse library of over 200 macrocyclic peptidomimetic compounds, each based around a distinct molecular scaffold and isolated in milligram quantities, from readily available building-blocks. To the best of our knowledge this represents an unprecedented level of scaffold diversity in a synthetically derived library of macrocyclic peptidomimetics. Cheminformatic analysis indicated that the library compounds access regions of chemical space that are distinct from those addressed by top-selling brand-name drugs and macrocyclic natural products, illustrating the value of our DOS approach to sample regions of chemical space underexploited in current drug discovery efforts. An analysis of three-dimensional molecular shapes illustrated that the DOS library has a relatively high level of shape diversity.

Copper/H2O2-mediated oxidation of 2'-deoxyguanosine in the presence of 2-naphthol leads to the formation of two distinct isomeric adducts.

PubMed

Fleming, Aaron M; Kannan, Arunkumar; Muller, James G; Liao, Yi; Burrows, Cynthia J

2011-10-07

Exposure of cells to phenolic compounds through exogenous and endogenous sources can lead to deleterious effects via nucleobase modifications of DNA occurring under oxidative conditions. 2'-Deoxyguanosine (dG) is the most electron rich of the four canonical bases and includes many nucleophilic sites; it is also susceptible to oxidation with numerous reactive oxygen species. In these studies, dG was allowed to react with 2-naphthol in the presence of copper or iron salts yielding two principal isomeric products. Spectroscopic analysis and reactions with alkylated nucleosides support the assignment of compound 1a/1b as a pair of atropisomer N(2) adducts and compound 2a/2b as a diastereomeric mixture of tricyclic [4.3.3.0] adducts. Both products are the result of an overall four-electron oxidation process and consequently have the same masses, though drastically different structures, providing mechanistic insight into their formation. Thus, dG alkylation by 2-naphthol under oxidative conditions yields products whose structural properties are altered, leading to potentially mutagenic effects in genomic DNA.

Discovery of novel, highly potent, and selective quinazoline-2-carboxamide-based matrix metalloproteinase (MMP)-13 inhibitors without a zinc binding group using a structure-based design approach.

PubMed

Nara, Hiroshi; Sato, Kenjiro; Naito, Takako; Mototani, Hideyuki; Oki, Hideyuki; Yamamoto, Yoshio; Kuno, Haruhiko; Santou, Takashi; Kanzaki, Naoyuki; Terauchi, Jun; Uchikawa, Osamu; Kori, Masakuni

2014-11-13

Matrix metalloproteinase-13 (MMP-13) has been implicated to play a key role in the pathology of osteoarthritis. On the basis of X-ray crystallography, we designed a series of potent MMP-13 selective inhibitors optimized to occupy the distinct deep S1' pocket including an adjacent branch. Among them, carboxylic acid inhibitor 21k exhibited excellent potency and selectivity for MMP-13 over other MMPs. An effort to convert compound 21k to the mono sodium salt 38 was promising in all animal species studied. Moreover, no overt toxicity was observed in a preliminary repeat dose oral toxicity study of compound 21k in rats. A single oral dose of compound 38 significantly reduced degradation products (CTX-II) released from articular cartilage into the joint cavity in a rat MIA model in vivo. In this article, we report the discovery of highly potent, selective, and orally bioavailable MMP-13 inhibitors as well as their detailed structure-activity data.

Synthesis, structure and characterization of two new organic template-directed gallium phosphate/phosphite-oxalates

NASA Astrophysics Data System (ADS)

Xue, Zhen-Zhen; Pan, Jie; Li, Jin-Hua; Wang, Zong-Hua; Wang, Guo-Ming

2017-06-01

Two new gallium phosphate/phosphite-oxalates hybrid solids, {[H2dmpip][Ga2(HPO4)2(PO4)(C2O4)0.5]·H2O} (1) and [H2apm][Ga2(H2PO3)2(HPO3)2(C2O4)] (2), where dmpip = 2,6-dimethyl-piperazine and apm = N-(3-aminopropyl)morpholine, have been synthesized and structurally characterized. Both of compounds 1 and 2 are formed by the connectivity of the Ga-based polyhedral, phosphite/phosphate groups as well as oxalate units. Compound 1 possesses a two-dimensional layer structure, in which the C2O4 units via an in-plane linkage connect two Ga center within the sheet. While in 2, the C2O4 units serve as bis-bidentates ligands bridging two GaO6 octahedra from two distinct gallium-phosphite chains to give rise to inorganic-organic hybrid layer with 8-membered rings. In these materials, the structure-directing amines reside in the interlayer region and interact with the layers by way of hydrogen-bonds.

(+)-Methyl 3β-acet­oxy-13-carb­oxy-19-hy­droxy-11-oxo-C-norolean-18-en-30-oate γ-lactone

PubMed Central

Gaware, Rawindra; Czollner, Laszlo; Jordis, Ulrich; Mereiter, Kurt

2010-01-01

The title compound, C33H46O7, is an unusual oxydation product of the therapeutic agent glycyrrhetinic acid that has, in comparison to the latter, a distinctly altered triterpene structure with one five- and four six-membered carbocycles complemented by a γ-lactone ring with a spiro-junction and a ring double bond. The junction between the five-membered ring C, a cyclo­penta­none ring, and the six-membered ring D, previously in question, was found to be cis, confirming earlier structure assignments based solely on chemical transformations. In the solid state, the compound exhibits five intra- and four inter­molecular C—H⋯O inter­actions with H⋯O distances less than or equal to 2.70 Å and C—H⋯O greater than 100°. PMID:21587575

A novel metal-organic coordination polymer with unprecedented floor-like structural configuration consisting of two kinds of independent building blocks of triple- and double-stranded braids

NASA Astrophysics Data System (ADS)

Che, Yun-Xia; Luo, Feng; Zheng, Ji-Min

2007-02-01

This paper presents a novel and distinctive metal-organic compound, {[Cd 4(bet) 4Cl 6(H 2O) 4][Cd 2Cl 6]} n (bet=(CH 3) 3NCH 2CO 2, namely betaine) 1, assembled from two independent building blocks of triple- and double-stranded braids, and characterized by an unprecedented floor-like structural configuration. Furthermore, IR, element analysis, and TG-DTA were employed to characterize it. Compound 1 belongs to triclinic system, space group P-1, a = 6.704(2) Å, b = 9.338(3) Å, c = 20.056(7) Å, α = 101.409(5)°, β = 96.650(5)°, γ = 93.148(5)°, V = 1218.5(7) Å 3, Z = 1, R1 = 0.0340, ωR2 = 0.1017.

Structure elucidation of organic compounds from natural sources using 1D and 2D NMR techniques

NASA Astrophysics Data System (ADS)

Topcu, Gulacti; Ulubelen, Ayhan

2007-05-01

In our continuing studies on Lamiaceae family plants including Salvia, Teucrium, Ajuga, Sideritis, Nepeta and Lavandula growing in Anatolia, many terpenoids, consisting of over 50 distinct triterpenoids and steroids, and over 200 diterpenoids, several sesterterpenoids and sesquiterpenoids along with many flavonoids and other phenolic compounds have been isolated. For Salvia species abietanes, for Teucrium and Ajuga species neo-clerodanes for Sideritis species ent-kaurane diterpenes are characteristic while nepetalactones are specific for Nepeta species. In this review article, only some interesting and different type of skeleton having constituents, namely rearranged, nor- or rare diterpenes, isolated from these species will be presented. For structure elucidation of these natural diterpenoids intensive one- and two-dimensional NMR techniques ( 1H, 13C, APT, DEPT, NOE/NOESY, 1H- 1H COSY, HETCOR, COLOC, HMQC/HSQC, HMBC, SINEPT) were used besides mass and some other spectroscopic methods.

Phytochemical constituents and chemosystematic significance of Chrozophora tinctoria (L.) Raf.

PubMed

Marzouk, Mona M; Hussein, Sameh R; Kassem, Mona E S; Kawashty, Salwa A; El Negoumy, Sabry I M

2016-07-01

Twelve compounds were isolated from Chrozophora tinctoria (L.) Raf. They were identified as kaempferol, kaempferol 3-O-β-glucopyranoside, kaempferol 3-O-(6″-α-rhamnopyranosyl)-β-glucopyranoside, quercetin, quercetin 3-O-β-glucopyranoside, quercetin 3-O-(6″-α-rhamnopyranosyl)-β-glucopyranoside, apigenin, apigenin 7-O-β-glucopyranoside, acacetin, gallic acid, methyl gallate and β-sitosterol-3-O-β-glucopyranoside. Their structures were elucidated by chemical and spectral methods. Furthermore, chemosystematics of the isolated compounds is briefly discussed. It was indicated that C. tinctoria is the only species of Chrozophora that has the capability to synthesis kaempferol aglycone and their glycosides, and the finding is supported by its distinct morphological and anatomical aspects.

High-Throughput Screening and Hit Validation of Extracellular-Related Kinase 5 (ERK5) Inhibitors.

PubMed

Myers, Stephanie M; Bawn, Ruth H; Bisset, Louise C; Blackburn, Timothy J; Cottyn, Betty; Molyneux, Lauren; Wong, Ai-Ching; Cano, Celine; Clegg, William; Harrington, Ross W; Leung, Hing; Rigoreau, Laurent; Vidot, Sandrine; Golding, Bernard T; Griffin, Roger J; Hammonds, Tim; Newell, David R; Hardcastle, Ian R

2016-08-08

The extracellular-related kinase 5 (ERK5) is a promising target for cancer therapy. A high-throughput screen was developed for ERK5, based on the IMAP FP progressive binding system, and used to identify hits from a library of 57 617 compounds. Four distinct chemical series were evident within the screening hits. Resynthesis and reassay of the hits demonstrated that one series did not return active compounds, whereas three series returned active hits. Structure-activity studies demonstrated that the 4-benzoylpyrrole-2-carboxamide pharmacophore had excellent potential for further development. The minimum kinase binding pharmacophore was identified, and key examples demonstrated good selectivity for ERK5 over p38α kinase.

Structure-Activity Relationships of the Human Immunodeficiency Virus Type 1 Maturation Inhibitor PF-46396.

PubMed

Murgatroyd, Christopher; Pirrie, Lisa; Tran, Fanny; Smith, Terry K; Westwood, Nicholas J; Adamson, Catherine S

2016-09-15

HIV-1 maturation inhibitors are a novel class of antiretroviral compounds that consist of two structurally distinct chemical classes: betulinic acid derivatives and the pyridone-based compound PF-46396. It is currently believed that both classes act by similar modes of action to generate aberrant noninfectious particles via inhibition of CA-SP1 cleavage during Gag proteolytic processing. In this study, we utilized a series of novel analogues with decreasing similarity to PF-46396 to determine the chemical groups within PF-46396 that contribute to antiviral activity, Gag binding, and the relationship between these essential properties. A spectrum of antiviral activity (active, intermediate, and inactive) was observed across the analogue series with respect to CA-SP1 cleavage and HIV-1 (NL4-3) replication kinetics in Jurkat T cells. We demonstrate that selected inactive analogues are incorporated into wild-type (WT) immature particles and that one inactive analogue is capable of interfering with PF-46396 inhibition of CA-SP1 cleavage. Mutations that confer PF-46396 resistance can impose a defective phenotype on HIV-1 that can be rescued in a compound-dependent manner. Some inactive analogues retained the capacity to rescue PF-46396-dependent mutants (SP1-A3V, SP1-A3T, and CA-P157S), implying that they can also interact with mutant Gag. The structure-activity relationships observed in this study demonstrate that (i) the tert-butyl group is essential for antiviral activity but is not an absolute requirement for Gag binding, (ii) the trifluoromethyl group is optimal but not essential for antiviral activity, and (iii) the 2-aminoindan group is important for antiviral activity and Gag binding but is not essential, as its replacement is tolerated. Combinations of antiretroviral drugs successfully treat HIV/AIDS patients; however, drug resistance problems make the development of new mechanistic drug classes an ongoing priority. HIV-1 maturation inhibitors are novel as they target the Gag protein, specifically by inhibiting CA-SP1 proteolytic cleavage. The lack of high-resolution structural information of the CA-SP1 target in Gag has hindered our understanding of the inhibitor-binding pocket and maturation inhibitor mode of action. Therefore, we utilized analogues of the maturation inhibitor PF-46396 as chemical tools to determine the chemical components of PF-46396 that contribute to antiviral activity and Gag binding and the relationship between these essential properties. This is the first study to report structure-activity relationships of the maturation inhibitor PF-46396. PF-46396 is chemically distinct from betulinic acid-derived maturation inhibitors; therefore, our data provide a foundation of knowledge that will aid our understanding of how structurally distinct maturation inhibitors act by similar modes of action. Copyright © 2016 Murgatroyd et al.

Design and Discovery of Functionally Selective Serotonin 2C (5-HT2C) Receptor Agonists.

PubMed

Cheng, Jianjun; McCorvy, John D; Giguere, Patrick M; Zhu, Hu; Kenakin, Terry; Roth, Bryan L; Kozikowski, Alan P

2016-11-10

On the basis of the structural similarity of our previous 5-HT 2C agonists with the melatonin receptor agonist tasimelteon and the putative biological cross-talk between serotonergic and melatonergic systems, a series of new (2,3-dihydro)benzofuran-based compounds were designed and synthesized. The compounds were evaluated for their selectivity toward 5-HT 2A , 5-HT 2B , and 5-HT 2C receptors in the calcium flux assay with the ultimate goal to generate selective 5-HT 2C agonists. Selected compounds were studied for their functional selectivity by comparing their transduction efficiency at the G protein signaling pathway versus β-arrestin recruitment. The most functionally selective compound (+)-7e produced weak β-arrestin recruitment and also demonstrated less receptor desensitization compared to serotonin in both calcium flux and phosphoinositide (PI) hydrolysis assays. We report for the first time that selective 5-HT 2C agonists possessing weak β-arrestin recruitment can produce distinct receptor desensitization properties.

Antioxidant activity, total phenolics and flavonoids contents: Should we ban in vitro screening methods?

PubMed

Granato, Daniel; Shahidi, Fereidoon; Wrolstad, Ronald; Kilmartin, Paul; Melton, Laurence D; Hidalgo, Francisco J; Miyashita, Kazuo; Camp, John van; Alasalvar, Cesarettin; Ismail, Amin B; Elmore, Stephen; Birch, Gordon G; Charalampopoulos, Dimitris; Astley, Sian B; Pegg, Ronald; Zhou, Peng; Finglas, Paul

2018-10-30

As many studies are exploring the association between ingestion of bioactive compounds and decreased risk of non-communicable diseases, the scientific community continues to show considerable interest in these compounds. In addition, as many non-nutrients with putative health benefits are reducing agents, hydrogen donors, singlet oxygen quenchers or metal chelators, measurement of antioxidant activity using in vitro assays has become very popular over recent decades. Measuring concentrations of total phenolics, flavonoids, and other compound (sub)classes using UV/Vis spectrophotometry offers a rapid chemical index, but chromatographic techniques are necessary to establish structure-activity. For bioactive purposes, in vivo models are required or, at the very least, methods that employ distinct mechanisms of action (i.e., single electron transfer, transition metal chelating ability, and hydrogen atom transfer). In this regard, better understanding and application of in vitro screening methods should help design of future research studies on 'bioactive compounds'. Copyright © 2018 Elsevier Ltd. All rights reserved.

Advances in the synthesis of inorganic nanotubes and fullerene-like nanoparticles.

PubMed

Tenne, Reshef

2003-11-03

In analogy to graphite, nanoparticles of inorganic compounds with lamellar two-dimensional structure, such as MoS(2), are not stable against folding, and can adopt nanotubular and fullerene-like structures, nicknamed inorganic fullerenes or IF. Various applications for such nanomaterials were proposed. For instance, IF-WS(2) nanoparticles were shown to have beneficial effects as solid lubricants and as part of tribological surfaces. Further applications of IF for high-tensile-strength fibers, hydrogen storage, rechargeable batteries, catalysis, and in nanotechnology are being contemplated. This Minireview highlights some of the latest developments in the synthesis of inorganic nanotubes and fullerene-like structures. Some structural aspects and properties of IF, which are distinct from the bulk materials, are briefly discussed.

Conserved Binding Mode of Human [beta subscript 2] Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-ray Crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wacker, Daniel; Fenalti, Gustavo; Brown, Monica A.

2010-11-15

G protein-coupled receptors (GPCRs) represent a large fraction of current pharmaceutical targets, and of the GPCRs, the {beta}{sub 2} adrenergic receptor ({beta}{sub 2}AR) is one of the most extensively studied. Previously, the X-ray crystal structure of {beta}{sub 2}AR has been determined in complex with two partial inverse agonists, but the global impact of additional ligands on the structure or local impacts on the binding site are not well-understood. To assess the extent of such ligand-induced conformational differences, we determined the crystal structures of a previously described engineered {beta}{sub 2}AR construct in complex with two inverse agonists: ICI 118,551 (2.8 {angstrom}),more » a recently described compound (2.8 {angstrom}) (Kolb et al, 2009), and the antagonist alprenolol (3.1 {angstrom}). The structures show the same overall fold observed for the previous {beta}{sub 2}AR structures and demonstrate that the ligand binding site can accommodate compounds of different chemical and pharmacological properties with only minor local structural rearrangements. All three compounds contain a hydroxy-amine motif that establishes a conserved hydrogen bond network with the receptor and chemically diverse aromatic moieties that form distinct interactions with {beta}{sub 2}AR. Furthermore, receptor ligand cross-docking experiments revealed that a single {beta}{sub 2}AR complex can be suitable for docking of a range of antagonists and inverse agonists but also indicate that additional ligand-receptor structures may be useful to further improve performance for in-silico docking or lead-optimization in drug design.« less

A UV resonance Raman (UVRR) spectroscopic study on the extractable compounds of Scots pine ( Pinus sylvestris) wood . Part I: Lipophilic compounds

NASA Astrophysics Data System (ADS)

Nuopponen, M.; Willför, S.; Jääskeläinen, A.-S.; Sundberg, A.; Vuorinen, T.

2004-11-01

The wood resin in Scots pine ( Pinus sylvestris) stemwood and branch wood were studied using UV resonance Raman (UVRR) spectroscopy. UVRR spectra of the sapwood and heartwood hexane extracts, solid wood samples and model compounds (six resin acids, three fatty acids, a fatty acid ester, sitosterol and sitosterol acetate) were collected using excitation wavelengths of 229, 244 and 257 nm. In addition, visible Raman spectra of the fatty and resin acids were recorded. Resin compositions of heartwood and sapwood hexane extracts were determined using gas chromatography. Raman signals of both conjugated and isolated double bonds of all the model compounds were resonance enhanced by UV excitation. The oleophilic structures showed strong bands in the region of 1660-1630 cm -1. Distinct structures were enhanced depending on the excitation wavelength. The UVRR spectra of the hexane extracts showed characteristic bands for resin and fatty acids. It was possible to identify certain resin acids from the spectra. UV Raman spectra collected from the solid wood samples containing wood resin showed a band at ˜1650 cm -1 due to unsaturated resin components. The Raman signals from extractives in the resin rich branch wood sample gave even more strongly enhanced signals than the aromatic lignin.

A UV resonance Raman (UVRR) spectroscopic study on the extractable compounds of Scots pine (Pinus sylvestris) wood. Part I: lipophilic compounds.

PubMed

Nuopponen, M; Willför, S; Jääskeläinen, A-S; Sundberg, A; Vuorinen, T

2004-11-01

The wood resin in Scots pine (Pinus sylvestris) stemwood and branch wood were studied using UV resonance Raman (UVRR) spectroscopy. UVRR spectra of the sapwood and heartwood hexane extracts, solid wood samples and model compounds (six resin acids, three fatty acids, a fatty acid ester, sitosterol and sitosterol acetate) were collected using excitation wavelengths of 229, 244 and 257 nm. In addition, visible Raman spectra of the fatty and resin acids were recorded. Resin compositions of heartwood and sapwood hexane extracts were determined using gas chromatography. Raman signals of both conjugated and isolated double bonds of all the model compounds were resonance enhanced by UV excitation. The oleophilic structures showed strong bands in the region of 1660-1630 cm(-1). Distinct structures were enhanced depending on the excitation wavelength. The UVRR spectra of the hexane extracts showed characteristic bands for resin and fatty acids. It was possible to identify certain resin acids from the spectra. UV Raman spectra collected from the solid wood samples containing wood resin showed a band at approximately 1650 cm(-1) due to unsaturated resin components. The Raman signals from extractives in the resin rich branch wood sample gave even more strongly enhanced signals than the aromatic lignin.

Towards the discovery of drug-like RNA ligands?

PubMed

Foloppe, Nicolas; Matassova, Natalia; Aboul-Ela, Fareed

2006-11-01

Targeting RNA with small molecule drugs is an area of great potential for therapeutic treatment of infections and possibly genetic and autoimmune diseases. However, a mature set of precedents and established methodology is lacking. The physicochemical properties of RNA raise specific issues and obstacles to development, and contribute to explain the distinct characteristics of natural RNA ligands, including antibiotics. Yet, RNA-targeting strategies are being implemented to reinvigorate antibacterial discovery by using the ribosomal X-ray structures to modify known antibiotics. To exploit further these structures, we suggest the use of existing protein kinase-directed libraries of drug-like compounds to target the A-site of the bacterial ribosome, on the basis of a specific structural hypothesis.

Anle138b and related compounds are aggregation specific fluorescence markers and reveal high affinity binding to α-synuclein aggregates.

PubMed

Deeg, Andreas A; Reiner, Anne M; Schmidt, Felix; Schueder, Florian; Ryazanov, Sergey; Ruf, Viktoria C; Giller, Karin; Becker, Stefan; Leonov, Andrei; Griesinger, Christian; Giese, Armin; Zinth, Wolfgang

2015-09-01

Special diphenyl-pyrazole compounds and in particular anle138b were found to reduce the progression of prion and Parkinson's disease in animal models. The therapeutic impact of these compounds was attributed to the modulation of α-synuclein and prion-protein aggregation related to these diseases. Photophysical and photochemical properties of the diphenyl-pyrazole compounds anle138b, anle186b and sery313b and their interaction with monomeric and aggregated α-synuclein were studied by fluorescence techniques. The fluorescence emission of diphenyl-pyrazole is strongly increased upon incubation with α-synuclein fibrils, while no change in fluorescence emission is found when brought in contact with monomeric α-synuclein. This points to a distinct interaction between diphenyl-pyrazole and the fibrillar structure with a high binding affinity (Kd=190±120nM) for anle138b. Several α-synuclein proteins form a hydrophobic binding pocket for the diphenyl-pyrazole compound. A UV-induced dehalogenation reaction was observed for anle138b which is modulated by the hydrophobic environment of the fibrils. Fluorescence of the investigated diphenyl-pyrazole compounds strongly increases upon binding to fibrillar α-synuclein structures. Binding at high affinity occurs to hydrophobic pockets in the fibrils. The observed particular fluorescence properties of the diphenyl-pyrazole molecules open new possibilities for the investigation of the mode of action of these compounds in neurodegenerative diseases. The high binding affinity to aggregates and the strong increase in fluorescence upon binding make the compounds promising fluorescence markers for the analysis of aggregation-dependent epitopes. Copyright © 2015 Elsevier B.V. All rights reserved.

Synthetic Cannabinoids: Pharmacology, Behavioral Effects, and Abuse Potential

PubMed Central

Tai, Sherrica; Fantegrossi, William E.

2015-01-01

Cannabis has been used throughout the world for centuries. The psychoactive effects of cannabis are largely attributable to Δ9-tetrahydrocannabinol (Δ9-THC), the prototypical cannabinoid that occurs naturally in the plant. More recently, chemically- and pharmacologically-distinct synthetic cannabinoids (SCBs) have emerged as drugs of abuse. As compared to Δ9-THC, the distinct structures of these compounds allow them to avoid legal restrictions (at least initially) and detection in standard drug screens. This has contributed to the popularity of SCBs among drug users who seek to avoid positive drug screens. Importantly, the distinct structures of the SCBs also typically result in increased affinity for and efficacy at cannabinoid CB1 receptors, which are thought to be responsible for the psychoactive effects of Δ9-THC and its analogues. Accordingly, it seems likely that these more powerful cannabimimetic effects could result in increased adverse reactions and toxicities not elicited by Δ9-THC in cannabis. Animal models useful for the study of emerging SCBs include the cannabinoid tetrad, drug discrimination, and assays of tolerance, dependence, and withdrawal. However, these in vivo procedures have not been particularly informative with regards to drug efficacy, where the majority of SCB effects are comparable to those of Δ9-THC. In contrast, essentially all in vitro measures of drug efficacy confirm Δ9-THC as a relatively weak CB1 partial agonist, while the majority of the SCBs detected in commercial preparations are full agonists at the CB1 receptor. As use of these emerging SCBs continues to rise, there is an urgent need to better understand the pharmacology and toxicology of these novel compounds. PMID:26413452

Inhalation TTC values: A new integrative grouping approach considering structural, toxicological and mechanistic features.

PubMed

Tluczkiewicz, I; Kühne, R; Ebert, R-U; Batke, M; Schüürmann, G; Mangelsdorf, I; Escher, S E

2016-07-01

The present publication describes an integrative grouping concept to derive threshold values for inhalation exposure. The classification scheme starts with differences in toxicological potency and develops criteria to group compounds into two potency classes, namely toxic (T-group) or low toxic (L-group). The TTC concept for inhalation exposure is based on the TTC RepDose data set, consisting of 296 organic compounds with 608 repeated-dose inhalation studies. Initially, 21 structural features (SFs) were identified as being characteristic for compounds of either high or low NOEC values (Schüürmann et al., 2016). In subsequent analyses these SF groups were further refined by taking into account structural homogeneity, type of toxicological effect observed, differences in absorption, metabolism and mechanism of action (MoA), to better define their structural and toxicological boundaries. Differentiation of a local or systemic mode of action did not improve the classification scheme. Finally, 28 groups were discriminated: 19 T-groups and 9 L-groups. Clearly distinct thresholds were derived for the T- and L-toxicity groups, being 2 × 10(-5) ppm (2 μg/person/day) and 0.05 ppm (4260 μg/person/day), respectively. The derived thresholds and the classification are compared to the initial mainly structure driven grouping (Schüürmann et al., 2016) and to the Cramer classification. Copyright © 2016 Elsevier Inc. All rights reserved.

Study Approach of Antioxidant Properties in Foods: Update and Considerations.

PubMed

Durazzo, Alessandra

2017-02-28

The assessment of interactions between natural antioxidants and other food matrix components represents the main step in the investigation of total antioxidant properties, in terms of potential health benefits. The diversity of chemical structures of natural compounds, besides their possible interactions, as well as the biological role and different modes of action makes it difficult to assess a single and reliable procedure for the evaluation of antioxidant activity. Today, much attention is given to the distinction between extractable and non-extractable antioxidants as a key tool in the description of the nutritional and healthy properties of food matrices. The starting point for the investigation of antioxidant effects of food extracts is the analysis of antioxidant properties of pure compounds and their interactions. Another complementary approach could be represented by the study of how different biologically active compound-rich extracts contribute to the total antioxidant capacity.

Study Approach of Antioxidant Properties in Foods: Update and Considerations

PubMed Central

Durazzo, Alessandra

2017-01-01

The assessment of interactions between natural antioxidants and other food matrix components represents the main step in the investigation of total antioxidant properties, in terms of potential health benefits. The diversity of chemical structures of natural compounds, besides their possible interactions, as well as the biological role and different modes of action makes it difficult to assess a single and reliable procedure for the evaluation of antioxidant activity. Today, much attention is given to the distinction between extractable and non-extractable antioxidants as a key tool in the description of the nutritional and healthy properties of food matrices. The starting point for the investigation of antioxidant effects of food extracts is the analysis of antioxidant properties of pure compounds and their interactions. Another complementary approach could be represented by the study of how different biologically active compound-rich extracts contribute to the total antioxidant capacity. PMID:28264480

Molecular Phenotyping Combines Molecular Information, Biological Relevance, and Patient Data to Improve Productivity of Early Drug Discovery.

PubMed

Drawnel, Faye Marie; Zhang, Jitao David; Küng, Erich; Aoyama, Natsuyo; Benmansour, Fethallah; Araujo Del Rosario, Andrea; Jensen Zoffmann, Sannah; Delobel, Frédéric; Prummer, Michael; Weibel, Franziska; Carlson, Coby; Anson, Blake; Iacone, Roberto; Certa, Ulrich; Singer, Thomas; Ebeling, Martin; Prunotto, Marco

2017-05-18

Today, novel therapeutics are identified in an environment which is intrinsically different from the clinical context in which they are ultimately evaluated. Using molecular phenotyping and an in vitro model of diabetic cardiomyopathy, we show that by quantifying pathway reporter gene expression, molecular phenotyping can cluster compounds based on pathway profiles and dissect associations between pathway activities and disease phenotypes simultaneously. Molecular phenotyping was applicable to compounds with a range of binding specificities and triaged false positives derived from high-content screening assays. The technique identified a class of calcium-signaling modulators that can reverse disease-regulated pathways and phenotypes, which was validated by structurally distinct compounds of relevant classes. Our results advocate for application of molecular phenotyping in early drug discovery, promoting biological relevance as a key selection criterion early in the drug development cascade. Copyright © 2017 Elsevier Ltd. All rights reserved.

Addressing Facts and Gaps in the Phenolics Chemistry of Winery By-Products.

PubMed

Machado, Nelson F L; Domínguez-Perles, Raúl

2017-02-14

Grape and wine phenolics display a noticeable structural diversity, encompassing distinct compounds ranging from simple molecules to oligomers, as well as polymers usually designated as tannins. Since these compounds contribute critically to the organoleptic properties of wines, their analysis and quantification are of primordial importance for winery industry operators. Besides, the occurrence of these compounds has been also extensively described in winery residues, which have been pointed as a valuable source of bioactive phytochemicals presenting potential for the development of new added value products that could fit the current market demands. Therefore, the cumulative knowledge generated during the last decades has allowed the identification of the most promising compounds displaying interesting biological functions, as well as the chemical features responsible for the observed bioactivities. In this regard, the present review explores the scope of the existing knowledge, concerning the compounds found in these winery by-products, as well as the chemical features presumably responsible for the biological functions already identified. Moreover, the present work will hopefully pave the way for further actions to develop new powerful applications to these materials, thus, contributing to more sustainable valorization procedures and the development of newly obtained compounds with enhanced biological properties.

Multifunctional glial support by Semper cells in the Drosophila retina

PubMed Central

Charlton-Perkins, Mark A.

2017-01-01

Glial cells play structural and functional roles central to the formation, activity and integrity of neurons throughout the nervous system. In the retina of vertebrates, the high energetic demand of photoreceptors is sustained in part by Müller glia, an intrinsic, atypical radial glia with features common to many glial subtypes. Accessory and support glial cells also exist in invertebrates, but which cells play this function in the insect retina is largely undefined. Using cell-restricted transcriptome analysis, here we show that the ommatidial cone cells (aka Semper cells) in the Drosophila compound eye are enriched for glial regulators and effectors, including signature characteristics of the vertebrate visual system. In addition, cone cell-targeted gene knockdowns demonstrate that such glia-associated factors are required to support the structural and functional integrity of neighboring photoreceptors. Specifically, we show that distinct support functions (neuronal activity, structural integrity and sustained neurotransmission) can be genetically separated in cone cells by down-regulating transcription factors associated with vertebrate gliogenesis (pros/Prox1, Pax2/5/8, and Oli/Olig1,2, respectively). Further, we find that specific factors critical for glial function in other species are also critical in cone cells to support Drosophila photoreceptor activity. These include ion-transport proteins (Na/K+-ATPase, Eaat1, and Kir4.1-related channels) and metabolic homeostatic factors (dLDH and Glut1). These data define genetically distinct glial signatures in cone/Semper cells that regulate their structural, functional and homeostatic interactions with photoreceptor neurons in the compound eye of Drosophila. In addition to providing a new high-throughput model to study neuron-glia interactions, the fly eye will further help elucidate glial conserved "support networks" between invertebrates and vertebrates. PMID:28562601

A Role for 2-Methyl Pyrrole in the Browning of 4-Oxopentanal and Limonene Secondary Organic Aerosol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aiona, Paige K.; Lee, Hyun Ji; Lin, Peng

“Brown Carbon” (BrC) is a type of organic particulate matter that absorbs visible and near ultraviolet radiation. Reactions of carbonyls in secondary organic aerosol (SOA) produced from limonene with ammonia (NH3) or ammonium sulfate (AS) are known to produce BrC with a distinctive absorption band at 500 nm. Although the general mechanism for this process has been proposed in previous studies, the specific molecular structures of the light-absorbing species remain unclear. This study examined the browning processes occurring in aqueous solutions of AS and 4-oxopentanal (4-OPA), which has a 1,4-dicarbonyl structural motif present in many limonene SOA compounds. The reactionmore » of 4-OPA with AS in a bulk aqueous solution produces a 2-methyl pyrrole (2-MP) intermediate, which is not a strong light absorber by itself, but can react further with carbonyl compounds leading to the eventual formation of BrC chromophores. The direct involvement of 2-MP in the browning process was demonstrated by reacting 2-MP with 4-OPA and with limonene SOA, both of which produced BrC chromophores with distinctive absorption bands at visible wavelengths. The formation of BrC in reaction of 4-OPA with AS and ammonium nitrate (AN) was found to be accelerated by evaporation of the solution suggesting an important role of the dehydration processes in BrC formation from 1,4- dicarbonyls. 4-OPA was also found to produce BrC in aqueous reactions with a broad spectrum of amino acids and amines. The results suggest that 4-OPA may be the smallest atmospherically relevant compound capable of browning by the same mechanism as limonene SOA.« less

Deciphering structure-activity relationships in a series of Tat/TAR inhibitors.

PubMed

Pascale, Lise; González, Alejandro López; Di Giorgio, Audrey; Gaysinski, Marc; Teixido Closa, Jordi; Tejedor, Roger Estrada; Azoulay, Stéphane; Patino, Nadia

2016-11-01

A series of pentameric "Polyamide Amino Acids" (PAAs) compounds derived from the same trimeric precursor have been synthesized and investigated as HIV TAR RNA ligands, in the absence and in the presence of a Tat fragment. All PAAs bind TAR with similar sub-micromolar affinities but their ability to compete efficiently with the Tat fragment strongly differs, IC50 ranging from 35 nM to >2 μM. While NMR and CD studies reveal that all PAA interact with TAR at the same site and induce globally the same RNA conformational change upon binding, a comparative thermodynamic study of PAA/TAR equilibria highlights distinct TAR binding modes for Tat competitor and non-competitor PAAs. This led us to suggest two distinct interaction modes that have been further validated by molecular modeling studies. While the binding of Tat competitor PAAs induces a contraction at the TAR bulge region, the binding of non-competitor ones widens it. This could account for the distinct PAA ability to compete with Tat fragment. Our work illustrates how comparative thermodynamic studies of a series of RNA ligands of same chemical family are of value for understanding their binding modes and for rationalizing structure-activity relationships.

An Unsymmetric Ligand Framework for Noncoupled Homo- and Heterobimetallic Complexes.

PubMed

Haas, Ruth M; Hern, Zachary; Sproules, Stephen; Hess, Corinna R

2017-12-18

We introduce a new unsymmetric ligand, PDIpCy (PDI = pyridyldiimine; Cy = cyclam), that offers two distinct, noncoupled coordination sites. A series of homo- and heterobimetallic complexes, [Zn 2 (PDIpCy)(THF)(OTf) 4 ] (1; THF = tetrahydrofuran and OTf = triflate), [Ni 2 (PDIpCy)(THF)(OTf) 2 ](OTf) 2 (2), and [NiZn(PDIpCy)(THF)(OTf) 4 ] (3), are described. The one-electron-reduced compounds, [Zn 2 (PDIpCy)(OTF) 3 ] (4), [Ni 2 (PDIpCy)(OTf)](OTf) 2 (5), and [NiZn(PDIpCy)(OTf) 3 ] (6), were isolated, and their electronic structures were characterized. The reduced compounds are charge-separated species, with electron storage at either the PDI ligand (4) or at the PDI-bound metal ion (5 and 6).

Chemical sensors based on N-substituted polyaniline derivatives: reactivity and adsorption studies via electronic structure calculations.

PubMed

Mandú, Larissa O; Batagin-Neto, Augusto

2018-06-09

Conjugated organic polymers represent an important class of materials for varied technological applications including in active layers of chemical sensors. In this context, polyaniline (PANI) derivatives are promising candidates, mainly due to their high chemical stability, good processability, versatility of synthesis, polymerization, and doping, as well as relative low cost. In this study, electronic structure calculations were carried out for varied N-substituted PANI derivatives in order to investigate the potential sensory properties of these materials. The opto-electronic properties of nine distinct compounds were evaluated and discussed in terms of the employed substituents. Preliminary reactivity studies were performed in order to identify adsorption centers on the oligomer structures via condensed-to-atoms Fukui indexes (CAFI). Finally, adsorption studies were carried out for selected derivatives considering five distinct gaseous analytes. The influence of the analytes on the oligomer properties were investigated via the evaluation of average binding energies and changes on the structural features, optical absorption spectra, frontier orbitals distribution, and total density of states in relation to the isolated oligomers. The obtained results indicate the derivatives PANI-NO 2 and PANI-C 6 H 5 as promising materials for the development of improved chemical sensors.

Discovery of potent and novel smoothened antagonists via structure-based virtual screening and biological assays.

PubMed

Lu, Wenfeng; Zhang, Dihua; Ma, Haikuo; Tian, Sheng; Zheng, Jiyue; Wang, Qin; Luo, Lusong; Zhang, Xiaohu

2018-05-23

The Hedgehog (Hh) signaling pathway plays a critical role in controlling patterning, growth and cell migration during embryonic development. Aberrant activation of Hh signaling has been linked to tumorigenesis in various cancers, such as basal cell carcinoma (BCC) and medulloblastoma. As a key member of the Hh pathway, the Smoothened (Smo) receptor, a member of the G protein-coupled receptor (GPCR) family, has emerged as an attractive therapeutic target for the treatment and prevention of human cancers. The recent determination of several crystal structures of Smo in complex with different antagonists offers the possibility to perform structure-based virtual screening for discovering potent Smo antagonists with distinct chemical scaffolds. In this study, based on the two Smo crystal complexes with the best capacity to distinguish the known Smo antagonists from decoys, the molecular docking-based virtual screening was conducted to identify promising Smo antagonists from ChemDiv library. A total of 21 structurally novel and diverse compounds were selected for experimental testing, and six of them exhibited significant inhibitory activity against the Hh pathway activation (IC 50  < 10 μM) in a GRE (Gli-responsive element) reporter gene assay. Specifically, the most potent compound (compound 20: 47 nM) showed comparable Hh signaling inhibition to vismodegib (46 nM). Compound 20 was further confirmed to be a potent Smo antagonist in a fluorescence based competitive binding assay. Optimization using substructure searching method led to the discovery of 12 analogues of compound 20 with decent Hh pathway inhibition activity, including four compounds with IC 50 lower than 1 μM. The important residues uncovered by binding free energy calculation (MM/GBSA) and binding free energy decomposition were highlighted and discussed. These findings suggest that the novel scaffold afforded by compound 20 can be used as a good starting point for further modification/optimization and the clarified interaction patterns may also guide us to find more potent Smo antagonists. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Solid-state synthesis in the system Na 0.8Nb yW 1-yO 3 with 0⩽ y⩽0.4: A new phase, Na 0.5NbO 2.75, with perovskite-type structure

NASA Astrophysics Data System (ADS)

Debnath, Tapas; Rüscher, Claus H.; Gesing, Thorsten M.; Koepke, Jürgen; Hussain, Altaf

2008-04-01

Series of compounds in the system Na xNb yW 1-yO 3 were prepared according to the appropriate molar ratio of Na 2WO 4, WO 3, WO 2 and Nb 2O 5 with x=0.80 and 0.0⩽ y⩽0.4 at 600 °C in evacuated silica glass tubes. These compounds were investigated by X-ray powder diffraction, optical microscopy, microprobe analysis, Raman and optical microspectroscopy. A y-dependent separation into three distinct coloured crystallites with cubic perovskite-type structures is observed: (i) red-orange crystallites with composition Na xWO 3 with slightly decreasing x (i.e. 0.8-0.72) with increasing nominal y, (ii) bluish solid solution of composition Na xNb yW 1-yO 3 and (iii) white crystallites of a new phase having defect perovskite-type structure with composition Na 0.5NbO 2.75.

Liquid structure of dibutyl sulfoxide

DOE PAGES

Lo Celso, Fabrizio; Aoun, Bachir; Triolo, Alessandro; ...

2016-05-16

We present experimental (x-ray diffraction) data on the structure of liquid dibutyl sulfoxide at 320 K and rationalize them by means of Molecular Dynamics simulations. Not unexpectedly, DBSO bearing a strong dipolar moiety and two medium length, apolar, butyl chains, this compound turns out to be characterised by a distinct degree of polar-vs-apolar structural differentiation at the nm spatial scale that is fingerprinted in a low Q peak in its x-ray diffraction pattern. Similarly to, but to a larger extent than its shorter chain family members (such as DMSO), DBSO is also characterised by an enhanced dipole-dipole correlation that ismore » responsible for the moderate Kirkwood correlation factor as well as for the self-association detected in this compound. In conclusion, we show however that the supposedly relevant hydrogen bonding correlations between oxygen and butyl chain hydrogens are of limited extent and only in the case of α-hydrogens appreciable indication of the existence of such an interaction is found, but it turns out to be a mere consequence of the strong dipole-dipole correlation.« less

Experimental Observation of Redox-Induced Fe-N Switching Behavior as a Determinant Role for Oxygen Reduction Activity.

PubMed

Jia, Qingying; Ramaswamy, Nagappan; Hafiz, Hasnain; Tylus, Urszula; Strickland, Kara; Wu, Gang; Barbiellini, Bernardo; Bansil, Arun; Holby, Edward F; Zelenay, Piotr; Mukerjee, Sanjeev

2015-12-22

The commercialization of electrochemical energy conversion and storage devices relies largely upon the development of highly active catalysts based on abundant and inexpensive materials. Despite recent achievements in this respect, further progress is hindered by the poor understanding of the nature of active sites and reaction mechanisms. Herein, by characterizing representative iron-based catalysts under reactive conditions, we identify three Fe-N4-like catalytic centers with distinctly different Fe-N switching behaviors (Fe moving toward or away from the N4-plane) during the oxygen reduction reaction (ORR), and show that their ORR activities are essentially governed by the dynamic structure associated with the Fe(2+/3+) redox transition, rather than the static structure of the bare sites. Our findings reveal the structural origin of the enhanced catalytic activity of pyrolyzed Fe-based catalysts compared to nonpyrolyzed Fe-macrocycle compounds. More generally, the fundamental insights into the dynamic nature of transition-metal compounds during electron-transfer reactions will potentially guide rational design of these materials for broad applications.

Exploring the structural basis of the selective inhibition of monoamine oxidase A by dicarbonitrile aminoheterocycles: role of Asn181 and Ile335 validated by spectroscopic and computational studies.

PubMed

Juárez-Jiménez, Jordi; Mendes, Eduarda; Galdeano, Carles; Martins, Carla; Silva, Daniel B; Marco-Contelles, José; do Carmo Carreiras, Maria; Luque, F Javier; Ramsay, Rona R

2014-02-01

Since cyanide potentiates the inhibitory activity of several monoamine oxidase (MAO) inhibitors, a series of carbonitrile-containing aminoheterocycles was examined to explore the role of nitriles in determining the inhibitory activity against MAO. Dicarbonitrile aminofurans were found to be potent, selective inhibitors against MAO A. The origin of the MAO A selectivity was identified by combining spectroscopic and computational methods. Spectroscopic changes induced in MAO A by mono- and dicarbonitrile inhibitors were different, providing experimental evidence for distinct binding modes to the enzyme. Similar differences were also found between the binding of dicarbonitrile compounds to MAO A and to MAO B. Stabilization of the flavin anionic semiquinone by monocarbonitrile compounds, but destabilization by dicarbonitriles, provided further support to the distinct binding modes of these compounds and their interaction with the flavin ring. Molecular modeling studies supported the role played by the nitrile and amino groups in anchoring the inhibitor to the binding cavity. In particular, the results highlight the role of Asn181 and Ile335 in assisting the interaction of the nitrile-containing aminofuran ring. The network of interactions afforded by the specific attachment of these functional groups provides useful guidelines for the design of selective, reversible MAO A inhibitors. Copyright © 2013 Elsevier B.V. All rights reserved.

Identification and Characterization of Inhibitors of West Nile Virus

PubMed Central

Puig-Basagoiti, Francesc; Qing, Min; Dong, Hongping; Zhang, Bo; Zou, Gang; Yuan, Zhiming

2011-01-01

Although flaviviruses cause significant human diseases, no antiviral therapy is currently available for clinical treatment of these pathogens. To identify flavivirus inhibitors, we performed a high-throughput screening of compound libraries using cells containing luciferase-reporting replicon of West Nile viruses (WNV). Five novel small molecular inhibitors of WNV were identified from libraries containing 96,958 compounds. The inhibitors suppress epidemic strain of WNV in cell culture, with EC50 (50% effective concentration) values of <10 µM and TI (therapeutic index) values of >10. Viral titer reduction assays, using various flaviviruses and nonflaviviruses, showed that the compounds have distinct antiviral spectra. Mode-of-action analysis showed that the inhibitors block distinct steps of WNV replication: four compounds inhibit viral RNA syntheses, while the other compound suppresses both viral translation and RNA syntheses. Biochemical enzyme assays showed that two compounds selectively inhibit viral RNA-dependent RNA polymerase (RdRp), while another compound specifically inhibits both RdRp and methyltransferase. The identified compounds could potentially be developed for treatment of flavivirus infections. PMID:19501258

Organics In Meteorites

NASA Technical Reports Server (NTRS)

Chang, Sherwood

1996-01-01

The variety of classes of organic compounds that occur in carbonaceous meteorites suggests a rich pre-planetary chemistry with possible connections to interstellar, solar nebular and parent body processes. Structural diversity prevails within all classes examined in detail. Among amino acids for instance, all possible isomers are found up to species containing 4-6 carbon atoms, with abundances decreasing with increasing molecular weight. Such diversity seems limited to those carbonaceous meteorites which show evidence of having been exposed to liquid water; meteorites lacking such evidence also show much lower abundances and less structural diversity in their organic contents. This apparent dependency on water suggests a role for cometary ices in the chemical evolution of organic compounds on parent bodies. Measurements of the stable isotope compositions of C, H, N and S in classes of compounds and at the individual compound level show strong deviations from average chondritic values. These deviations are difficult to explain by solar system or parent body processes, and precedents for some of these isotopic anomalies exist in interstellar (e.g., high D/H ratios) and circumstellar chemistry. Therefore, presolar origins for much if not all of the meteoritic organic compounds (or their precursors) is a distinct possibility. In contrast, evidence of solar nebular origins is either lacking or suspect. Results from molecular and isotopic analyses of meteoritic organics, from laboratory simulations and from a model of interstellar grain reactions will be used to flesh out the hypothesis that this material originated with interstellar chemistry, was distributed within the early solar system as cometary ices, and was subsequently altered on meteorite parent bodies to yield the observed compounds.

Crystal structure of langbeinite-related Rb0.743K0.845Co0.293Ti1.707(PO4)3.

PubMed

Strutynska, Nataliia Yu; Bondarenko, Marina A; Ogorodnyk, Ivan V; Baumer, Vyacheslav N; Slobodyanik, Nikolay S

2015-03-01

Potassium rubidium cobalt(II)/titanium(IV) tris-(orthophosphate), Rb0.743K0.845Co0.293Ti1.707(PO4)3, has been obtained using a high-temperature crystallization method. The obtained compound has a langbeinite-type structure. The three-dimensional framework is built up from mixed-occupied (Co/Ti(IV))O6 octa-hedra (point group symmetry .3.) and PO4 tetra-hedra. The K(+) and Rb(+) cations are statistically distributed over two distinct sites (both with site symmetry .3.) in the large cavities of the framework. They are surrounded by 12 O atoms.

General Platform for Systematic Quantitative Evaluation of Small-Molecule Permeability in Bacteria

PubMed Central

2015-01-01

The chemical features that impact small-molecule permeability across bacterial membranes are poorly understood, and the resulting lack of tools to predict permeability presents a major obstacle to the discovery and development of novel antibiotics. Antibacterials are known to have vastly different structural and physicochemical properties compared to nonantiinfective drugs, as illustrated herein by principal component analysis (PCA). To understand how these properties influence bacterial permeability, we have developed a systematic approach to evaluate the penetration of diverse compounds into bacteria with distinct cellular envelopes. Intracellular compound accumulation is quantitated using LC-MS/MS, then PCA and Pearson pairwise correlations are used to identify structural and physicochemical parameters that correlate with accumulation. An initial study using 10 sulfonyladenosines in Escherichia coli, Bacillus subtilis, and Mycobacterium smegmatis has identified nonobvious correlations between chemical structure and permeability that differ among the various bacteria. Effects of cotreatment with efflux pump inhibitors were also investigated. This sets the stage for use of this platform in larger prospective analyses of diverse chemotypes to identify global relationships between chemical structure and bacterial permeability that would enable the development of predictive tools to accelerate antibiotic drug discovery. PMID:25198656

Computer-Assisted Inverse Design of Inorganic Electrides

NASA Astrophysics Data System (ADS)

Zhang, Yunwei; Wang, Hui; Wang, Yanchao; Zhang, Lijun; Ma, Yanming

2017-01-01

Electrides are intrinsic electron-rich materials enabling applications as excellent electron emitters, superior catalysts, and strong reducing agents. There are a number of organic electrides; however, their instability at room temperature and sensitivity to moisture are bottlenecks for their practical uses. Known inorganic electrides are rare, but they appear to have greater thermal stability at ambient conditions and are thus better characterized for application. Here, we develop a computer-assisted inverse-design method for searching for a large variety of inorganic electrides unbiased by any known electride structures. It uses the intrinsic property of interstitial electron localization of electrides as the global variable function for swarm intelligence structure searches. We construct two rules of thumb on the design of inorganic electrides pointing to electron-rich ionic systems and low electronegativity of the cationic elements involved. By screening 99 such binary compounds through large-scale computer simulations, we identify 24 stable and 65 metastable new inorganic electrides that show distinct three-, two-, and zero-dimensional conductive properties, among which 18 are existing compounds that have not been pointed to as electrides. Our work reveals the rich abundance of inorganic electrides by providing 33 hitherto unexpected structure prototypes of electrides, of which 19 are not in the known structure databases.

Current Status and Future Prospects of Marine Natural Products (MNPs) as Antimicrobials.

PubMed

Choudhary, Alka; Naughton, Lynn M; Montánchez, Itxaso; Dobson, Alan D W; Rai, Dilip K

2017-08-28

The marine environment is a rich source of chemically diverse, biologically active natural products, and serves as an invaluable resource in the ongoing search for novel antimicrobial compounds. Recent advances in extraction and isolation techniques, and in state-of-the-art technologies involved in organic synthesis and chemical structure elucidation, have accelerated the numbers of antimicrobial molecules originating from the ocean moving into clinical trials. The chemical diversity associated with these marine-derived molecules is immense, varying from simple linear peptides and fatty acids to complex alkaloids, terpenes and polyketides, etc. Such an array of structurally distinct molecules performs functionally diverse biological activities against many pathogenic bacteria and fungi, making marine-derived natural products valuable commodities, particularly in the current age of antimicrobial resistance. In this review, we have highlighted several marine-derived natural products (and their synthetic derivatives), which have gained recognition as effective antimicrobial agents over the past five years (2012-2017). These natural products have been categorized based on their chemical structures and the structure-activity mediated relationships of some of these bioactive molecules have been discussed. Finally, we have provided an insight into how genome mining efforts are likely to expedite the discovery of novel antimicrobial compounds.

A Dinitroaniline-Resistant Mutant of Eleusine indica Exhibits Cross-Resistance and Supersensitivity to Antimicrotubule Herbicides and Drugs 1

PubMed Central

Vaughn, Kevin C.; Marks, M. David; Weeks, Donald P.

1987-01-01

A dinitroaniline-resistant (R) biotype of Eleusine indica (L.) Gaertner. (goosegrass) is demonstrated to be cross-resistant to a structurally non-related herbicide, amiprophosmethyl, and supersensitive to two other classes of compounds which disrupt mitosis. These characteristics of the R biotype were discovered in a comparative test of the effects of 24 different antimitotic compounds on the R biotype and susceptible (S) wild-type Eleusine. The compounds tested could be classified into three groups based upon their effects on mitosis in root tips of the susceptible (S) biotype. Class I compounds induced effects like the well known mitotic disrupter colchicine: absence of cortical and spindle microtubules, mitosis arrested at prometaphase, and the formation of polymorphic nuclei after arrested mitosis. The R biotype was resistant to treatment with some class I inhibitors (all dinitroaniline herbicides and amiprophosmethyl) but not all (e.g. colchicine, podophyllotoxin, vinblastine, and pronamide). Roots of the R biotype, when treated with either dinitroaniline herbicides or amiprophosmethyl, exhibited no or only small increases in the mitotic index nor were the spindle and cortical microtubules affected. Compounds of class II (carbamate herbicides and griseofulvin) cause misorientation of microtubules which results in multinucleated cells. Compounds of class III (caffeine and structually related alkaloids) cause imcomplete cell walls to form at telophase. Each of these last two classes of compounds affected the R biotype more than the S biotype (supersensitivity). The cross-resistance and high levels of resistance of the R biotype of Eleusine to the dinitroaniline herbicides and the structurally distinct herbicide, amiprophosmethyl, indicate that a mechanism of resistance based upon metabolic modification, translocation, or compartmentation of the herbicides is probably not operative. Images Fig. 1 Fig. 2 Fig. 3 Fig. 5 Fig. 6 PMID:16665371

A Dinitroaniline-Resistant Mutant of Eleusine indica Exhibits Cross-Resistance and Supersensitivity to Antimicrotubule Herbicides and Drugs.

PubMed

Vaughn, K C; Marks, M D; Weeks, D P

1987-04-01

A dinitroaniline-resistant (R) biotype of Eleusine indica (L.) Gaertner. (goosegrass) is demonstrated to be cross-resistant to a structurally non-related herbicide, amiprophosmethyl, and supersensitive to two other classes of compounds which disrupt mitosis. These characteristics of the R biotype were discovered in a comparative test of the effects of 24 different antimitotic compounds on the R biotype and susceptible (S) wild-type Eleusine. The compounds tested could be classified into three groups based upon their effects on mitosis in root tips of the susceptible (S) biotype. Class I compounds induced effects like the well known mitotic disrupter colchicine: absence of cortical and spindle microtubules, mitosis arrested at prometaphase, and the formation of polymorphic nuclei after arrested mitosis. The R biotype was resistant to treatment with some class I inhibitors (all dinitroaniline herbicides and amiprophosmethyl) but not all (e.g. colchicine, podophyllotoxin, vinblastine, and pronamide). Roots of the R biotype, when treated with either dinitroaniline herbicides or amiprophosmethyl, exhibited no or only small increases in the mitotic index nor were the spindle and cortical microtubules affected. Compounds of class II (carbamate herbicides and griseofulvin) cause misorientation of microtubules which results in multinucleated cells. Compounds of class III (caffeine and structually related alkaloids) cause imcomplete cell walls to form at telophase. Each of these last two classes of compounds affected the R biotype more than the S biotype (supersensitivity). The cross-resistance and high levels of resistance of the R biotype of Eleusine to the dinitroaniline herbicides and the structurally distinct herbicide, amiprophosmethyl, indicate that a mechanism of resistance based upon metabolic modification, translocation, or compartmentation of the herbicides is probably not operative.

Hybrid gels by conjugation of hyaluronic acid with poly(itaconic anhydride-co-3,9-divinyl-2,4,8,10-tetraoxaspiro (5.5)undecane) copolymers.

PubMed

Chiriac, Aurica P; Nita, Loredana Elena; Diaconu, Alina; Bercea, Maria; Tudorachi, Nita; Pamfil, Daniela; Mititelu-Tartau, Liliana

2017-05-01

The approach of covalent conjugation for coupling synthetic polymers with biomolecules represents an appealing strategy to produce new compounds with distinctive properties for biomedical applications. In the present study we generated hybrid gels with tunable characteristics by using hyaluronic acid (HA) and four variants of poly(itaconic anhydride-co-3,9-divinyl-2,4,8,10-tetraoxaspiro[5.5] undecane) (PITAU) copolymers, differing through the molar ratios between comonomers. The new bioconjugate compounds were realized by using a ″grafting to″ strategy, for further ensuring new ways for coupling of various bioactive compounds, taking into account that the grafted copolymers are dual sensitive to pH and temperature. The procedure of chemical crosslinking, by opening the anhydride cycle of the copolymer with the hydroxyl groups of hyaluronic acid, was used to prepare the bioconjugates. The chemical conjugation between HA and PITAU copolymers, as well as the structure of the new compounds, was confirmed by FTIR and NMR techniques. The physical properties of the new gels as thermal stability, swelling capacity, and rheological properties were investigated. The bioconjugate networks were also investigated as drug delivery carriers by using indomethacin as a model drug. In vitro and in vivo tests attested the homogeneity of the bioactive compounds as well as a good biochemical response, showing good biocompatibility for the new structures. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural and Functional Analysis of Two New Positive Allosteric Modulators of GluA2 Desensitization and Deactivation

PubMed Central

Timm, David E.; Benveniste, Morris; Weeks, Autumn M.; Nisenbaum, Eric S.

2011-01-01

At the dimer interface of the extracellular ligand-binding domain of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptors a hydrophilic pocket is formed that is known to interact with two classes of positive allosteric modulators, represented by cyclothiazide and the ampakine 2H,3H,6aH-pyrrolidino(2,1–3′,2′)1,3-oxazino(6′,5′-5,4)benzo(e)1,4-dioxan-10-one (CX614). Here, we present structural and functional data on two new positive allosteric modulators of AMPA receptors, phenyl-1,4-bis-alkylsulfonamide (CMPDA) and phenyl-1,4-bis-carboxythiophene (CMPDB). Crystallographic data show that these compounds bind within the modulator-binding pocket and that substituents of each compound overlap with distinct moieties of cyclothiazide and CX614. The goals of the present study were to determine 1) the degree of modulation by CMPDA and CMPDB of AMPA receptor deactivation and desensitization; 2) whether these compounds are splice isoform-selective; and 3) whether predictions of mechanism of action could be inferred by comparing molecular interactions between the ligand-binding domain and each compound with those of cyclothiazide and CX614. CMPDB was found to be more isoform-selective than would be predicted from initial binding assays. It is noteworthy that these new compounds are both more potent and more effective and may be more clinically relevant than the AMPA receptor modulators described previously. PMID:21543522

Small structural changes on a hydroquinone scaffold determine the complex I inhibition or uncoupling of tumoral oxidative phosphorylation.

PubMed

Urra, Félix A; Córdova-Delgado, Miguel; Lapier, Michel; Orellana-Manzano, Andrea; Acevedo-Arévalo, Luis; Pessoa-Mahana, Hernán; González-Vivanco, Jaime M; Martínez-Cifuentes, Maximiliano; Ramírez-Rodríguez, Oney; Millas-Vargas, Juan Pablo; Weiss-López, Boris; Pavani, Mario; Ferreira, Jorge; Araya-Maturana, Ramiro

2016-01-15

Mitochondria participate in several distinctiveness of cancer cell, being a promising target for the design of anti-cancer compounds. Previously, we described that ortho-carbonyl hydroquinone scaffold 14 inhibits the complex I-dependent respiration with selective anti-proliferative effect on mouse mammary adenocarcinoma TA3/Ha cancer cells; however, the structural requirements of this hydroquinone scaffold to affect the oxidative phosphorylation (OXPHOS) of cancer cells have not been studied in detail. Here, we characterize the mitochondrial metabolism of TA3/Ha cancer cells, which exhibit a high oxidative metabolism, and evaluate the effect of small structural changes of the hydroquinone scaffold 14 on the respiration of this cell line. Our results indicate that these structural changes modify the effect on OXPHOS, obtaining compounds with three alternative actions: inhibitors of complex I-dependent respiration, uncoupler of OXPHOS and compounds with both actions. To confirm this, the effect of a bicyclic hydroquinone (9) was evaluated in isolated mitochondria. Hydroquinone 9 increased mitochondrial respiration in state 4o without effects on the ADP-stimulated respiration (state 3ADP), decreasing the complexes I and II-dependent respiratory control ratio. The effect on mitochondrial respiration was reversed by 6-ketocholestanol addition, indicating that this hydroquinone is a protonophoric uncoupling agent. In intact TA3/Ha cells, hydroquinone 9 caused mitochondrial depolarization, decreasing intracellular ATP and NAD(P)H levels and GSH/GSSG ratio, and slightly increasing the ROS levels. Moreover, it exhibited selective NAD(P)H availability-dependent anti-proliferative effect on cancer cells. Therefore, our results indicate that the ortho-carbonyl hydroquinone scaffold offers the possibility to design compounds with specific actions on OXPHOS of cancer cells.

A Novel, “Double-Clamp” Binding Mode for Human Heme Oxygenase-1 Inhibition

PubMed Central

Rahman, Mona N.; Vlahakis, Jason Z.; Vukomanovic, Dragic; Lee, Wallace; Szarek, Walter A.; Nakatsu, Kanji; Jia, Zongchao

2012-01-01

The development of heme oxygenase (HO) inhibitors is critical in dissecting and understanding the HO system and for potential therapeutic applications. We have established a program to design and optimize HO inhibitors using structure-activity relationships in conjunction with X-ray crystallographic analyses. One of our previous complex crystal structures revealed a putative secondary hydrophobic binding pocket which could be exploited for a new design strategy by introducing a functional group that would fit into this potential site. To test this hypothesis and gain further insights into the structural basis of inhibitor binding, we have synthesized and characterized 1-(1H-imidazol-1-yl)-4,4-diphenyl-2-butanone (QC-308). Using a carbon monoxide (CO) formation assay on rat spleen microsomes, the compound was found to be ∼15 times more potent (IC50 = 0.27±0.07 µM) than its monophenyl analogue, which is already a potent compound in its own right (QC-65; IC50 = 4.0±1.8 µM). The crystal structure of hHO-1 with QC-308 revealed that the second phenyl group in the western region of the compound is indeed accommodated by a definitive secondary proximal hydrophobic pocket. Thus, the two phenyl moieties are each stabilized by distinct hydrophobic pockets. This “double-clamp” binding offers additional inhibitor stabilization and provides a new route for improvement of human heme oxygenase inhibitors. PMID:22276118

A novel, "double-clamp" binding mode for human heme oxygenase-1 inhibition.

PubMed

Rahman, Mona N; Vlahakis, Jason Z; Vukomanovic, Dragic; Lee, Wallace; Szarek, Walter A; Nakatsu, Kanji; Jia, Zongchao

2012-01-01

The development of heme oxygenase (HO) inhibitors is critical in dissecting and understanding the HO system and for potential therapeutic applications. We have established a program to design and optimize HO inhibitors using structure-activity relationships in conjunction with X-ray crystallographic analyses. One of our previous complex crystal structures revealed a putative secondary hydrophobic binding pocket which could be exploited for a new design strategy by introducing a functional group that would fit into this potential site. To test this hypothesis and gain further insights into the structural basis of inhibitor binding, we have synthesized and characterized 1-(1H-imidazol-1-yl)-4,4-diphenyl-2-butanone (QC-308). Using a carbon monoxide (CO) formation assay on rat spleen microsomes, the compound was found to be ∼15 times more potent (IC(50) = 0.27±0.07 µM) than its monophenyl analogue, which is already a potent compound in its own right (QC-65; IC(50) = 4.0±1.8 µM). The crystal structure of hHO-1 with QC-308 revealed that the second phenyl group in the western region of the compound is indeed accommodated by a definitive secondary proximal hydrophobic pocket. Thus, the two phenyl moieties are each stabilized by distinct hydrophobic pockets. This "double-clamp" binding offers additional inhibitor stabilization and provides a new route for improvement of human heme oxygenase inhibitors.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, Aaron A.; Liu, Wei; Chun, Eugene

Members of the opioid receptor family of G-protein-coupled receptors (GPCRs) are found throughout the peripheral and central nervous system, where they have key roles in nociception and analgesia. Unlike the 'classical' opioid receptors, {delta}, {kappa} and {mu} ({delta}-OR, {kappa}-OR and {mu}-OR), which were delineated by pharmacological criteria in the 1970s and 1980s, the nociceptin/orphanin FQ (N/OFQ) peptide receptor (NOP, also known as ORL-1) was discovered relatively recently by molecular cloning and characterization of an orphan GPCR. Although it shares high sequence similarity with classical opioid GPCR subtypes ({approx}60%), NOP has a markedly distinct pharmacology, featuring activation by the endogenous peptidemore » N/OFQ, and unique selectivity for exogenous ligands. Here we report the crystal structure of human NOP, solved in complex with the peptide mimetic antagonist compound-24 (C-24) (ref. 4), revealing atomic details of ligand-receptor recognition and selectivity. Compound-24 mimics the first four amino-terminal residues of the NOP-selective peptide antagonist UFP-101, a close derivative of N/OFQ, and provides important clues to the binding of these peptides. The X-ray structure also shows substantial conformational differences in the pocket regions between NOP and the classical opioid receptors {kappa} (ref. 5) and {mu} (ref. 6), and these are probably due to a small number of residues that vary between these receptors. The NOP-compound-24 structure explains the divergent selectivity profile of NOP and provides a new structural template for the design of NOP ligands.« less

Systematic assessment of scaffold hopping versus activity cliff formation across bioactive compound classes following a molecular hierarchy.

PubMed

Stumpfe, Dagmar; Dimova, Dilyana; Bajorath, Jürgen

2015-07-01

Scaffold hopping and activity cliff formation define opposite ends of the activity landscape feature spectrum. To rationalize these events at the level of scaffolds, active compounds involved in scaffold hopping were required to contain topologically distinct scaffolds but have only limited differences in potency, whereas compounds involved in activity cliffs were required to share the same scaffold but have large differences in potency. A systematic search was carried out for compounds involved in scaffold hopping and/or activity cliff formation. Results obtained for compound data sets covering more than 300 human targets revealed clear trends. If scaffolds represented multiple but fewer than 10 active compounds, nearly 90% of all scaffolds were exclusively involved in hopping events. With increasing compound coverage, the fraction of scaffolds involved in both scaffold hopping and activity cliff formation significantly increased to more than 50%. However, ∼40% of the scaffolds representing large numbers of active compounds continued to be exclusively involved in scaffold hopping. More than 200 scaffolds with broad target coverage were identified that consistently represented potent compounds and yielded an abundance of scaffold hops in the low-nanomolar range. These and other subsets of scaffolds we characterized are of prime interest for structure-activity relationship (SAR) exploration and compound design. Therefore, the complete scaffold classification generated in the course of our analysis is made freely available. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Modification of Compounds by Attributive Adjectives

ERIC Educational Resources Information Center

Berg, Thomas

2011-01-01

This paper examines the modification of nominal compounds by attributive adjectives in English. It draws on a distinction between compound-external (i.e. syntactic) and compound-internal (i.e. morphological) modification. An analysis is presented of more than 1000 pertinent cases, which are roughly equally divided into two-, three- and four-noun…

Design, synthesis, and biological evaluation of novel dipeptide-type SARS-CoV 3CL protease inhibitors: structure-activity relationship study.

PubMed

Thanigaimalai, Pillaiyar; Konno, Sho; Yamamoto, Takehito; Koiwai, Yuji; Taguchi, Akihiro; Takayama, Kentaro; Yakushiji, Fumika; Akaji, Kenichi; Kiso, Yoshiaki; Kawasaki, Yuko; Chen, Shen-En; Naser-Tavakolian, Aurash; Schön, Arne; Freire, Ernesto; Hayashi, Yoshio

2013-07-01

This work describes the design, synthesis, and evaluation of low-molecular weight peptidic SARS-CoV 3CL protease inhibitors. The inhibitors were designed based on the potent tripeptidic Z-Val-Leu-Ala(pyrrolidone-3-yl)-2-benzothiazole (8; Ki = 4.1 nM), in which the P3 valine unit was substituted with a variety of distinct moieties. The resulting series of dipeptide-type inhibitors displayed moderate to good inhibitory activities against 3CL(pro). In particular, compounds 26m and 26n exhibited good inhibitory activities with Ki values of 0.39 and 0.33 μM, respectively. These low-molecular weight compounds are attractive leads for the further development of potent peptidomimetic inhibitors with pharmaceutical profiles. Docking studies were performed to model the binding interaction of the compound 26m with the SARS-CoV 3CL protease. The preliminary SAR study of the peptidomimetic compounds with potent inhibitory activities revealed several structural features that boosted the inhibitory activity: (i) a benzothiazole warhead at the S1' position, (ii) a γ-lactam unit at the S1-position, (iii) an appropriately hydrophobic leucine moiety at the S2-position, and (iv) a hydrogen bond between the N-arylglycine unit and a backbone hydrogen bond donor at the S3-position. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Nontargeted Screening of Halogenated Organic Compounds in Bottlenose Dolphins (Tursiops truncatus) from Rio de Janeiro, Brazil.

PubMed

Alonso, Mariana B; Maruya, Keith A; Dodder, Nathan G; Lailson-Brito, José; Azevedo, Alexandre; Santos-Neto, Elitieri; Torres, Joao P M; Malm, Olaf; Hoh, Eunha

2017-02-07

To catalog the diversity and abundance of halogenated organic compounds (HOCs) accumulating in high trophic marine species from the southwestern Atlantic Ocean, tissue from bottlenose dolphins (Tursiops truncatus) stranded or incidentally captured along the coast of Rio de Janeiro, Brazil, were analyzed by a nontargeted approach based on GC×GC/TOF-MS. A total of 158 individual HOCs from 32 different structural classes were detected in the blubber of 4 adult male T. truncatus. Nearly 90% of the detected compounds are not routinely monitored in the environment. DDT-related and mirex/dechlorane-related compounds were the most abundant classes of anthropogenic origin. Methoxy-brominated diphenyl ethers (MeO-BDEs) and chlorinated methyl- and dimethyl bipyrroles (MBPs and DMBPs) were the most abundant natural products. Reported for the first time in southwestern Atlantic cetaceans and in contrast to North American marine mammals, chlorinated MBPs and DMBPs were more abundant than their brominated and/or mixed halogenated counterparts. HOC profiles in coastal T. truncatus from Brazil and California revealed a distinct difference, with a higher abundance of MeO-BDEs, mirex/dechloranes and chlorinated bipyrroles in the Brazilian dolphins. Thirty-six percent of the detected HOCs had an unknown structure. These results suggest broad geographical differences in the patterns of bioaccumulative chemicals found in the marine environment and indicate the need to develop more complete catalogs of HOCs from various marine environments.

Kinetic control of intralayer cobalt coordination in layered hydroxides: Co(1-0.5x)(oct) Co(x)(tet) (OH)2 (Cl)x (H2O)n.

PubMed

Neilson, James R; Schwenzer, Birgit; Seshadri, Ram; Morse, Daniel E

2009-12-07

We report the synthesis and characterization of new structural variants of the isotypic compound with the generic chemical formula, Co(1-0.5x)(oct) Co(x)(tet) (OH)2 (Cl)x (H2O)n, all modifications of an alpha-Co(OH)2 lattice. We show that the occupancy of tetrahedrally coordinated cobalt sites and associated chloride ligands, x, is modulated by the rate of formation of the respective layered hydroxide salts from kinetically controlled aqueous hydrolysis at an air-water interface. This new level of structural control is uniquely enabled by the slow diffusion of a hydrolytic catalyst, a simple technique. Independent structural characterizations of the compounds separately describe various attributes of the materials on different length scales, revealing details hidden by the disordered average structures. The precise control over the population of distinct octahedrally and tetrahedrally coordinated cobalt ions in the lattice provides a gentle, generic method for modulating the coordination geometry of cobalt in the material without disturbing the lattice or using additional reagents. A mechanism is proposed to reconcile the observation of the kinetic control of the structure with competing interactions during the initial stages of hydrolysis and condensation.

Cadmium-1,4-cyclohexanedicarboxylato coordination polymers bearing different di-alkyl-2,2'-bipyridines: syntheses, crystal structures and photoluminescence studies.

PubMed

Rosales-Vázquez, Luis D; Sánchez-Mendieta, Víctor; Dorazco-González, Alejandro; Martínez-Otero, Diego; García-Orozco, Iván; Morales-Luckie, Raúl A; Jaramillo-Garcia, Jonathan; Téllez-López, Antonio

2017-09-26

Four coordination polymers have been synthesized using self-assembly solution reactions under ambient conditions, reacting Cd(ii) ions with 1,4-cyclohexanedicarboxylic acid in the presence of different 2,2'-bipyridine co-ligands: {[Cd(H 2 O)(e,a-cis-1,4-chdc)(2,2'-bpy)]·H 2 O} n (1); [Cd 2 (H 2 O) 2 (e,a-cis-1,4-chdc) 2 (4,4'-dmb) 2 ] n (2); {[Cd(e,a-cis-1,4-chdc)(5,5'-dmb)]·H 2 O·CH 3 OH} n (3) and {[Cd(e,e-trans-1,4-chdc)(4,4'-dtbb)]·CH 3 OH} n (4), where 1,4-chdc = 1,4-cyclohexanedicarboxylato, 2,2'-bpy = 2,2'-bipyridine, 4,4'-dmb = 4,4'-dimethyl-2,2'-bipyridine, 5,5'-dmb = 5,5'-dimethyl-2,2'-bipyridine and 4,4'-dtbb = 4,4'-di-tert-butyl-2,2'-bipyridine. Crystallographic studies show that compound 1 has a 1D structure propagating along the crystallographic b-axis; the Cd ion in 1 is six-coordinated with a distorted-octahedral coordination sphere. Compound 2 has two crystallographic different Cd ions and both are six-coordinated with a distorted-octahedral coordination sphere. Compound 3 exhibits a seven-coordinated Cd ion having a distinctive distorted-monocapped trigonal prismatic geometry. In compound 4, the Cd ion is also seven-coordinated in a distorted monocapped octahedral geometry. Compounds 2, 3 and 4 possess rhombic-shaped dinuclear units (Cd 2 O 2 ) as nodes to generate larger cycles made up of four dinuclear units, a Cd 4 motif, bridged by four 1,4-chdc ligands, accomplishing, thus, 2D structures. Remarkably, in compound 4 the 1,4-chdc ligand conformation changes to the equatorial, equatorial trans, unlike the other compounds where the bridging ligand conformation is the more typical equatorial, axial cis. The solid state luminescence properties of 1-4 were investigated; polymers 3 and 4 exhibited a strong blue emission (λ em = 410-414 nm) compared to 1 and 2; structure-related photoluminescence is attributed to the degree of hydration of the compounds. Furthermore, Cd-polymer 3 suspended in acetone allows the fluorescence selective sensing of acetonitrile over common organic solvents such as alcohols and DMF, based on turn-on fluorescence intensity with a limit of 53 μmol L -1 .

Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals

NASA Astrophysics Data System (ADS)

Pham, Cong-Huy; Kucukbenli, Emine; de Gironcoli, Stefano

2015-03-01

Ab initio crystal structure prediction of even small organic compounds is extremely challenging due to polymorphism, molecular flexibility and difficulties in addressing the dispersion interaction from first principles. We recently implemented vdW-aware density functionals and demonstrated their success in energy ordering of aminoacid crystals. In this work we combine this development with the evolutionary structure prediction method to study cholesterol polymorphs. Cholesterol crystals have paramount importance in various diseases, from cancer to atherosclerosis. The structure of some polymorphs (e.g. ChM, ChAl, ChAh) have already been resolved while some others, which display distinct NMR spectra and are involved in disease formation, are yet to be determined. Here we thoroughly assess the applicability of evolutionary structure prediction to address such real world problems. We validate the newly predicted structures with ab initio NMR chemical shift data using secondary referencing for an improved comparison with experiments.

Thermally Induced Structural Evolution and Performance of Mesoporous Block Copolymer-Directed Alumina Perovskite Solar Cells

PubMed Central

2015-01-01

Structure control in solution-processed hybrid perovskites is crucial to design and fabricate highly efficient solar cells. Here, we utilize in situ grazing incidence wide-angle X-ray scattering and scanning electron microscopy to investigate the structural evolution and film morphologies of methylammonium lead tri-iodide/chloride (CH3NH3PbI3–xClx) in mesoporous block copolymer derived alumina superstructures during thermal annealing. We show the CH3NH3PbI3–xClx material evolution to be characterized by three distinct structures: a crystalline precursor structure not described previously, a 3D perovskite structure, and a mixture of compounds resulting from degradation. Finally, we demonstrate how understanding the processing parameters provides the foundation needed for optimal perovskite film morphology and coverage, leading to enhanced block copolymer-directed perovskite solar cell performance. PMID:24684494

New copper(I) complexes bearing lomefloxacin motif: Spectroscopic properties, in vitro cytotoxicity and interactions with DNA and human serum albumin.

PubMed

Komarnicka, Urszula K; Starosta, Radosław; Kyzioł, Agnieszka; Płotek, Michał; Puchalska, Małgorzata; Jeżowska-Bojczuk, Małgorzata

2016-12-01

In this paper we present lomefloxacin's (HLm, 2nd generation fluoroquinolone antibiotic agent) organic and inorganic derivatives: aminomethyl(diphenyl)phosphine (PLm), its oxide as well as new copper(I) iodide or copper(I) thiocyanate complexes with PLm and 2,9-dimethyl-1,10-phenanthroline (dmp) or 2,2'-biquinoline (bq) as the auxiliary ligands. The synthesized compounds were fully characterised by NMR, UV-Vis and luminescence spectroscopies. Selected structures were analysed by theoretical DFT (density functional theory) methods. High stability of the complexes in aqueous solutions in the presence of atmosferic oxygen was proven. Cytotoxic activity of all compounds was tested towards three cancer cell lines (CT26 - mouse colon carcinoma, A549 - human lung adenocarcinoma, and MCF7 - human breast adenocarcinoma). All complexes are characterised by cytotoxic activity higher than the activity of the parent drug and its organic derivatives as well as cisplatin. Studied derivatives as well as parent drug do not intercalate to DNA, except Cu(I) complexes with bq ligand. All studied complexes caused single-stranded cleavage of the sugar-phosphate backbone of plasmid DNA. The addition of H 2 O 2 caused distinct changes in the plasmid structure and led to single- and/or double-strain plasmid cleavage. Studied compounds interact with human serum albumin without affecting its secondary structure. Copyright © 2016 Elsevier Inc. All rights reserved.

Exploring the binding mechanisms of diaminopimelic acid analogs to meso-diaminopimelate dehydrogenase by molecular modeling.

PubMed

Wang, Huiqun; Kellogg, Glen E; Xu, Ping; Zhang, Yan

2018-06-02

Meso-Diaminopimelic acid (meso-2,6-diamino-heptanedioic acid, DAP) is an important component of the cell wall of many bacteria. Meso-diaminopimelate dehydrogenase (m-Ddh) is a critical enzyme in the process of converting tetrahydrodipicolinate to DAP. Here, we are proposing that DAP analogs targeting m-Ddh may be considered as potential antibiotics. Four DAP analogs without significant structural change from DAP have been obtained and their inhibitory potencies against m-Ddh from the P. gingivalis strain W83 show significant differences from that of DAP. However, their inhibitory mechanisms as for how simple structural change influences the inhibitory potency remain unknown. Therefore, we employed molecular modeling methods to obtain insight into the inhibitory mechanisms of DAP and analogs with m-Ddh. The predicted binding mode of DAP was highly consistent with the experimental structural data and disclosed the important roles played by the binding pocket residues. According to our predictions, the isoxazoline ring of compounds 1 and 2 and the double bonds in compounds 3 and 4 had distinct influences on these compounds' binding to m-Ddh. This enriched understanding of the inhibitory mechanisms of DAP and these four analogs to m-Ddh has provided new and relevant information for future rational development of potent inhibitors targeting m-Ddh. Copyright © 2018. Published by Elsevier Inc.

Curcumin and derivatives function through protein phosphatase 2A and presenilin orthologues in Dictyostelium discoideum

PubMed Central

Cocorocchio, Marco; Baldwin, Amy J.; Stewart, Balint; Kim, Lou; Harwood, Adrian J.; Thompson, Christopher R. L.; Andrews, Paul L. R.

2018-01-01

ABSTRACT Natural compounds often have complex molecular structures and unknown molecular targets. These characteristics make them difficult to analyse using a classical pharmacological approach. Curcumin, the main curcuminoid of turmeric, is a complex molecule possessing wide-ranging biological activities, cellular mechanisms and roles in potential therapeutic treatment, including Alzheimer's disease and cancer. Here, we investigate the physiological effects and molecular targets of curcumin in Dictyostelium discoideum. We show that curcumin exerts acute effects on cell behaviour, reduces cell growth and slows multicellular development. We employed a range of structurally related compounds to show the distinct role of different structural groups in curcumin's effects on cell behaviour, growth and development, highlighting active moieties in cell function, and showing that these cellular effects are unrelated to the well-known antioxidant activity of curcumin. Molecular mechanisms underlying the effect of curcumin and one synthetic analogue (EF24) were then investigated to identify a curcumin-resistant mutant lacking the protein phosphatase 2A regulatory subunit (PsrA) and an EF24-resistant mutant lacking the presenilin 1 orthologue (PsenB). Using in silico docking analysis, we then showed that curcumin might function through direct binding to a key regulatory region of PsrA. These findings reveal novel cellular and molecular mechanisms for the function of curcumin and related compounds. PMID:29361519

Curcumin and derivatives function through protein phosphatase 2A and presenilin orthologues in Dictyostelium discoideum.

PubMed

Cocorocchio, Marco; Baldwin, Amy J; Stewart, Balint; Kim, Lou; Harwood, Adrian J; Thompson, Christopher R L; Andrews, Paul L R; Williams, Robin S B

2018-01-29

Natural compounds often have complex molecular structures and unknown molecular targets. These characteristics make them difficult to analyse using a classical pharmacological approach. Curcumin, the main curcuminoid of turmeric, is a complex molecule possessing wide-ranging biological activities, cellular mechanisms and roles in potential therapeutic treatment, including Alzheimer's disease and cancer. Here, we investigate the physiological effects and molecular targets of curcumin in Dictyostelium discoideum We show that curcumin exerts acute effects on cell behaviour, reduces cell growth and slows multicellular development. We employed a range of structurally related compounds to show the distinct role of different structural groups in curcumin's effects on cell behaviour, growth and development, highlighting active moieties in cell function, and showing that these cellular effects are unrelated to the well-known antioxidant activity of curcumin. Molecular mechanisms underlying the effect of curcumin and one synthetic analogue (EF24) were then investigated to identify a curcumin-resistant mutant lacking the protein phosphatase 2A regulatory subunit (PsrA) and an EF24-resistant mutant lacking the presenilin 1 orthologue (PsenB). Using in silico docking analysis, we then showed that curcumin might function through direct binding to a key regulatory region of PsrA. These findings reveal novel cellular and molecular mechanisms for the function of curcumin and related compounds. © 2018. Published by The Company of Biologists Ltd.

Distinct Spacing Between Anionic Groups: An Essential Chemical Determinant for Achieving Thiophene-Based Ligands to Distinguish β-Amyloid or Tau Polymorphic Aggregates

PubMed Central

Klingstedt, Therése; Shirani, Hamid; Mahler, Jasmin; Wegenast-Braun, Bettina M; Nyström, Sofie; Goedert, Michel; Jucker, Mathias; Nilsson, K Peter R

2015-01-01

The accumulation of protein aggregates is associated with many devastating neurodegenerative diseases and the existence of distinct aggregated morphotypes has been suggested to explain the heterogeneous phenotype reported for these diseases. Thus, the development of molecular probes able to distinguish such morphotypes is essential. We report an anionic tetrameric oligothiophene compound that can be utilized for spectral assignment of different morphotypes of β-amyloid or tau aggregates present in transgenic mice at distinct ages. The ability of the ligand to spectrally distinguish between the aggregated morphotypes was reduced when the spacing between the anionic substituents along the conjugated thiophene backbone was altered, which verified that specific molecular interactions between the ligand and the protein aggregate are necessary to detect aggregate polymorphism. Our findings provide the structural and functional basis for the development of new fluorescent ligands that can distinguish between different morphotypes of protein aggregates. PMID:26013403

Optimization of Allosteric With-No-Lysine (WNK) Kinase Inhibitors and Efficacy in Rodent Hypertension Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamada, Ken; Levell, Julian; Yoon, Taeyong

The observed structure–activity relationship of three distinct ATP noncompetitive With-No-Lysine (WNK) kinase inhibitor series, together with a crystal structure of a previously disclosed allosteric inhibitor bound to WNK1, led to an overlay hypothesis defining core and side-chain relationships across the different series. This in turn enabled an efficient optimization through scaffold morphing, resulting in compounds with a good balance of selectivity, cellular potency, and pharmacokinetic profile, which were suitable for in vivo proof-of-concept studies. When dosed orally, the optimized compound reduced blood pressure in mice overexpressing human WNK1, and induced diuresis, natriuresis and kaliuresis in spontaneously hypertensive rats (SHR), confirmingmore » that this mechanism of inhibition of WNK kinase activity is effective at regulating cardiovascular homeostasis.« less

Phase diagram and electrical behavior of silicon-rich iridium silicide compounds

NASA Technical Reports Server (NTRS)

Allevato, C. E.; Vining, Cronin B.

1992-01-01

The iridium-silicon phase diagram on the silicon-rich side was investigated by means of X-ray powder diffraction, density, differential thermal analysis, metalography, microprobe analysis, and electrical resistivity. Attempts were made to prepare eight previously reported silicon-rich iridium silicide compounds by arc melting and Bridgman-like growth. However, microprobe analysis identified only four distinct compositions: IrSi, Ir3Si4, Ir3Si5 and IrSi sub about 3. The existence of Ir4Si5 could not be confirmed in this study, even though the crystal structure has been previously reported. Differential thermal analysis (DTA) in conjunction with X-ray powder diffraction confirm polymorphism in IrSi sub about 3, determined to have orthorhombic and monoclinic unit cells in the high and low temperature forms. A eutectic composition alloy of 83 +/- 1 atomic percent silicon was observed between IrSi sub about 3 and silicon. Ir3Si4 exhibits distinct metallic behavior while Ir3Si5 is semiconducting. Both and IrSi and IrSi sub about 3 exhibit nearly temperature independent electrical resistivities on the order of 5-10 x 10 exp -6 ohms-m.

Thiol reactivity and its impact on the ciliate toxicity of α,β-unsaturated aldehydes, ketones, and esters.

PubMed

Böhme, Alexander; Thaens, Diana; Schramm, Franziska; Paschke, Albrecht; Schüürmann, Gerrit

2010-12-20

A recently introduced chemoassay has been used to determine second-order rate constants of the electrophile-nucleophile reaction of 15 α,β-unsaturated aldehydes with glutathione. The respective kGSH values vary for more than 3 orders of magnitude, and are within the range determined previously for 31 α,β-unsaturated ketones and esters. Structure-reactivity analyses yield distinct relationships between kGSH and structural features of the compounds. Moreover, increasing kGSH increases the aldehyde toxicity toward ciliates in terms of 48 h-EC50 values (effective concentration yielding 50% growth inhibition of Tetrahymena pyriformis within 48 h). A respective log-log regression equation including both kGSH and the octanol/water partition coefficient, Kow, yields a squared correlation coefficient of 0.96. Comparative analysis with corresponding data for 15 ketones and 16 esters reveals systematic differences between the three compound classes with regard to the individual contributions of hydrophobicity and electrophilic reactivity to aquatic toxicity. The former is particularly pronounced for aldehydes, while the ester toxicity is largely governed by reactivity, with ketones showing an intermediate pattern that is more similar to the one of esters than of aldehydes. It follows that within the Michael acceptor domain of α,β-unsaturated carbonyls, a distinction between aldehydes and nonaldehydic derivatives appears necessary when employing electrophilic reactivity as a component for the quantitative prediction of their reactive toxicity toward aquatic organisms.

A diversity-oriented synthesis strategy enabling the combinatorial-type variation of macrocyclic peptidomimetic scaffolds† †Electronic supplementary information (ESI) available: Experimental procedures, characterization data and details of the computational analyses. See DOI: 10.1039/c5ob00371g Click here for additional data file.

PubMed Central

Isidro-Llobet, Albert; Hadje Georgiou, Kathy; Galloway, Warren R. J. D.; Giacomini, Elisa; Hansen, Mette R.; Méndez-Abt, Gabriela; Tan, Yaw Sing; Carro, Laura; Sore, Hannah F.

2015-01-01

Macrocyclic peptidomimetics are associated with a broad range of biological activities. However, despite such potentially valuable properties, the macrocyclic peptidomimetic structural class is generally considered as being poorly explored within drug discovery. This has been attributed to the lack of general methods for producing collections of macrocyclic peptidomimetics with high levels of structural, and thus shape, diversity. In particular, there is a lack of scaffold diversity in current macrocyclic peptidomimetic libraries; indeed, the efficient construction of diverse molecular scaffolds presents a formidable general challenge to the synthetic chemist. Herein we describe a new, advanced strategy for the diversity-oriented synthesis (DOS) of macrocyclic peptidomimetics that enables the combinatorial variation of molecular scaffolds (core macrocyclic ring architectures). The generality and robustness of this DOS strategy is demonstrated by the step-efficient synthesis of a structurally diverse library of over 200 macrocyclic peptidomimetic compounds, each based around a distinct molecular scaffold and isolated in milligram quantities, from readily available building-blocks. To the best of our knowledge this represents an unprecedented level of scaffold diversity in a synthetically derived library of macrocyclic peptidomimetics. Cheminformatic analysis indicated that the library compounds access regions of chemical space that are distinct from those addressed by top-selling brand-name drugs and macrocyclic natural products, illustrating the value of our DOS approach to sample regions of chemical space underexploited in current drug discovery efforts. An analysis of three-dimensional molecular shapes illustrated that the DOS library has a relatively high level of shape diversity. PMID:25778821

Structure-dependent binding and activation of perfluorinated compounds on human peroxisome proliferator-activated receptor γ

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Lianying; College of Life Science, Dezhou University, Dezhou 253023; Ren, Xiao-Min

2014-09-15

Perfluorinated compounds (PFCs) have been shown to disrupt lipid metabolism and even induce cancer in rodents through activation of peroxisome proliferator-activated receptors (PPARs). Lines of evidence showed that PPARα was activated by PFCs. However, the information on the binding interactions between PPARγ and PFCs and subsequent alteration of PPARγ activity is still limited and sometimes inconsistent. In the present study, in vitro binding of 16 PFCs to human PPARγ ligand binding domain (hPPARγ-LBD) and their activity on the receptor in cells were investigated. The results showed that the binding affinity was strongly dependent on their carbon number and functional group.more » For the eleven perfluorinated carboxylic acids (PFCAs), the binding affinity increased with their carbon number from 4 to 11, and then decreased slightly. The binding affinity of the three perfluorinated sulfonic acids (PFSAs) was stronger than their PFCA counterparts. No binding was detected for the two fluorotelomer alcohols (FTOHs). Circular dichroim spectroscopy showed that PFC binding induced distinctive structural change of the receptor. In dual luciferase reporter assays using transiently transfected Hep G2 cells, PFCs acted as hPPARγ agonists, and their potency correlated with their binding affinity with hPPARγ-LBD. Molecular docking showed that PFCs with different chain length bind with the receptor in different geometry, which may contribute to their differences in binding affinity and transcriptional activity. - Highlights: • Binding affinity between PFCs and PPARγ was evaluated for the first time. • The binding strength was dependent on fluorinated carbon chain and functional group. • PFC binding induced distinctive structural change of the receptor. • PFCs could act as hPPARγ agonists in Hep G2 cells.« less

First-order metal-insulator transitions in vanadates from first principles

NASA Astrophysics Data System (ADS)

Kumar, Anil; Rabe, Karin

2013-03-01

Materials that exhibit first-order metal-insulator transitions, with the accompanying abrupt change in the conductivity, have potential applications as switches in future electronic devices. Identification of materials and exploration of the atomic-scale mechanisms for switching between the two electronic states is a focus of current research. In this work, we search for first-order metal-insulator transitions in transition metal compounds, with a particular focus on d1 and d2 systems, by using first principles calculations to screen for an alternative low-energy state having not only a electronic character opposite to that of the ground state, but a distinct structure and/or magnetic ordering which would permit switching by an applied field or stress. We will present the results of our investigation of the perovskite compounds SrVO3, LaVO3, CaVO3, YVO3, LaTiO3 and related layered phase, including superlattices and Ruddlesden-Popper phases. While the pure compounds do not satisfy the search criteria, the layered phases show promising results.

The Ba 4d-4f giant dipole resonance in complex Ba/Si compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sahle, Ch. J.; Sternemann, C.; Sternemann, H.

2014-08-06

The shape of the Ba 4d–4f giant dipole resonance is studied for Ba atoms embedded inside complex Si networks covering structures consisting of Si nanocages and nanotubes, i.e. the clathrate Ba 8Si 46, the complex compound BaSi 6, and the semiconducting BaSi 2. Here, non-resonant x-ray Raman scattering is used to investigate confinement effects on the shape of the giant resonance in the vicinity of the Ba NIV, V-edge. The distinct momentum transfer dependence of the spectra is analyzed and discussed. The measurements are compared to calculations of the giant resonance within time-dependent local density approximation in the dipole limit.more » No modulation of the giant resonance's shape for Ba atoms confined in different local environments was observed, in contrast to the calculations. The absence of such shape modulation for complex Ba/Si compounds is discussed providing important implications for further studies of giant resonance phenomena utilizing both theory and experiment.« less

The Ba 4d-4f giant dipole resonance in complex Ba/Si compounds

NASA Astrophysics Data System (ADS)

Sahle, Ch J.; Sternemann, C.; Sternemann, H.; Tse, J. S.; Gordon, R. A.; Desgreniers, S.; Maekawa, S.; Yamanaka, S.; Lehmkühler, F.; Wieland, D. C. F.; Mende, K.; Huotari, S.; Tolan, M.

2014-02-01

The shape of the Ba 4d-4f giant dipole resonance is studied for Ba atoms embedded inside complex Si networks covering structures consisting of Si nanocages and nanotubes, i.e. the clathrate Ba8Si46, the complex compound BaSi6, and the semiconducting BaSi2. Here, non-resonant x-ray Raman scattering is used to investigate confinement effects on the shape of the giant resonance in the vicinity of the Ba NIV, V-edge. The distinct momentum transfer dependence of the spectra is analyzed and discussed. The measurements are compared to calculations of the giant resonance within time-dependent local density approximation in the dipole limit. No modulation of the giant resonance’s shape for Ba atoms confined in different local environments was observed, in contrast to the calculations. The absence of such shape modulation for complex Ba/Si compounds is discussed providing important implications for further studies of giant resonance phenomena utilizing both theory and experiment.

Volatile compounds released by disturbed and undisturbed adults of Anchomenus dorsalis (Coleoptera, Carabidae, Platynini) and structure of the pygidial gland

PubMed Central

Bonacci, Teresa; Brandmayr, Pietro; Zetto, Tullia; Perrotta, Ida Daniela; Guarino, Salvatore; Peri, Ezio; Colazza, Stefano

2011-01-01

Abstract Volatile compounds produced by adults of Anchomenus dorsalis under undisturbed and disturbed conditions were investigated with an all-glass aeration apparatus. GC-MS analysis of the crude extracts from undisturbed and disturbed adults highlighted four major volatile compounds, undecane, heneicosane, Z-9 tricosene and tricosane, of which significantly more undecane was released by disturbed adults compared to undisturbed beetles. The pygidial glands of adults of Anchomenus dorsalis were investigated using light and Transmission Electron Microscopy (TEM). Each gland showed dense aggregates of secretory cells organized into visually distinct lobes; a long collecting canal that drains the secretion towards the reservoir, a bean-shaped double lobed muscular reservoir in which secretion is stored and a short duct (efferent duct) through which the secretion is discharged. The function of the pygidial glands and the possible role played by undecane as a defensive allomone and/or chemical signalling molecule are discussed. PMID:21594158

New antimuscarinic agents for improved treatment of poisoning by cholinesterase inhibitors. Annual report, 1 November 1983-1 August 1984

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stubbins, J.F.

The object of this project is to find a more effective antimuscarinic agent than atropine for use as an antidote for poisoning by organophosphate cholinesterase inhibitors. To start this search, 30 structurally diverse antimuscarinic agents have been selected for initial testing. These compounds are to be evaluated for peripheral and central antimuscarinic activity in a variety of in vitro and in vivo tests in addition to determining their effectiveness as antidotes (in combination with an oxime reactivator) for poisoning by soman. Twenty-two of the compounds have now been evaluated for their ability to block acetylcholine-induced contractions in guinea pig intestinalmore » smooth muscle when compared to atropine. Ability to displace radiolabeled quinuclidinyl benzilate from muscarinic receptors of mouse brain homogenate has been determined for atropine, hyoscine and 26 of the compounds. Only triflupromazine appeared to have a distinctly greater affinity for brain receptors than muscle receptors to atropine. Intestinal smooth muscle blockade; oxotremorine tremor inhibition; muscarinic receptor subtypes.« less

Efficient Syntheses of Novel Fluoro-Substituted Pentacenes and Azapentacenes: Molecular and Solid-State Properties.

PubMed

Schwaben, Jonas; Münster, Niels; Klues, Michael; Breuer, Tobias; Hofmann, Philipp; Harms, Klaus; Witte, Gregor; Koert, Ulrich

2015-09-21

Non-symmetrical 6,13-disubstituted pentacenes bearing trifluoromethyl and aryl substituents have been synthesized starting from pentacenequinone. Diazapentacenes with a variety of fluorine substituents were prepared either via a Hartwig-Buchwald aryl amination route or by a SNAr strategy. As a result of a non-symmetric substitution pattern containing electron-donating substituents in combination with electron-accepting fluorine substituents, the synthesized compounds feature distinct molecular dipoles. All compounds are analyzed regarding their optoelectronic properties in solution with special focus on the frontier orbital energies as well as their molecular packing in the crystal structures. The analyses of isolated molecules are complemented by thin-film studies to examine their solid-state properties. A precise comparison between these and the molecular properties gave detailed insights into the exciton binding energies of these compounds, which are explained by means of a simple model considering the molecular packing and polarizabilities. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparative Environmental Performance of Two-Diesel-Fuel Oxygenates: Dibutyl Maleate (DBM) and Triproplyene Glycol Monomethyl Ether (TGME)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Layton, D.W.; Marchetti, A.A.

2001-10-01

Many studies have shown that the addition of oxygen bearing compounds to diesel fuel can significantly reduce particulate emissions. To assist in the evaluation of the environmental performance of diesel-fuel oxygenates, we have implemented a suite of diagnostic models for simulating the transport of compounds released to air, water, and soils/groundwater as well as regional landscapes. As a means of studying the comparative performance of DBM and TGME, we conducted a series of simulations for selected environmental media. Benzene and methyl tertiary butyl ether (MTBE) were also addressed because they represent benchmark fuel-related compounds that have been the subject ofmore » extensive environmental measurements and modeling. The simulations showed that DBM and TGME are less mobile in soil because of reduced vapor-phase transport and increased retention on soil particles. The key distinction between these two oxygenates is that DBM is predicted to have a greater potential than TGME for aerobic biodegradation, based on chemical structure.« less

A diversity oriented synthesis of natural product inspired molecular libraries.

PubMed

Chauhan, Jyoti; Luthra, Tania; Gundla, Rambabu; Ferraro, Antonio; Holzgrabe, Ulrike; Sen, Subhabrata

2017-11-07

Natural products are the source of innumerable pharmaceutical drug candidates and also form an important aspect of herbal remedies. They are also a source of various bioactive compounds. Herein we have leveraged the structural attributes of several natural products in building a library of architecturally diverse chiral molecules by harnessing R-tryptophan as the chiral auxiliary. It is converted to its corresponding methyl ester 1 which in turn provided a bevy of 1-aryl-tetrahydro-β-carbolines 2a-d, which were then converted to chiral compounds via a diversity oriented synthetic strategy (DOS). In general, intermolecular and intramolecular ring rearrangements facilitated the formation of the final compounds. Four different classes of molecules with distinct architectures were generated, adding up to nearly twenty-two individual molecules. Phenotypic screening of a representative section of the library revealed two molecules that selectively inhibit MCF7 breast cancer cells with IC 50 of ∼5 μg mL -1 potency.

Estrogenicity of halogenated bisphenol A: in vitro and in silico investigations.

PubMed

Zhang, Jie; Li, Tiezhu; Wang, Tuoyi; Yuan, Cuiping; Zhong, Shuning; Guan, Tianzhu; Li, Zhuolin; Wang, Yongzhi; Yu, Hansong; Luo, Quan; Wang, Yongjun; Zhang, Tiehua

2018-03-01

The binding interactions of bisphenol A (BPA) and its halogenated derivatives (halogenated BPAs) to human estrogen receptor α ligand binding domain (hERα-LBD) was investigated using a combined in vitro and in silico approach. First, the recombinant hERα-LBD was prepared as a soluble protein in Escherichia coli BL21(DE3)pLysS. A native fluorescent phytoestrogen, coumestrol, was employed as tracer for the fluorescence polarization assay. The results of the in vitro binding assay showed that bisphenol compounds could bind to hERα-LBD as the affinity ligands. All the tested halogenated BPAs exhibited weaker receptor binding than BPA, which might be explained by the steric effect of substituents. Molecular docking studies elucidated that the halogenated BPAs adopted different conformations in the flexible hydrophobic ligand binding pocket (LBP), which is mainly dependent on their distinct halogenation patterns. The compounds with halogen substituents on the phenolic rings and on the bridging alkyl moiety acted as agonists and antagonists for hERα, respectively. Interestingly, all the compounds in the agonist conformation of hERα formed a hydrogen bond with His524, while the compounds in the antagonist conformation formed a hydrogen bond with Thr347. These docking results suggested a pivotal role of His524/Thr347 in maintaining the hERα structure in the biologically active agonist/antagonist conformation. Comparison of the calculated binding energies vs. experimental binding affinities yielded a good correlation, which might be applicable for the structure-based design of novel bisphenol compounds with reduced toxicities and for environmental risk assessment. In addition, based on hERα-LBD as a recognition element, the proposed fluorescence polarization assay may offer an alternative to chromatographic techniques for the multi-residue determination of bisphenol compounds.

Structure-activity models of oral clearance, cytotoxicity, and LD50: a screen for promising anticancer compounds

PubMed Central

Boik, John C; Newman, Robert A

2008-01-01

Background Quantitative structure-activity relationship (QSAR) models have become popular tools to help identify promising lead compounds in anticancer drug development. Few QSAR studies have investigated multitask learning, however. Multitask learning is an approach that allows distinct but related data sets to be used in training. In this paper, a suite of three QSAR models is developed to identify compounds that are likely to (a) exhibit cytotoxic behavior against cancer cells, (b) exhibit high rat LD50 values (low systemic toxicity), and (c) exhibit low to modest human oral clearance (favorable pharmacokinetic characteristics). Models were constructed using Kernel Multitask Latent Analysis (KMLA), an approach that can effectively handle a large number of correlated data features, nonlinear relationships between features and responses, and multitask learning. Multitask learning is particularly useful when the number of available training records is small relative to the number of features, as was the case with the oral clearance data. Results Multitask learning modestly but significantly improved the classification precision for the oral clearance model. For the cytotoxicity model, which was constructed using a large number of records, multitask learning did not affect precision but did reduce computation time. The models developed here were used to predict activities for 115,000 natural compounds. Hundreds of natural compounds, particularly in the anthraquinone and flavonoids groups, were predicted to be cytotoxic, have high LD50 values, and have low to moderate oral clearance. Conclusion Multitask learning can be useful in some QSAR models. A suite of QSAR models was constructed and used to screen a large drug library for compounds likely to be cytotoxic to multiple cancer cell lines in vitro, have low systemic toxicity in rats, and have favorable pharmacokinetic properties in humans. PMID:18554402

Structure-activity models of oral clearance, cytotoxicity, and LD50: a screen for promising anticancer compounds.

PubMed

Boik, John C; Newman, Robert A

2008-06-13

Quantitative structure-activity relationship (QSAR) models have become popular tools to help identify promising lead compounds in anticancer drug development. Few QSAR studies have investigated multitask learning, however. Multitask learning is an approach that allows distinct but related data sets to be used in training. In this paper, a suite of three QSAR models is developed to identify compounds that are likely to (a) exhibit cytotoxic behavior against cancer cells, (b) exhibit high rat LD50 values (low systemic toxicity), and (c) exhibit low to modest human oral clearance (favorable pharmacokinetic characteristics). Models were constructed using Kernel Multitask Latent Analysis (KMLA), an approach that can effectively handle a large number of correlated data features, nonlinear relationships between features and responses, and multitask learning. Multitask learning is particularly useful when the number of available training records is small relative to the number of features, as was the case with the oral clearance data. Multitask learning modestly but significantly improved the classification precision for the oral clearance model. For the cytotoxicity model, which was constructed using a large number of records, multitask learning did not affect precision but did reduce computation time. The models developed here were used to predict activities for 115,000 natural compounds. Hundreds of natural compounds, particularly in the anthraquinone and flavonoids groups, were predicted to be cytotoxic, have high LD50 values, and have low to moderate oral clearance. Multitask learning can be useful in some QSAR models. A suite of QSAR models was constructed and used to screen a large drug library for compounds likely to be cytotoxic to multiple cancer cell lines in vitro, have low systemic toxicity in rats, and have favorable pharmacokinetic properties in humans.

The chemistry of gold as an anion.

PubMed

Jansen, Martin

2008-09-01

Due to relativistic and classical shell structure effects, the 6s orbital of gold is significantly contracted and energetically stabilized. This is reflected by a strikingly high electron affinity, and a distinct tendency to adopt negatively polarized valence states. This tutorial review focuses on the chemistry of gold as an anion, displaying the integral ionic charge number of 1-. Two synthetic approaches to compounds containing monoatomic gold anions have become available: (1) reacting elemental gold with molten caesium and an oxide, e.g. Cs2O; (2) metathesis reactions involving Au- dissolved in liquid ammonia. Both procedures have proven to be rather versatile. Aurides synthesized along these routes are surveyed, in particular with respect to their structures and bonding properties.

Crystal structure of langbeinite-related Rb0.743K0.845Co0.293Ti1.707(PO4)3

PubMed Central

Strutynska, Nataliia Yu.; Bondarenko, Marina A.; Ogorodnyk, Ivan V.; Baumer, Vyacheslav N.; Slobodyanik, Nikolay S.

2015-01-01

Potassium rubidium cobalt(II)/titanium(IV) tris­(orthophosphate), Rb0.743K0.845Co0.293Ti1.707(PO4)3, has been obtained using a high-temperature crystallization method. The obtained compound has a langbeinite-type structure. The three-dimensional framework is built up from mixed-occupied (Co/TiIV)O6 octa­hedra (point group symmetry .3.) and PO4 tetra­hedra. The K+ and Rb+ cations are statistically distributed over two distinct sites (both with site symmetry .3.) in the large cavities of the framework. They are surrounded by 12 O atoms. PMID:25844179

Morphological, structural, and spectral characteristics of amorphous iron sulfates

PubMed Central

Sklute, E. C.; Jensen, H. B.; Rogers, A. D.; Reeder, R. J.

2018-01-01

Current or past brine hydrologic activity on Mars may provide suitable conditions for the formation of amorphous ferric sulfates. Once formed, these phases would likely be stable under current Martian conditions, particularly at low- to mid-latitudes. Therefore, we consider amorphous iron sulfates (AIS) as possible components of Martian surface materials. Laboratory AIS were created through multiple synthesis routes and characterized with total X-ray scattering, thermogravimetric analysis, scanning electron microscopy, visible/near-infrared (VNIR), thermal infrared (TIR), and Mössbauer techniques. We synthesized amorphous ferric sulfates (Fe(III)2(SO4)3 · ~ 6–8H2O) from sulfate-saturated fluids via vacuum dehydration or exposure to low relative humidity (<11%). Amorphous ferrous sulfate (Fe(II)SO4 · ~1H2O) was synthesized via vacuum dehydration of melanterite. All AIS lack structural order beyond 11 Å. The short-range (<5 Å) structural characteristics of amorphous ferric sulfates resemble all crystalline reference compounds; structural characteristics for the amorphous ferrous sulfate are similar to but distinct from both rozenite and szomolnokite. VNIR and TIR spectral data for all AIS display broad, muted features consistent with structural disorder and are spectrally distinct from all crystalline sulfates considered for comparison. Mössbauer spectra are also distinct from crystalline phase spectra available for comparison. AIS should be distinguishable from crystalline sulfates based on the position of their Fe-related absorptions in the visible range and their spectral characteristics in the TIR. In the NIR, bands associated with hydration at ~1.4 and 1.9 μm are significantly broadened, which greatly reduces their detectability in soil mixtures. AIS may contribute to the amorphous fraction of soils measured by the Curiosity rover. PMID:29675340

Vibrational spectroscopic analyses of unique yellow feather pigments (spheniscins) in penguins.

PubMed

Thomas, Daniel B; McGoverin, Cushla M; McGraw, Kevin J; James, Helen F; Madden, Odile

2013-06-06

Many animals extract, synthesize and refine chemicals for colour display, where a range of compounds and structures can produce a diverse colour palette. Feather colours, for example, span the visible spectrum and mostly result from pigments in five chemical classes (carotenoids, melanins, porphyrins, psittacofulvins and metal oxides). However, the pigment that generates the yellow colour of penguin feathers appears to represent a sixth, poorly characterized class of feather pigments. This pigment class, here termed 'spheniscin', is displayed by half of the living penguin genera; the larger and richer colour displays of the pigment are highly attractive. Using Raman and mid-infrared spectroscopies, we analysed yellow feathers from two penguin species (king penguin, Aptenodytes patagonicus; macaroni penguin, Eudyptes chrysolophus) to further characterize spheniscin pigments. The Raman spectrum of spheniscin is distinct from spectra of other feather pigments and exhibits 17 distinctive spectral bands between 300 and 1700 cm(-1). Spectral bands from the yellow pigment are assigned to aromatically bound carbon atoms, and to skeletal modes in an aromatic, heterocyclic ring. It has been suggested that the penguin pigment is a pterin compound; Raman spectra from yellow penguin feathers are broadly consistent with previously reported pterin spectra, although we have not matched it to any known compound. Raman spectroscopy can provide a rapid and non-destructive method for surveying the distribution of different classes of feather pigments in the avian family tree, and for correlating the chemistry of spheniscin with compounds analysed elsewhere. We suggest that the sixth class of feather pigments may have evolved in a stem-lineage penguin and endowed modern penguins with a costly plumage trait that appears to be chemically unique among birds.

Vibrational spectroscopic analyses of unique yellow feather pigments (spheniscins) in penguins

PubMed Central

Thomas, Daniel B.; McGoverin, Cushla M.; McGraw, Kevin J.; James, Helen F.; Madden, Odile

2013-01-01

Many animals extract, synthesize and refine chemicals for colour display, where a range of compounds and structures can produce a diverse colour palette. Feather colours, for example, span the visible spectrum and mostly result from pigments in five chemical classes (carotenoids, melanins, porphyrins, psittacofulvins and metal oxides). However, the pigment that generates the yellow colour of penguin feathers appears to represent a sixth, poorly characterized class of feather pigments. This pigment class, here termed ‘spheniscin’, is displayed by half of the living penguin genera; the larger and richer colour displays of the pigment are highly attractive. Using Raman and mid-infrared spectroscopies, we analysed yellow feathers from two penguin species (king penguin, Aptenodytes patagonicus; macaroni penguin, Eudyptes chrysolophus) to further characterize spheniscin pigments. The Raman spectrum of spheniscin is distinct from spectra of other feather pigments and exhibits 17 distinctive spectral bands between 300 and 1700 cm−1. Spectral bands from the yellow pigment are assigned to aromatically bound carbon atoms, and to skeletal modes in an aromatic, heterocyclic ring. It has been suggested that the penguin pigment is a pterin compound; Raman spectra from yellow penguin feathers are broadly consistent with previously reported pterin spectra, although we have not matched it to any known compound. Raman spectroscopy can provide a rapid and non-destructive method for surveying the distribution of different classes of feather pigments in the avian family tree, and for correlating the chemistry of spheniscin with compounds analysed elsewhere. We suggest that the sixth class of feather pigments may have evolved in a stem-lineage penguin and endowed modern penguins with a costly plumage trait that appears to be chemically unique among birds. PMID:23516063

EF24, a novel curcumin analog, disrupts the microtubule cytoskeleton and inhibits HIF-1

PubMed Central

Thomas, Shala L.; Zhong, Diansheng; Zhou, Wei; Malik, Sanna; Liotta, Dennis; Snyder, James P.; Hamel, Ernest; Giannakakou, Paraskevi

2008-01-01

Curcumin, the yellow pigment of the spice turmeric, has emerged as a promising anticancer agent due to its antiproliferative and antiangiogenic properties. However, the molecular mechanism of action of this compound remains a subject of debate. In addition, curcumin’s low bioavailability and efficacy profile in vivo further hinders its clinical development. This study focuses on the mechanism of action of EF24, a novel curcumin analog with greater than curcumin biological activity and bioavailability, but no increased toxicity. Treatment of MDA-MB231 breast and PC3 prostate cancer cells with EF24 or curcumin led to inhibition of HIF-1α protein levels and, consequently, inhibition of HIF transcriptional activity. This drug-induced HIF inhibition occurred in a VHL-dependent but proteasome-independent manner. We found that, while curcumin inhibited HIF-1α gene transcription, EF24 exerted its activity by inhibiting HIF-1α posttranscriptionally. This result suggested that the two compounds are structurally similar but mechanistically distinct. Another cellular effect that further differentiated the two compounds was the ability of EF24, but not curcumin, to induce microtubule stabilization in cells. EF24 had no stabilizing effect on tubulin polymerization in an in vitro assay using purified bovine brain tubulin, suggesting that the EF24-induced cytoskeletal disruption in cells may be the result of upstream signaling events rather than EF24 direct binding to tubulin. In summary, our study identifies EF24 as a novel curcumin-related compound possessing a distinct mechanism of action, which we believe contributes to the potent anticancer activity of this agent and can be further exploited to investigate the therapeutic potential of EF24. PMID:18682687

EF24, a novel curcumin analog, disrupts the microtubule cytoskeleton and inhibits HIF-1.

PubMed

Thomas, Shala L; Zhong, Diansheng; Zhou, Wei; Malik, Sanna; Liotta, Dennis; Snyder, James P; Hamel, Ernest; Giannakakou, Paraskevi

2008-08-01

Curcumin, the yellow pigment of the spice turmeric, has emerged as a promising anticancer agent due to its antiproliferative and antiangiogenic properties. However, the molecular mechanism of action of this compound remains a subject of debate. In addition, curcumin's low bioavailability and efficacy profile in vivo further hinders its clinical development. This study focuses on the mechanism of action of EF24, a novel curcumin analog with greater than curcumin biological activity and bioavailability, but no increased toxicity. Treatment of MDA-MB231 breast and PC3 prostate cancer cells with EF24 or curcumin led to inhibition of HIF-1alpha protein levels and, consequently, inhibition of HIF transcriptional activity. This drug-induced HIF inhibition occurred in a VHL-dependent but proteasome-independent manner. We found that, while curcumin inhibited HIF-1alpha gene transcription, EF24 exerted its activity by inhibiting HIF-1alpha posttranscriptionally. This result suggested that the two compounds are structurally similar but mechanistically distinct. Another cellular effect that further differentiated the two compounds was the ability of EF24, but not curcumin, to induce microtubule stabilization in cells. EF24 had no stabilizing effect on tubulin polymerization in an in vitro assay using purified bovine brain tubulin, suggesting that the EF24-induced cytoskeletal disruption in cells may be the result of upstream signaling events rather than EF24 direct binding to tubulin. In summary, our study identifies EF24 as a novel curcumin-related compound possessing a distinct mechanism of action, which we believe contributes to the potent anticancer activity of this agent and can be further exploited to investigate the therapeutic potential of EF24.

Aroma characterization of tangerine hybrids by gas-chromatography-olfactometry and sensory evaluation.

PubMed

Miyazaki, Takayuki; Plotto, Anne; Baldwin, Elizabeth A; Reyes-De-Corcuera, José I; Gmitter, Fred G

2012-03-15

Tangerines have a distinct flavor among citrus fruit. However, information on tangerine volatiles remains limited. Volatile compounds from a breeding population of tangerines were earlier identified by gas chromatography-mass spectrometry. In this study, five hybrids with a distinct volatile profile were analyzed by gas-chromatography-olfactometry (GC-O) and descriptive sensory analysis. Forty-nine aroma active compounds were found in a consensus by GC-O. Aldehydes were the most important group with odor activity, as well as monoterpenes, esters, alcohols and ketones. 1,8-Cineole, β-myrcene, (E,E)-2,4-nonadienal, hexanal, ethyl-2-methylbutanoate, and linalool were perceived with high intensity in most samples. Two 'Clementine' × 'Minneola' and one 'Fortune' × 'Murcott' hybrids with tangerine, sulfury and woody/spicy flavors had aroma active compounds with terpeney, fatty/vegetable and metallic/rubber descriptors. A tangerine with 'Valencia' orange in its parentage had a characteristic orange flavor, which could be explained by esters and ketones, high in fruity and floral odor intensities. A hybrid of unknown origin had a distinct fruity-non-citrus and pumpkin/fatty flavor; that sample had the lowest amount of aroma-active volatiles, with the least compounds with terpeney odors. There was no one compound characteristic of tangerine flavor. Nevertheless, each sample sensory characteristic could be explained by a set of aroma-active volatile compounds.

Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: predicting affinity and conformational sampling.

PubMed

Bazeley, Peter S; Prithivi, Sridevi; Struble, Craig A; Povinelli, Richard J; Sem, Daniel S

2006-01-01

Cytochrome P450 2D6 (CYP2D6) is used to develop an approach for predicting affinity and relevant binding conformation(s) for highly flexible binding sites. The approach combines the use of docking scores and compound properties as attributes in building a neural network (NN) model. It begins by identifying segments of CYP2D6 that are important for binding specificity, based on structural variability among diverse CYP enzymes. A family of distinct, low-energy conformations of CYP2D6 are generated using simulated annealing (SA) and a collection of 82 compounds with known CYP2D6 affinities are docked. Interestingly, docking poses are observed on the backside of the heme as well as in the known active site. Docking scores for the active site binders, along with compound-specific attributes, are used to train a neural network model to properly bin compounds as strong binders, moderate binders, or nonbinders. Attribute selection is used to preselect the most important scores and compound-specific attributes for the model. A prediction accuracy of 85+/-6% is achieved. Dominant attributes include docking scores for three of the 20 conformations in the ensemble as well as the compound's formal charge, number of aromatic rings, and AlogP. Although compound properties were highly predictive attributes (12% improvement over baseline) in the NN-based prediction of CYP2D6 binders, their combined use with docking score attributes is synergistic (net increase of 23% above baseline). Beyond prediction of affinity, attribute selection provides a way to identify the most relevant protein conformation(s), in terms of binding competence. In the case of CYP2D6, three out of the ensemble of 20 SA-generated structures are found to be the most predictive for binding.

Specific attraction of fig-pollinating wasps: role of volatile compounds released by tropical figs.

PubMed

Grison-Pigé, Laure; Bessière, Jean-Marie; Hossaert-McKey, Martine

2002-02-01

Floral scents often act as pollinator attractants. In the case of obligate and specific plant-pollinator relationships, the role of floral signals may be crucial in allowing the encounter of the partners. About 750 Ficus species (Moraceae) are involved in such interactions, each with a distinct species of pollinating wasp (Chalcidoidea, Agaonidae). Several species have been shown to release volatile compounds, but their role in pollinator attraction has rarely been simultaneously tested. We investigated the floral scents of four tropical fig species and combined chemical analysis with biological tests of stimulation of insects. Pollinators of three species were stimulated by the odor of their associated fig species and generally not by the odor of another species. The fourth actually comprised two distinct varieties. The main compound was often a different one in each species. Floral blends of different species always shared compounds, but ratios of these compounds varied among species.

Mass Spectra-Based Framework for Automated Structural Elucidation of Metabolome Data to Explore Phytochemical Diversity

PubMed Central

Matsuda, Fumio; Nakabayashi, Ryo; Sawada, Yuji; Suzuki, Makoto; Hirai, Masami Y.; Kanaya, Shigehiko; Saito, Kazuki

2011-01-01

A novel framework for automated elucidation of metabolite structures in liquid chromatography–mass spectrometer metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method. PMID:22645535

Synthesis and structure-activity relationship of histone deacetylase (HDAC) inhibitors with triazole-linked cap group.

PubMed

Chen, Po C; Patil, Vishal; Guerrant, William; Green, Patience; Oyelere, Adegboyega K

2008-05-01

Histone deacetylase (HDAC) inhibition is a recent, clinically validated therapeutic strategy for cancer treatment. Small molecule HDAC inhibitors identified so far fall in to three distinct structural motifs: the zinc-binding group (ZBG), a hydrophobic linker, and a recognition cap group. Here we report the suitability of a 1,2,3-triazole ring as a surface recognition cap group-linking moiety in suberoylanilide hydroxamic acid-like (SAHA-like) HDAC inhibitors. Using "click" chemistry (Huisgen cycloaddition reaction), several triazole-linked SAHA-like hydroxamates were synthesized. Structure-activity relationship revealed that the position of the triazole moiety as well as the identity of the cap group markedly affected the in vitro HDAC inhibition and cell growth inhibitory activities of this class of compounds.

Homology Models of Melatonin Receptors: Challenges and Recent Advances

PubMed Central

Pala, Daniele; Lodola, Alessio; Bedini, Annalida; Spadoni, Gilberto; Rivara, Silvia

2013-01-01

Melatonin exerts many of its actions through the activation of two G protein-coupled receptors (GPCRs), named MT1 and MT2. So far, a number of different MT1 and MT2 receptor homology models, built either from the prototypic structure of rhodopsin or from recently solved X-ray structures of druggable GPCRs, have been proposed. These receptor models differ in the binding modes hypothesized for melatonin and melatonergic ligands, with distinct patterns of ligand-receptor interactions and putative bioactive conformations of ligands. The receptor models will be described, and they will be discussed in light of the available information from mutagenesis experiments and ligand-based pharmacophore models. The ability of these ligand-receptor complexes to rationalize structure-activity relationships of known series of melatonergic compounds will be commented upon. PMID:23584026

Redox chromophore compounds and electrodes of metal containing substituted bipyridines

DOEpatents

Elliott, Cecil M.; Redepenning, Jody G.

1986-01-01

Chromophoric compounds, each having a wide range of distinct color changes in response to changes in the oxidation states thereof, are provided in the form of polymerizable monomers, and polymers thereof, of certain metal containing, and electron group substituted, 2,2'-bipyridine compounds.

Structural and Spectroscopic Analysis of the Kinase Inhibitor Bosutinib and an Isomer of Bosutinib Binding to the Abl Tyrosine Kinase Domain

PubMed Central

Levinson, Nicholas M.; Boxer, Steven G.

2012-01-01

Chronic myeloid leukemia (CML) is caused by the kinase activity of the BCR-Abl fusion protein. The Abl inhibitors imatinib, nilotinib and dasatinib are currently used to treat CML, but resistance to these inhibitors is a significant clinical problem. The kinase inhibitor bosutinib has shown efficacy in clinical trials for imatinib-resistant CML, but its binding mode is unknown. We present the 2.4 Å structure of bosutinib bound to the kinase domain of Abl, which explains the inhibitor's activity against several imatinib-resistant mutants, and reveals that similar inhibitors that lack a nitrile moiety could be effective against the common T315I mutant. We also report that two distinct chemical compounds are currently being sold under the name “bosutinib”, and report spectroscopic and structural characterizations of both. We show that the fluorescence properties of these compounds allow inhibitor binding to be measured quantitatively, and that the infrared absorption of the nitrile group reveals a different electrostatic environment in the conserved ATP-binding sites of Abl and Src kinases. Exploiting such differences could lead to inhibitors with improved selectivity. PMID:22493660

The Tropical Biominer Project: mining old sources for new drugs.

PubMed

Artiguenave, François; Lins, André; Maciel, Wesley Dias; Junior, Antonio Celso Caldeira; Nacif-Coelho, Carla; de Souza Linhares, Maria Margarida Ribeiro; de Oliveira, Guilherme Correa; Barbosa, Luis Humberto Rezende; Lopes, Júlio César Dias; Junior, Claudionor Nunes Coelho

2005-01-01

The Tropical Biominer Project is a recent initiative from the Federal University of Minas Gerais (UFMG) and the Oswaldo Cruz foundation, with the participation of the Biominas Foundation (Belo Horizonte, Minas Gerais, Brazil) and the start-up Homologix. The main objective of the project is to build a new resource for the chemogenomics research, on chemical compounds, with a strong emphasis on natural molecules. Adopted technologies include the search of information from structured, semi-structured, and non-structured documents (the last two from the web) and datamining tools in order to gather information from different sources. The database is the support for developing applications to find new potential treatments for parasitic infections by using virtual screening tools. We present here the midpoint of the project: the conception and implementation of the Tropical Biominer Database. This is a Federated Database designed to store data from different resources. Connected to the database, a web crawler is able to gather information from distinct, patented web sites and store them after automatic classification using datamining tools. Finally, we demonstrate the interest of the approach, by formulating new hypotheses on specific targets of a natural compound, violacein, using inferences from a Virtual Screening procedure.

Diversity of exophillic acid derivatives in strains of an endophytic Exophiala sp.

PubMed

Cheikh-Ali, Zakaria; Glynou, Kyriaki; Ali, Tahir; Ploch, Sebastian; Kaiser, Marcel; Thines, Marco; Bode, Helge B; Maciá-Vicente, Jose G

2015-10-01

Members of the fungal genus Exophiala are common saprobes in soil and water environments, opportunistic pathogens of animals, or endophytes in plant roots. Their ecological versatility could imply a capacity to produce diverse secondary metabolites, but only a few studies have aimed at characterizing their chemical profiles. Here, we assessed the secondary metabolites produced by five Exophiala sp. strains of a particular phylotype, isolated from roots of Microthlaspi perfoliatum growing in different European localities. Exophillic acid and two previously undescribed compounds were isolated from these strains, and their structures were elucidated by spectroscopic methods using MS, 1D and 2D NMR. Bioassays revealed a weak activity of these compounds against disease-causing protozoa and mammalian cells. In addition, 18 related structures were identified by UPLC/MS based on comparisons with the isolated structures. Three Exophiala strains produced derivatives containing a β-d-glucopyranoside moiety, and their colony morphology was distinct from the other two strains, which produced derivatives lacking β-d-glucopyranoside. Whether the chemical/morphological strain types represent variants of the same genotype or independent genetic populations within Exophiala remains to be evaluated. Copyright © 2015 Elsevier Ltd. All rights reserved.

Identification of Novel Fusion Inhibitors of Influenza A Virus by Chemical Genetics

PubMed Central

Lai, Kin Kui; Cheung, Nam Nam; Yang, Fang; Dai, Jun; Liu, Li; Chen, Zhiwei; Sze, Kong Hung; Chen, Honglin

2015-01-01

ABSTRACT A previous screening of more than 50,000 compounds led to the identification of a pool of bioactive small molecules with inhibitory effect on the influenza A virus. One of these compounds, now widely known as nucleozin, is a small molecule that targets the influenza A virus nucleoprotein. Here we identify and characterize two structurally different novel fusion inhibitors of the influenza A virus group 1 hemagglutinin (HA), FA-583 and FA-617, with low nanomolar activities. Escape mutants that are highly resistant to each of these compounds were generated, and both were found to carry mutations localized in close proximity to the B-loop of the hemagglutinin 2 protein, which plays a crucial role in the virion-host cell fusion process. Recombinant virus, generated through reverse genetics, confirmed the resistance phenotype. In addition, the proposed binding pockets predicted by molecular docking studies are in accordance with the resistance-bearing mutation sites. We show through mechanistic studies that FA-583 and FA-617 act as fusion inhibitors by prohibiting the low-pH-induced conformational change of hemagglutinin. Our study has offered concrete biological and mechanistic explorations for the strategic development of novel fusion inhibitors of influenza A viruses. IMPORTANCE Here we report two structurally distinctive novel fusion inhibitors of influenza A virus that act by interfering with the structural change of HA at acidic pH, a process necessary for successful entry of the virus. Mutational and molecular docking studies have identified their binding pockets situated in close proximity to the B-loop region of hemagglutinin 2. The reduced sensitivity of FA-583- or FA-617-associated mutants to another compound suggests a close proximity and even partial overlap of their binding sites on hemagglutinin. Amino acid sequence alignments and crystal structure analyses of group 1 and group 2 hemagglutinins have shed light on the possible binding mode of these two compounds. This report offers new lead compounds for the design of fusion inhibitors for influenza A viruses and further shows that analysis by forward chemical genetics is a highly effective approach for the identification of novel compounds that can perturb the infectivity of viruses and to probe new druggable targets or druggable domains in various viruses. PMID:26676787

Likelihood of atom-atom contacts in crystal structures of halogenated organic compounds.

PubMed

Jelsch, Christian; Soudani, Sarra; Ben Nasr, Cherif

2015-05-01

The likelihood of occurrence of intermolecular contacts in crystals of halogenated organic compounds has been analysed statistically using tools based on the Hirshfeld surface. Several families of small halogenated molecules (containing organic F, Cl, Br or I atoms) were analysed, based on chemical composition and aromatic or aliphatic character. The behaviour of crystal contacts was also probed for molecules containing O or N. So-called halogen bonding (a halogen making short interactions with O or N, or a π interaction with C) is generally disfavoured, except when H is scarce on the molecular surface. Similarly, halogen⋯halogen contacts are more rare than expected, except for molecules that are poor in H. In general, the H atom is found to be the preferred partner of organic halogen atoms in crystal structures. On the other hand, C⋯C interactions in parallel π-stacking have a high propensity to occur in halogenated aromatic molecules. The behaviour of the four different halogen species (F, Cl, Br, I) is compared in several chemical composition contexts. The analysis tool can be refined by distinguishing several types for a given chemical species, such as H atoms bound to O or C. Such distinction shows, for instance, that C-H⋯Cl and O-H⋯O are the preferred interactions in compounds containing both O and Cl.

Current Status and Future Prospects of Marine Natural Products (MNPs) as Antimicrobials

PubMed Central

Choudhary, Alka; Naughton, Lynn M.; Montánchez, Itxaso

2017-01-01

The marine environment is a rich source of chemically diverse, biologically active natural products, and serves as an invaluable resource in the ongoing search for novel antimicrobial compounds. Recent advances in extraction and isolation techniques, and in state-of-the-art technologies involved in organic synthesis and chemical structure elucidation, have accelerated the numbers of antimicrobial molecules originating from the ocean moving into clinical trials. The chemical diversity associated with these marine-derived molecules is immense, varying from simple linear peptides and fatty acids to complex alkaloids, terpenes and polyketides, etc. Such an array of structurally distinct molecules performs functionally diverse biological activities against many pathogenic bacteria and fungi, making marine-derived natural products valuable commodities, particularly in the current age of antimicrobial resistance. In this review, we have highlighted several marine-derived natural products (and their synthetic derivatives), which have gained recognition as effective antimicrobial agents over the past five years (2012–2017). These natural products have been categorized based on their chemical structures and the structure-activity mediated relationships of some of these bioactive molecules have been discussed. Finally, we have provided an insight into how genome mining efforts are likely to expedite the discovery of novel antimicrobial compounds. PMID:28846659

Syntheses and Chemosensory of Anthracene and Phenanthrene Bisimide Derivatives

NASA Technical Reports Server (NTRS)

Bogusz, Zachary A.

2004-01-01

As the present technology of biochemical weapons advances, it is essential for science to attempt to prepare our nation for such an occurrence. Various areas of current research are devoted to precautionary measures and potential antidotes for national security. A practical application of these precautions would be the development of a chemical capable of detecting harmful gas. The benefits of being capable to synthesis a chemical compound that would warn and identify potentially deadly gases would ensure a higher level of safety. The chemicals in question can be generalized as bisimide anthracene derivatives. The idea behind these compounds is that in the presence of certain nerve gases, the compound will actually fluoresce, giving an indication that there is a strong likelihood of the presence of a nerve gas and ensure the proper precautionary measures are taken. The fluorescence is due to the quenching of an electric proton transfer within the structure of the molecule. The system proves to be very unique on account of the fact that the fluorescence can be "turned off" by reducing the system. By utilizing the synthesis designed by Dr. Faysal Ilhan, four distinct compounds can be synthesized through photochemical reactions involving para- and ortho- diketones. The photochemistry involved is very modem and much research is being devoted to fully understanding the possibilities and alternative applications of such materials. and meta-nitro anthracene bisimide (ABI-NO2), the amine of each (ABI-NH2), a para- and meta-nitro phenanthrene bisimjde (PBI-NO2), and the amine of each (PBI-NH2). Upon synthesizing these distinct compounds, I must then purify and analyze them in order to obtain any relevant trends, behaviors, and characteristics. The chemical composition analyses that will be conducted are the procedures taken by Dr. Daniel Tyson on previous experiments. The results generated from the data will point further research in the correct direction and hopefully provide enough information to possibly create a stepping-stone for a brand new area in an unexplored frontier of chemistry.

A dysmorphology score system for assessing embryo abnormalities in rat whole embryo culture.

PubMed

Zhang, Cindy X; Danberry, Tracy; Jacobs, Mary Ann; Augustine-Rauch, Karen

2010-12-01

The rodent whole embryo culture (WEC) system is a well-established model for characterizing developmental toxicity of test compounds and conducting mechanistic studies. Laboratories have taken various approaches in describing type and severity of developmental findings of organogenesis-stage rodent embryos, but the Brown and Fabro morphological score system is commonly used as a quantitative approach. The associated score criteria is based upon developmental stage and growth parameters, where a series of embryonic structures are assessed and assigned respective scores relative to their gestational stage, with a Total Morphological Score (TMS) assigned to the embryo. This score system is beneficial because it assesses a series of stage-specific anatomical landmarks, facilitating harmonized evaluation across laboratories. Although the TMS provides a quantitative approach to assess growth and determine developmental delay, it is limited to its ability to identify and/or delineate subtle or structure-specific abnormalities. Because of this, the TMS may not be sufficiently sensitive for identifying compounds that induce structure or organ-selective effects. This study describes a distinct morphological score system called the "Dysmorphology Score System (DMS system)" that has been developed for assessing gestation day 11 (approximately 20-26 somite stage) rat embryos using numerical scores to differentiate normal from abnormal morphology and define the respective severity of dysmorphology of specific embryonic structures and organ systems. This method can also be used in scoring mouse embryos of the equivalent developmental stage. The DMS system enhances capabilities to rank-order compounds based upon teratogenic potency, conduct structure- relationships of chemicals, and develop statistical prediction models to support abbreviated developmental toxicity screens. © 2010 Wiley-Liss, Inc.

Structural flexibility in magnetocaloric RE 5T 4 (RE=rare-earth; T=Si,Ge,Ga) materials: Effect of chemical substitution on structure, bonding and properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Misra, Sumohan

The binary, ternary and multicomponent intermetallic compounds of rare-earth metals (RE) with group 14 elements (Tt) at the RE 5Tt 4 stoichiometry have been known for over 30 years, but only in the past decade have these materials become a gold mine for solid-state chemistry, materials science and condensed matter physics. It all started with the discovery of a giant magnetocaloric effect in Gd 5Si 2Ge 2, along with other extraordinary magnetic properties, such as a colossal magnetostriction and giant magnetoresistance. The distinctiveness of this series is in the remarkable flexibility of the chemical bonding between well-defined, subnanometer-thick slabs andmore » the resultant magnetic, transport, and thermodynamic properties of these materials. This can be controlled by varying either or both RE and Tt elements, including mixed rare-earth elements on the RE sites and different group 14 (or T = group 13 or 15) elements occupying the Tt sites. In addition to chemical means, the interslab interactions are also tunable by temperature, pressure, and magnetic field. Thus, this system provides a splendid 'playground' to investigate the interrelationships among composition, structure, physical properties, and chemical bonding. The work presented in this dissertation involving RE 5T 4 materials has resulted in the successful synthesis, characterization, property measurements, and theoretical analyses of various new intermetallic compounds. The results provide significant insight into the fundamental magnetic and structural behavior of these materials and help us better understand the complex link between a compound's composition, its observed structure, and its properties.« less

Comparison of the Manganese Cluster in Oxygen-Evolving Photosystem II with Distorted Cubane Manganese Compounds through X-ray Absorption Spectroscopy

PubMed Central

Cinco, Roehl M.; Rompel, Annette; Visser, Hendrik; Aromí, Guillem; Christou, George; Sauer, Kenneth; Klein, Melvin P.; Yachandra, Vittal K.

2014-01-01

X-ray absorption spectroscopy has been employed to assess the degree of similarity between the oxygen-evolving complex (OEC) in photosystem II (PS II) and a family of synthetic manganese complexes containing the distorted cubane [Mn4O3X] core (X = benzoate, acetate, methoxide, hydroxide, azide, fluoride, chloride, or bromide). These [Mn4(μ3-O)3(μ3-X)] cubanes possess C3v symmetry except for the X = benzoate species, which is slightly more distorted with only Cs symmetry. In addition, Mn4O3Cl complexes containing three or six terminal Cl ligands at three of the Mn were included in this study. The Mn K-edge X-ray absorption near edge structure (XANES) from the oxygen-ligated complexes begin to resemble general features of the PS II (S1 state) spectrum, although the second derivatives are distinct from those in PS II. The extended X-ray absorption fine structure (EXAFS) of these Mn compounds also displays superficial resemblance to that of PS II, but major differences emerge on closer examination of the phases and amplitudes. The most obvious distinction is the smaller magnitude of the Fourier transform (FT) of the PS II EXAFS compared to the FTs from the distorted cubanes. Curve fitting of the Mn EXAFS spectra verifies the known core structures of the Mn cubanes, and shows that the number of the crucial 2.7 and 3.3 Å Mn–Mn distances differs from that observed in the OEC. The EXAFS method detects small changes in the core structures as X is varied in this series, and serves to exclude the distorted cubane of C3v symmetry as a topological model for the Mn catalytic cluster of the OEC. Instead, the method shows that even more distortion of the cubane framework, altering the ratio of the Mn–Mn distances, is required to resemble the Mn cluster in PS II. PMID:11671305

The crystal structures of Ni{sub 3+x}Sn{sub 4}Zn and Ni{sub 6+x}Sn{sub 8}Zn and their structural relations to Ni{sub 3+x}Sn{sub 4}, NiSn and Ni{sub 5−δ}ZnSn{sub 4}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schmetterer, Clemens, E-mail: clemens.schmetterer@univie.ac.at; Effenberger, Herta Silvia; Rajamohan, Divakar

2016-06-15

The crystal structures of two new compounds were determined from single-crystal X-ray diffraction measurements: Ni{sub 3+x}Sn{sub 4}Zn, (x~1.35, a=7.110(2) Å, b=4.123(1) Å, c=10.346(3) Å, β=90.23(2)°, space group I2/m, Z=2. R1=0.025, wR2=0.059 for 748 unique reflections, 35 variable parameters) and Ni{sub 6+x}Sn{sub 8}Zn, x~1.35 (a=12.379(3) Å, b=4.095(1) Å, c=12.155(3) Å, β=116.25(3)°, space group C2/m, Z=2. R1=0.026, wR2=0.052 for 1346 unique reflections, 60 variable parameters). In addition, a structural refinement was performed for Ni{sub 3+x}Sn{sub 4}, x~0.13 (a=12.264(3) Å, b=4.066(1) Å, c=5.223(2) Å, β=104.85(3)°, space group C2/m, Z=2. R1=0.019, wR2=0.046 for 617 unique reflections, 29 variable parameters). The three compounds show pronouncedmore » similarities among each other as well as to the crystal structures of surrounding binary Ni–Sn and ternary Ni–Sn–Zn compounds. In particular, the two new compounds form a homologous series with Ni{sub 3+x}Sn{sub 4}, x~0.13. They contain “Ni{sub 4}Sn{sub 4}” and “Ni{sub 2}Sn{sub 4}” building blocks which by different interconnection build up the distinct structures. Topological relations with NiSn and Ni{sub 5−δ}Sn{sub 4}Zn, δ~0.25 are evident. - Graphical abstract: Projection of the structure of Ni{sub 6+x}ZnSn{sub 8}, x~1.35 and constituent building blocks. Display Omitted - Highlights: • The crystal structures of Ni{sub 6+x}Sn{sub 8}Zn and Ni{sub 3+x}Sn{sub 4}Zn were determined using single crystal XRD. • Topological relations to Ni–Sn and Ni–Sn–Zn compounds were established and discussed. • Common structural units were identified and their interconnection patterns described.« less

Poly(acrylic acid) to induce competitive crystallization of a theophylline/oxalic acid cocrystal and a theophylline polymorph

NASA Astrophysics Data System (ADS)

Jang, Jisun; Kim, Il Won

2016-01-01

Polymeric additives to induce competitive crystallization of pharmaceutical compounds were explored. A cocrystal of theophylline and oxalic acid was used as a model system, and poly(acrylic acid), poly(caprolactone), and poly(ethylene glycol) were the additives. The cocrystal formation was selectively hindered with addition of poly(acrylic acid). First the size of the cocrystals were reduced, and eventually the cocrystallization was inhibited to generate neat theophylline crystals. The theophylline crystals were of a distinctively different crystal structure from known polymorphs, based on powder X-ray diffraction. They were also obtained in nanoscale size, when millimeter-scale crystals formed without poly(acrylic acid). Polymeric additives that could form specific interactions with crystallizing compounds seem to be useful tools for the phase and size control of pharmaceutical crystals.

Thermal behaviour and microanalysis of coal subbituminus

NASA Astrophysics Data System (ADS)

Heriyanti; Prendika, W.; Ashyar, R.; Sutrisno

2018-04-01

Differential scanning calorimetry (DSC) and X-ray powder diffraction (XRD) is used to study the thermal behaviour of sub-bituminous coal. The DSC experiment was performed in air atmosphere up to 125 °C at a heating rate of 25 °C min1. The DSC curve showed that the distinct transitional stages in the coal samples studied. Thermal heating temperature intervals, peak and dissociation energy of the coal samples were also determined. The XRD analysis was used to evaluate the diffraction pattern and crystal structure of the compounds in the coal sample at various temperatures (25-350 °C). The XRD analysis of various temperatures obtained compounds from the coal sample, dominated by quartz (SiO2) and corundum (Al2O3). The increase in temperature of the thermal treatment showed a better crystal formation.

Natural compounds interacting with nicotinic acetylcholine receptors: from low-molecular weight ones to peptides and proteins.

PubMed

Kudryavtsev, Denis; Shelukhina, Irina; Vulfius, Catherine; Makarieva, Tatyana; Stonik, Valentin; Zhmak, Maxim; Ivanov, Igor; Kasheverov, Igor; Utkin, Yuri; Tsetlin, Victor

2015-05-14

Nicotinic acetylcholine receptors (nAChRs) fulfill a variety of functions making identification and analysis of nAChR subtypes a challenging task. Traditional instruments for nAChR research are d-tubocurarine, snake venom protein α-bungarotoxin (α-Bgt), and α-conotoxins, neurotoxic peptides from Conus snails. Various new compounds of different structural classes also interacting with nAChRs have been recently identified. Among the low-molecular weight compounds are alkaloids pibocin, varacin and makaluvamines C and G. 6-Bromohypaphorine from the mollusk Hermissenda crassicornis does not bind to Torpedo nAChR but behaves as an agonist on human α7 nAChR. To get more selective α-conotoxins, computer modeling of their complexes with acetylcholine-binding proteins and distinct nAChRs was used. Several novel three-finger neurotoxins targeting nAChRs were described and α-Bgt inhibition of GABA-A receptors was discovered. Information on the mechanisms of nAChR interactions with the three-finger proteins of the Ly6 family was found. Snake venom phospholipases A2 were recently found to inhibit different nAChR subtypes. Blocking of nAChRs in Lymnaea stagnalis neurons was shown for venom C-type lectin-like proteins, appearing to be the largest molecules capable to interact with the receptor. A huge nAChR molecule sensible to conformational rearrangements accommodates diverse binding sites recognizable by structurally very different compounds.

Interrogating alkyl and arylalkylpolyamino (bis)urea and (bis)thiourea isosteres as potent antimalarial chemotypes against multiple lifecycle forms of Plasmodium falciparum parasites.

PubMed

Verlinden, Bianca K; de Beer, Marna; Pachaiyappan, Boobalan; Besaans, Ethan; Andayi, Warren A; Reader, Janette; Niemand, Jandeli; van Biljon, Riette; Guy, Kiplin; Egan, Timothy; Woster, Patrick M; Birkholtz, Lyn-Marie

2015-08-15

A new series of potent potent aryl/alkylated (bis)urea- and (bis)thiourea polyamine analogues were synthesized and evaluated in vitro for their antiplasmodial activity. Altering the carbon backbone and terminal substituents increased the potency of analogues in the compound library 3-fold, with the most active compounds, 15 and 16, showing half-maximal inhibitory concentrations (IC50 values) of 28 and 30 nM, respectively, against various Plasmodium falciparum parasite strains without any cross-resistance. In vitro evaluation of the cytotoxicity of these analogues revealed marked selectivity towards targeting malaria parasites compared to mammalian HepG2 cells (>5000-fold lower IC50 against the parasite). Preliminary biological evaluation of the polyamine analogue antiplasmodial phenotype revealed that (bis)urea compounds target parasite asexual proliferation, whereas (bis)thiourea compounds of the same series have the unique ability to block transmissible gametocyte forms of the parasite, indicating pluripharmacology against proliferative and non-proliferative forms of the parasite. In this manuscript, we describe these results and postulate a refined structure-activity relationship (SAR) model for antiplasmodial polyamine analogues. The terminally aryl/alkylated (bis)urea- and (bis)thiourea-polyamine analogues featuring a 3-5-3 or 3-6-3 carbon backbone represent a structurally novel and distinct class of potential antiplasmodials with activities in the low nanomolar range, and high selectivity against various lifecycle forms of P. falciparum parasites. Copyright © 2015 Elsevier Ltd. All rights reserved.

Natural Compounds Interacting with Nicotinic Acetylcholine Receptors: From Low-Molecular Weight Ones to Peptides and Proteins

PubMed Central

Kudryavtsev, Denis; Shelukhina, Irina; Vulfius, Catherine; Makarieva, Tatyana; Stonik, Valentin; Zhmak, Maxim; Ivanov, Igor; Kasheverov, Igor; Utkin, Yuri; Tsetlin, Victor

2015-01-01

Nicotinic acetylcholine receptors (nAChRs) fulfill a variety of functions making identification and analysis of nAChR subtypes a challenging task. Traditional instruments for nAChR research are d-tubocurarine, snake venom protein α-bungarotoxin (α-Bgt), and α-conotoxins, neurotoxic peptides from Conus snails. Various new compounds of different structural classes also interacting with nAChRs have been recently identified. Among the low-molecular weight compounds are alkaloids pibocin, varacin and makaluvamines C and G. 6-Bromohypaphorine from the mollusk Hermissenda crassicornis does not bind to Torpedo nAChR but behaves as an agonist on human α7 nAChR. To get more selective α-conotoxins, computer modeling of their complexes with acetylcholine-binding proteins and distinct nAChRs was used. Several novel three-finger neurotoxins targeting nAChRs were described and α-Bgt inhibition of GABA-A receptors was discovered. Information on the mechanisms of nAChR interactions with the three-finger proteins of the Ly6 family was found. Snake venom phospholipases A2 were recently found to inhibit different nAChR subtypes. Blocking of nAChRs in Lymnaea stagnalis neurons was shown for venom C-type lectin-like proteins, appearing to be the largest molecules capable to interact with the receptor. A huge nAChR molecule sensible to conformational rearrangements accommodates diverse binding sites recognizable by structurally very different compounds. PMID:26008231

Structural characterization of nonactive site, TrkA-selective kinase inhibitors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Su, Hua-Poo; Rickert, Keith; Burlein, Christine

Current therapies for chronic pain can have insufficient efficacy and lead to side effects, necessitating research of novel targets against pain. Although originally identified as an oncogene, Tropomyosin-related kinase A (TrkA) is linked to pain and elevated levels of NGF (the ligand for TrkA) are associated with chronic pain. Antibodies that block TrkA interaction with its ligand, NGF, are in clinical trials for pain relief. Here, we describe the identification of TrkA-specific inhibitors and the structural basis for their selectivity over other Trk family kinases. The X-ray structures reveal a binding site outside the kinase active site that uses residuesmore » from the kinase domain and the juxtamembrane region. Three modes of binding with the juxtamembrane region are characterized through a series of ligand-bound complexes. The structures indicate a critical pharmacophore on the compounds that leads to the distinct binding modes. The mode of interaction can allow TrkA selectivity over TrkB and TrkC or promiscuous, pan-Trk inhibition. This finding highlights the difficulty in characterizing the structure-activity relationship of a chemical series in the absence of structural information because of substantial differences in the interacting residues. These structures illustrate the flexibility of binding to sequences outside of—but adjacent to—the kinase domain of TrkA. This knowledge allows development of compounds with specificity for TrkA or the family of Trk proteins.« less

Structure and thermodynamic stability of UTa 3 O 10 , a U( v )-bearing compound

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Xiaofeng; Lipp, Christian; Tiferet, Eitan

Heating a mixture of uranyl(VI) nitrate and tantalum(V) oxide in the molar ratio of 2 : 3 to 1400 °C resulted in the formation of a new compound, UTa 3O 10. The honey colored to yellow brown crystals of UTa 3O 10 crystallize in an orthorhombic structure with the space group Fddd (no. 70), lattice parameters a = 7.3947(1), b = 12.7599(2), c = 15.8156(2) Å, and Z = 8. Vertex sharing [TaO 6] 7- octahedra of two crystallographically distinct Ta cations form a three dimensional tantalate framework. Within this framework, six membered rings of [TaO 6] 7- octahedra aremore » formed within the (001) plane. The center of these rings is occupied by the uranyl cations [UO 2] +, with an oxidation state of +5 for uranium. The pentavalence of U and Ta was confirmed by X-ray photoelectron spectroscopy and X-ray adsorption spectroscopy. The enthalpy of formation of UTa 3O 10 from Ta 2O 5, β-U 3O 7, and U 3O 8 has been determined to be 13.1 ± 18.1 kJ mol -1 using high temperature oxide melt solution calorimetry with sodium molybdate as the solvent at 700 °C. The close to zero enthalpy of formation of UTa 3O 10 can be explained by closely balanced structural stabilizing and destabilizing factors, which may also apply to other UM 3O 10 compounds.« less

Analytical characterization and structure elucidation of metabolites from Aspergillus ochraceus MP2 fungi.

PubMed

Meenupriya, J; Thangaraj, M

2011-10-01

To isolate and characterize the bioactive secondary metabolites from Aspergillus ochraceus (A. ochraceus) MP2 fungi. The anti bacterial activity of marine sponge derived fungi A. ochraceus MP2 was thoroughly investigated against antagonistic human pathogens. The optimum inhibitory concentration of the fungi in the elite solvent was also determined. The promising extracts that showed good antimicrobial activity were subjected to further analytical separation to get individual distinct metabolites and the eluants were further identified by GC MS instrumental analysis. The molecular characterization of the elite fungal strains were done by isolating their genomic DNA and amplify the internal transcribed spacer (ITS) region of 5.8s rRNA using specific ITS primer. The novelty of the strain was proved by homology search tools and elite sequences was submitted to GENBANK. Three bioactive compounds were characterized to reveal their identity, chemical formula and structure. The first elutant was identified asα- Campholene aldehyde with chemical formula C10 H16 O and molecular weight 152 Da. The second elutant was identified as Lucenin-2 and chemical formula C27 H30 O16 and molecular weight 610 Da. The third elutant was identified as 6-Ethyloct- 3-yl- 2- ethylhexyl ester with Chemical formula C26 H42 O4 with molecular weight 418 Da. The isolated compounds showed significant antimicrobial activity against potential human pathogens. Microbial secondary metabolites represent a large source of compounds endowed with ingenious structures and potent biological activities.

Two-temperature synthesis of non-linear optical compound CdGeAs2

NASA Astrophysics Data System (ADS)

Zhu, Chongqiang; Verozubova, G. A.; Mironov, Yuri P.; Lei, Zuotao; Song, Liangcheng; Ma, Tianhui; Okunev, A. O.; Yang, Chunhui

2016-12-01

In this work, we report on a new approach to synthesize large-scale nonlinear optical chalcopyrite compound CdGeAs2 (cadmium germanium arsenide), in which the arsenic (As) precursor and the mixture of the cadmium (Cd) and the germanium (Ge) were separated in two distinct temperature-defined zones of a furnace. Through probing the intermediate product prepared at pre-set temperature points of hot-zone area, it was revealed that the ternary compound CdGeAs2 was formed through chemical reactions among Cd3As2, CdAs2, GeAs, GeAs2 and Ge. A new intermediate crystalline compound, with determined crystal parameter c=0.9139 nm and unknown a parameter, was identified when the temperature of the mixture of Cd and Ge was set to 680 °C, which, however, disappeared when the temperature was set to 770 °C, yielding pure CdGeAs2 product. Most likely, the identified new intermediate compound has layered graphite-like structure. Moreover, we show that the described two-temperature synthesis method allows us to produce near 250 g CdGeAs2 product during one run in a horizontal furnace and 500 g in a tilted horizontal furnace with rotated reactor.

Indications of Transformation Products from Hydraulic Fracturing Additives in Shale-Gas Wastewater.

PubMed

Hoelzer, Kathrin; Sumner, Andrew J; Karatum, Osman; Nelson, Robert K; Drollette, Brian D; O'Connor, Megan P; D'Ambro, Emma L; Getzinger, Gordon J; Ferguson, P Lee; Reddy, Christopher M; Elsner, Martin; Plata, Desiree L

2016-08-02

Unconventional natural gas development (UNGD) generates large volumes of wastewater, the detailed composition of which must be known for adequate risk assessment and treatment. In particular, transformation products of geogenic compounds and disclosed additives have not been described. This study investigated six Fayetteville Shale wastewater samples for organic composition using a suite of one- and two-dimensional gas chromatographic techniques to capture a broad distribution of chemical structures. Following the application of strict compound-identification-confidence criteria, we classified compounds according to their putative origin. Samples displayed distinct chemical distributions composed of typical geogenic substances (hydrocarbons and hopane biomarkers), disclosed UNGD additives (e.g., hydrocarbons, phthalates such as diisobutyl phthalate, and radical initiators such as azobis(isobutyronitrile)), and undisclosed compounds (e.g., halogenated hydrocarbons, such as 2-bromohexane or 4-bromoheptane). Undisclosed chloromethyl alkanoates (chloromethyl propanoate, pentanoate, and octanoate) were identified as potential delayed acids (i.e., those that release acidic moieties only after hydrolytic cleavage, the rate of which could be potentially controlled), suggesting they were deliberately introduced to react in the subsurface. In contrast, the identification of halogenated methanes and acetones suggested that those compounds were formed as unintended byproducts. Our study highlights the possibility that UNGD operations generate transformation products and underscores the value of disclosing additives injected into the subsurface.

Synthesis of New Ba Complex as Metalorganic Source for Metalorganic Chemical Vapor Deposition and Optimization of Its Molecule Structure

NASA Astrophysics Data System (ADS)

Zama, Hideaki; Morishita, Tadataka

2000-10-01

New Ba(DPM)2-amine (DPM=dipivaloylmethane) adduct compounds were attempted to be synthesized from Ba(DPM)2 and amines. Complexes obtained were evaluated based on decreases of their weight with increasing temperature by thermogravimetry. The simple vaporizing phenomenon, showing a one-step weight-reduction curve, was observed only in the case of using tetraethylenepentamine and pentaethylenehexamine (pentaen) as adduct molecules, which have a simple chain structure and five to six primary and secondary amine radicals. From the viewpoint of applicability to film growth, they have the best structure based on a survey in this study using sixteen amine molecules with distinctive structures. When we used Ba(DPM)2-pentaen as a metalorganic source for a metalorganic chemical vapor deposition method at a vaporizing temperature of 140°C, the Ba supply rate remained stable within a standard deviation of 1.6% for over 300 h.

The proposal of architecture for chemical splitting to optimize QSAR models for aquatic toxicity.

PubMed

Colombo, Andrea; Benfenati, Emilio; Karelson, Mati; Maran, Uko

2008-06-01

One of the challenges in the field of quantitative structure-activity relationship (QSAR) analysis is the correct classification of a chemical compound to an appropriate model for the prediction of activity. Thus, in previous studies, compounds have been divided into distinct groups according to their mode of action or chemical class. In the current study, theoretical molecular descriptors were used to divide 568 organic substances into subsets with toxicity measured for the 96-h lethal median concentration for the Fathead minnow (Pimephales promelas). Simple constitutional descriptors such as the number of aliphatic and aromatic rings and a quantum chemical descriptor, maximum bond order of a carbon atom divide compounds into nine subsets. For each subset of compounds the automatic forward selection of descriptors was applied to construct QSAR models. Significant correlations were achieved for each subset of chemicals and all models were validated with the leave-one-out internal validation procedure (R(2)(cv) approximately 0.80). The results encourage to consider this alternative way for the prediction of toxicity using QSAR subset models without direct reference to the mechanism of toxic action or the traditional chemical classification.

A forward chemical screen in zebrafish identifies a retinoic acid derivative with receptor specificity.

PubMed

Das, Bhaskar C; McCartin, Kellie; Liu, Ting-Chun; Peterson, Randall T; Evans, Todd

2010-04-02

Retinoids regulate key developmental pathways throughout life, and have potential uses for differentiation therapy. It should be possible to identify novel retinoids by coupling new chemical reactions with screens using the zebrafish embryonic model. We synthesized novel retinoid analogues and derivatives by amide coupling, obtaining 80-92% yields. A small library of these compounds was screened for bioactivity in living zebrafish embryos. We found that several structurally related compounds significantly affect development. Distinct phenotypes are generated depending on time of exposure, and we characterize one compound (BT10) that produces specific cardiovascular defects when added 1 day post fertilization. When compared to retinoic acid (ATRA), BT10 shows similar but not identical changes in the expression pattern of embryonic genes that are known targets of the retinoid pathway. Reporter assays determined that BT10 interacts with all three RAR receptor sub-types, but has no activity for RXR receptors, at all concentrations tested. Our screen has identified a novel retinoid with specificity for retinoid receptors. This lead compound may be useful for manipulating components of retinoid signaling networks, and may be further derivatized for enhanced activity.

Rational Quantitative Structure-Activity Relationship (RQSAR) Screen for PXR and CAR Isoform-Specific Nuclear Receptor Ligands

PubMed Central

Dring, Ann M.; Anderson, Linnea E.; Qamar, Saima; Stoner, Matthew A.

2010-01-01

Constitutive androstane receptor (CAR) and pregnane X receptor (PXR) are closely related orphan nuclear receptor proteins that share several ligands and target overlapping sets of genes involved in homeostasis and all phases of drug metabolism. CAR and PXR are involved in the development of certain diseases, including diabetes, metabolic syndrome and obesity. Ligand screens for these receptors so far have typically focused on steroid hormone analogs with pharmacophore-based approaches, only to find relatively few new hits. Multiple CAR isoforms have been detected in human liver, with the most abundant being the constitutively active reference, CAR1, and the ligand-dependent isoform CAR3. It has been assumed that any compound that binds CAR1 should also activate CAR3, and so CAR3 can be used as a ligand-activated surrogate for CAR1 studies. The possibility of CAR3-specific ligands has not, so far, been addressed. To investigate the differences between CAR1, CAR3 and PXR, and to look for more CAR ligands that may be of use in quantitative structure-activity relationship (QSAR) studies, we performed a luciferase transactivation assay screen of 60 mostly non-steroid compounds. Known active compounds with different core chemistries were chosen as starting points and structural variants were rationally selected for screening. Distinct differences in agonist versus inverse agonist/antagonist effects were seen in 49 compounds that had some ligand effect on at least one receptor and 18 that had effects on all three receptors; eight were CAR1 ligands only, three were CAR3 only ligands and four affected PXR only. This work provides evidence for new CAR ligands, some of which have CAR3-specific effects, and provides observational data on CAR and PXR ligands with which to inform in silico strategies. Compounds that demonstrated unique activity on any one receptor are potentially valuable diagnostic tools for the investigation of in vivo molecular targets. PMID:20869355

Synthesizing new, high-temperature superconductors

NASA Astrophysics Data System (ADS)

Weaver, Claire; Aronson, Meigan

2015-03-01

Currently, there is no accepted theory behind type-II, high-temperature superconductors, but there is a distinct relationship between anti-ferromagnetism and superconductivity. Our research focuses on synthesizing new superconducting materials by observing the link between atomic structure and magnetic moments of anti-ferromagnetic compounds and attempting to reproduce the molecular physics of these known materials in new compounds. Consider the square-planar arrangement of the transition metal Fe in the Fe-pnictide superconductors of the ZrCuSiAs ``11 11'' and the ThCr2Si2 ``122'' structure types. We believe that the physics behind this superconductor, where Fe has d6 valence electrons, contributes to the superconducting state, not the presence of Fe itself. For this reason, we are synthesizing materials containing neighboring transition metals, like Mn and Co, combined with other elements in similar crystal lattice arrangements, having ionization properties that hopefully impose d6 valence electrons on the transition metals. This project was supported in part by the U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists (WDTS) under the Science Undergraduate Laboratory Internships Program (SULI).

[Study on mechanism of SOM stabilization of paddy soils under long-term fertilizations].

PubMed

Luo, Lu; Zhou, Ping; Tong, Cheng-Li; Shi, Hui; Wu, Jin-Shui; Huang, Tie-Ping

2013-02-01

Fourier transform infrared spectroscopy (FTIR) was applied to study the structure of soil organic matter (SOM) of paddy soils under long-term different fertilization treatments. The aim was to clarify the different distribution of SOM between different fertilization methods and between topsoil and subsoil, and to explore the stability mechanism of SOM under different fertilization treatments. The results showed that the content of topsoil organic carbon (SOC) was the highest under organic-inorganic fertilizations, with the increment of SOC by 18.5%, 12.9% and 18.4% under high organic manure (HOM), low organic manure (LOM) and straw returning (STW) respectively compared with no fertilization treatment (CK). The long-term fertilizations also changed the chemical structure of SOM. As compared with CK, different fertilization treatments increased the functional group absorbing intensity of chemical resistance compounds (aliphatic, aromaticity), carbohydrate and organo-silicon compounds, which was the most distinctive under treatments of HOM, LOM and STW. For example, the absorbing intensity of alkyl was 0.30, 0.25 and 0.29 under HOM, LOM and STW, respectively. These values were increased by 87% , 56% and 81% as compared with that under CK treatment. The functional group absorbing intensity of SOM in the topsoil was stronger than that in the subsoil, with the most distinctive difference under HOM, LOM and STW treatments. The present research indicated that the enhanced chemical resistance of functional group of SOM may contribute to the high contents of SOC in the paddy soils under long-term organic-inorganic fertilizations, which also suggested a chemical stabilization mechanism of SOM in the paddy soils.

Enhanced magnetization in morphologically and magnetically distinct BiFeO3 and La0.7Sr0.3MnO3 composites

NASA Astrophysics Data System (ADS)

Pillai, Shreeja; Reshi, Hilal Ahmad; Bagwaiya, Toshi; Banerjee, Alok; Shelke, Vilas

2017-09-01

Nanomaterials exhibit properties different from those of their bulk counterparts. The modified magnetic characteristics of manganite nanoparticles were exploited to improve magnetization in multiferroic BiFeO3 compound. We studied the composite of two morphologically and magnetically distinct compounds BiFeO3 (BFO) and La0.7Sr0.3MnO3 (LSMO). The microcrystalline BiFeO3 sample was prepared by solid state reaction method and the nanocrystalline La0.7Sr0.3MnO3 by sol-gel method. Composites with nominal compositions (1-x)BiFeO3-(x)La0.7Sr0.3MnO3 were prepared by modified solid state reaction method. The phase purity and crystal structures were checked by using X-ray diffraction. The formation of composites with phase separated BFO and LSMO was confirmed using Raman and Fourier Transform Infrared spectroscopy studies. The composite samples showed relatively high value of magnetization with finite coercivity. This improvement in magnetic behavior is ascribed to the coexistence of multiple magnetic orderings in composite samples. We scrutinized the possibility of oxygen vacancy or Fe mixed valency formation in the samples using X-ray photoelectron spectroscopy technique.

Trialkylphosphine-stabilized copper(I) gallium(III) phenylchalcogenolate complexes: crystal structures and generation of ternary semiconductors by thermolysis.

PubMed

Kluge, Oliver; Krautscheid, Harald

2012-06-18

A series of organometallic trialkylphosphine-stabilized copper gallium phenylchalcogenolate complexes [(R(3)P)(m)Cu(n)Me(2-x)Ga(EPh)(n+x+1)] (R = Me, Et, (i)Pr, (t)Bu; E = S, Se, Te; x = 0, 1) has been prepared and structurally characterized by X-ray diffraction. From their molecular structures three groups of compounds can be distinguished: ionic compounds, ring systems, and cage structures. All these complexes contain one gallium atom bound to one or two methyl groups, whereas the number of copper atoms, and therefore the nuclearity of the complexes, is variable and depends mainly on size and amount of phosphine ligand used in synthesis. The Ga-E bonds are relatively rigid, in contrast to flexible Cu-E bonds. The lengths of the latter are controlled by the coordination number and steric influences. The Ga-E bond lengths depend systematically on the number of methyl groups bound to the gallium atom, with somewhat shorter bonds in monomethyl compounds compared to dimethyl compounds. Quantum chemical computations reproduce this trend and show furthermore that the rotation of one phenyl group around the Ga-E bond is a low energy process with two distinct minima, corresponding to two different conformations found experimentally. Mixtures of different types of chalcogen atoms on molecular scale are possible, and then ligand exchange reactions in solution lead to mixed site occupation. In thermogravimetric studies the complexes were converted into the ternary semiconductors CuGaE(2). The thermolysis reaction is completed at temperatures between 250 and 400 °C, typically with lower temperatures for the heavier chalcogens. Because of significant release of Me(3)Ga during the thermolysis process, and especially in case of copper excess in the precursor complexes, binary copper chalcogenides are obtained as additional thermolysis products. Quaternary semiconductors can be obtained from mixed chalcogen precursors.

Lead identification for the K-Ras protein: virtual screening and combinatorial fragment-based approaches

PubMed Central

Pathan, Akbar Ali Khan; Panthi, Bhavana; Khan, Zahid; Koppula, Purushotham Reddy; Alanazi, Mohammed Saud; Sachchidanand; Parine, Narasimha Reddy; Chourasia, Mukesh

2016-01-01

Objective Kirsten rat sarcoma (K-Ras) protein is a member of Ras family belonging to the small guanosine triphosphatases superfamily. The members of this family share a conserved structure and biochemical properties, acting as binary molecular switches. The guanosine triphosphate-bound active K-Ras interacts with a range of effectors, resulting in the stimulation of downstream signaling pathways regulating cell proliferation, differentiation, and apoptosis. Efforts to target K-Ras have been unsuccessful until now, placing it among high-value molecules against which developing a therapy would have an enormous impact. K-Ras transduces signals when it binds to guanosine triphosphate by directly binding to downstream effector proteins, but in case of guanosine diphosphate-bound conformation, these interactions get disrupted. Methods In the present study, we targeted the nucleotide-binding site in the “on” and “off” state conformations of the K-Ras protein to find out suitable lead compounds. A structure-based virtual screening approach has been used to screen compounds from different databases, followed by a combinatorial fragment-based approach to design the apposite lead for the K-Ras protein. Results Interestingly, the designed compounds exhibit a binding preference for the “off” state over “on” state conformation of K-Ras protein. Moreover, the designed compounds’ interactions are similar to guanosine diphosphate and, thus, could presumably act as a potential lead for K-Ras. The predicted drug-likeness properties of these compounds suggest that these compounds follow the Lipinski’s rule of five and have tolerable absorption, distribution, metabolism, excretion and toxicity values. Conclusion Thus, through the current study, we propose targeting only “off” state conformations as a promising strategy for the design of reversible inhibitors to pharmacologically inhibit distinct conformations of K-Ras protein. PMID:27217775

Different phenolic compounds activate distinct human bitter taste receptors.

PubMed

Soares, Susana; Kohl, Susann; Thalmann, Sophie; Mateus, Nuno; Meyerhof, Wolfgang; De Freitas, Victor

2013-02-20

Bitterness is a major sensory attribute of several common foods and beverages rich in polyphenol compounds. These compounds are reported as very important for health as chemopreventive compounds, but they are also known to taste bitter. In this work, the activation of the human bitter taste receptors, TAS2Rs, by six polyphenol compounds was analyzed. The compounds chosen are present in a wide range of plant-derived foods and beverages, namely, red wine, beer, tea, and chocolate. Pentagalloylglucose (PGG) is a hydrolyzable tannin, (-)-epicatechin is a precursor of condensed tannins, procyanidin dimer B3 and trimer C2 belong to the condensed tannins, and malvidin-3-glucoside and cyanidin-3-glucoside are anthocyanins. The results show that the different compounds activate different combinations of the ~25 TAS2Rs. (-)-Epicatechin activated three receptors, TAS2R4, TAS2R5, and TAS2R39, whereas only two receptors, TAS2R5 and TAS2R39, responded to PGG. In contrast, malvidin-3-glucoside and procyanidin trimer stimulated only one receptor, TAS2R7 and TAS2R5, respectively. Notably, tannins are the first natural agonists found for TAS2R5 that display high potency only toward this receptor. The catechol and/or galloyl groups appear to be important structural determinants that mediate the interaction of these polyphenolic compounds with TAS2R5. Overall, the EC(50) values obtained for the different compounds vary 100-fold, with the lowest values for PGG and malvidin-3-glucoside compounds, suggesting that they could be significant polyphenols responsible for the bitterness of fruits, vegetables, and derived products even if they are present in very low concentrations.

Rational Design of Novel Allosteric Dihydrofolate Reductase Inhibitors Showing Antibacterial Effects on Drug-Resistant Escherichia coli Escape Variants.

PubMed

Srinivasan, Bharath; Rodrigues, João V; Tonddast-Navaei, Sam; Shakhnovich, Eugene; Skolnick, Jeffrey

2017-07-21

In drug discovery, systematic variations of substituents on a common scaffold and bioisosteric replacements are often used to generate diversity and obtain molecules with better biological effects. However, this could saturate the small-molecule diversity pool resulting in drug resistance. On the other hand, conventional drug discovery relies on targeting known pockets on protein surfaces leading to drug resistance by mutations of critical pocket residues. Here, we present a two-pronged strategy of designing novel drugs that target unique pockets on a protein's surface to overcome the above problems. Dihydrofolate reductase, DHFR, is a critical enzyme involved in thymidine and purine nucleotide biosynthesis. Several classes of compounds that are structural analogues of the substrate dihydrofolate have been explored for their antifolate activity. Here, we describe 10 novel small-molecule inhibitors of Escherichia coli DHFR, EcDHFR, belonging to the stilbenoid, deoxybenzoin, and chalcone family of compounds discovered by a combination of pocket-based virtual ligand screening and systematic scaffold hopping. These inhibitors show a unique uncompetitive or noncompetitive inhibition mechanism, distinct from those reported for all known inhibitors of DHFR, indicative of binding to a unique pocket distinct from either substrate or cofactor-binding pockets. Furthermore, we demonstrate that rescue mutants of EcDHFR, with reduced affinity to all known classes of DHFR inhibitors, are inhibited at the same concentration as the wild-type. These compounds also exhibit antibacterial activity against E. coli harboring the drug-resistant variant of DHFR. This discovery is the first report on a novel class of inhibitors targeting a unique pocket on EcDHFR.

Spatial and Temporal Patterns of Biocide Action against Staphylococcus epidermidis Biofilms▿ ‡

PubMed Central

Davison, William M.; Pitts, Betsey; Stewart, Philip S.

2010-01-01

The dynamic antimicrobial action of chlorine, a quaternary ammonium compound, glutaraldehyde, and nisin within biofilm cell clusters of Staphylococcus epidermidis was investigated using time-lapse confocal scanning laser microscopy. The technique allowed for the simultaneous imaging of changes in biofilm structure and disruption of cellular membrane integrity through the loss of an unbound fluorophore loaded into bacterial cells prior to antimicrobial challenge. Each of the four antimicrobial agents produced distinct spatial and temporal patterns of fluorescence loss. The antimicrobial action of chlorine was localized around the periphery of biofilm cell clusters. Chlorine was the only antimicrobial agent that caused any biofilm removal. Treatment with the quaternary ammonium compound caused membrane permeabilization that started at the periphery of cell clusters, then migrated steadily inward. A secondary pattern superimposed on the penetration dynamic suggested a subpopulation of less-susceptible cells. These bacteria lost fluorescence much more slowly than the majority of the population. Nisin caused a rapid and uniform loss of green fluorescence from all parts of the biofilm without any removal of biofilm. Glutaraldehyde caused no biofilm removal and also no loss of membrane integrity. Measurements of biocide penetration and action time at the center of cell clusters yielded 46 min for 10 mg liter−1 chlorine, 21 min for 50 mg liter−1 chlorine, 25 min for the quaternary ammonium compound, and 4 min for nisin. These results underscore the distinction between biofilm removal and killing and reinforce the critical role of biocide reactivity in determining the rate of biofilm penetration. PMID:20457816

The structures of cytosolic and plastid-located glutamine synthetases from Medicago truncatula reveal a common and dynamic architecture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Torreira, Eva; Seabra, Ana Rita; Marriott, Hazel

The experimental models of dicotyledonous cytoplasmic and plastid-located glutamine synthetases unveil a conserved eukaryotic-type decameric architecture, with subtle structural differences in M. truncatula isoenzymes that account for their distinct herbicide resistance. The first step of nitrogen assimilation in higher plants, the energy-driven incorporation of ammonia into glutamate, is catalyzed by glutamine synthetase. This central process yields the readily metabolizable glutamine, which in turn is at the basis of all subsequent biosynthesis of nitrogenous compounds. The essential role performed by glutamine synthetase makes it a prime target for herbicidal compounds, but also a suitable intervention point for the improvement of cropmore » yields. Although the majority of crop plants are dicotyledonous, little is known about the structural organization of glutamine synthetase in these organisms and about the functional differences between the different isoforms. Here, the structural characterization of two glutamine synthetase isoforms from the model legume Medicago truncatula is reported: the crystallographic structure of cytoplasmic GSII-1a and an electron cryomicroscopy reconstruction of plastid-located GSII-2a. Together, these structural models unveil a decameric organization of dicotyledonous glutamine synthetase, with two pentameric rings weakly connected by inter-ring loops. Moreover, rearrangement of these dynamic loops changes the relative orientation of the rings, suggesting a zipper-like mechanism for their assembly into a decameric enzyme. Finally, the atomic structure of M. truncatula GSII-1a provides important insights into the structural determinants of herbicide resistance in this family of enzymes, opening new avenues for the development of herbicide-resistant plants.« less

Structure of aryl O -demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kohler, Amanda C.; Mills, Matthew J. L.; Adams, Paul D.

Some strains of soil and marine bacteria have evolved intricate metabolic pathways for using environmentally derived aromatics as a carbon source. Many of these metabolic pathways go through intermediates such as vanillate, 3-O-methylgallate, and syringate. Demethylation of these compounds is essential for downstream aryl modification, ring opening, and subsequent assimilation of these compounds into the tricarboxylic acid (TCA) cycle, and, correspondingly, there are a variety of associated aryl demethylase systems that vary in complexity. Intriguingly, only a basic understanding of the least complex system, the tetrahydrofolate-dependent aryl demethylase LigM from Sphingomonas paucimobilis, a bacterial strain that metabolizes lignin-derived aromatics, wasmore » previously available. LigM-catalyzed demethylation enables further modification and rin g opening of the single-ring aromatics vanillate and 3-Omethylgallate, which are common byproducts of biofuel production. We characterize aryl O-demethylation by LigM and report its 1.81-Å crystal structure, revealing a unique demethylase fold and a canonical folate-binding domain. Structural homology and geometry optimization calculations enabled the identification of LigM's tetrahydrofolate-binding site and protein-folate interactions. Computationally guided mutagenesis and kinetic analyses allowed the identification of the enzyme's aryl-binding site location and determination of its unique, catalytic tyrosine-dependent reaction mechanism. This work defines LigM as a distinct demethylase, both structurally and functionally, and provides insight into demethylation and its reaction requirements. Our results afford the mechanistic details required for efficient utilization of LigM as a tool for aryl O-demethylation and as a component of synthetic biology efforts to valorize previously underused aromatic compounds.« less

Structure of aryl O -demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism

DOE PAGES

Kohler, Amanda C.; Mills, Matthew J. L.; Adams, Paul D.; ...

2017-04-03

Some strains of soil and marine bacteria have evolved intricate metabolic pathways for using environmentally derived aromatics as a carbon source. Many of these metabolic pathways go through intermediates such as vanillate, 3-O-methylgallate, and syringate. Demethylation of these compounds is essential for downstream aryl modification, ring opening, and subsequent assimilation of these compounds into the tricarboxylic acid (TCA) cycle, and, correspondingly, there are a variety of associated aryl demethylase systems that vary in complexity. Intriguingly, only a basic understanding of the least complex system, the tetrahydrofolate-dependent aryl demethylase LigM from Sphingomonas paucimobilis, a bacterial strain that metabolizes lignin-derived aromatics, wasmore » previously available. LigM-catalyzed demethylation enables further modification and rin g opening of the single-ring aromatics vanillate and 3-Omethylgallate, which are common byproducts of biofuel production. We characterize aryl O-demethylation by LigM and report its 1.81-Å crystal structure, revealing a unique demethylase fold and a canonical folate-binding domain. Structural homology and geometry optimization calculations enabled the identification of LigM's tetrahydrofolate-binding site and protein-folate interactions. Computationally guided mutagenesis and kinetic analyses allowed the identification of the enzyme's aryl-binding site location and determination of its unique, catalytic tyrosine-dependent reaction mechanism. This work defines LigM as a distinct demethylase, both structurally and functionally, and provides insight into demethylation and its reaction requirements. Our results afford the mechanistic details required for efficient utilization of LigM as a tool for aryl O-demethylation and as a component of synthetic biology efforts to valorize previously underused aromatic compounds.« less

Tunable Gas Sensing Gels by Cooperative Assembly

PubMed Central

Hussain, Abid; Semeano, Ana T. S.; Palma, Susana I. C. J.; Pina, Ana S.; Almeida, José; Medrado, Bárbara F.; Pádua, Ana C. C. S.; Carvalho, Ana L.; Dionísio, Madalena; Li, Rosamaria W. C.; Gamboa, Hugo; Ulijn, Rein V.; Gruber, Jonas; Roque, Ana C. A.

2017-01-01

The cooperative assembly of biopolymers and small molecules can yield functional materials with precisely tunable properties. Here, the fabrication, characterization, and use of multicomponent hybrid gels as selective gas sensors are reported. The gels are composed of liquid crystal droplets self-assembled in the presence of ionic liquids, which further coassemble with biopolymers to form stable matrices. Each individual component can be varied and acts cooperatively to tune gels’ structure and function. The unique molecular environment in hybrid gels is explored for supramolecular recognition of volatile compounds. Gels with distinct compositions are used as optical and electrical gas sensors, yielding a combinatorial response conceptually mimicking olfactory biological systems, and tested to distinguish volatile organic compounds and to quantify ethanol in automotive fuel. The gel response is rapid, reversible, and reproducible. These robust, versatile, modular, pliant electro-optical soft materials possess new possibilities in sensing triggered by chemical and physical stimuli. PMID:28747856

Compartmentalization of gypsum and halite associated with cyanobacteria in saline soil crusts.

PubMed

Canfora, Loredana; Vendramin, Elisa; Vittori Antisari, Livia; Lo Papa, Giuseppe; Dazzi, Carmelo; Benedetti, Anna; Iavazzo, Pietro; Adamo, Paola; Jungblut, Anne D; Pinzari, Flavia

2016-06-01

The interface between biological and geochemical components in the surface crust of a saline soil was investigated using X-ray diffraction, and variable pressure scanning electron microscopy in combination with energy dispersive X-ray spectrometry. Mineral compounds such as halite and gypsum were identified crystallized around filaments of cyanobacteria. A total of 92 genera were identified from the bacterial community based on 16S gene pyrosequencing analysis. The occurrence of the gypsum crystals, their shapes and compartmentalization suggested that they separated NaCl from the immediate microenvironment of the cyanobacteria, and that some cyanobacteria and communities of sulfur bacteria may had a physical control over the distinctive halite and gypsum structures produced. This suggests that cyanobacteria might directly or indirectly promote the formation of a protective envelope made of calcium and sulfur-based compounds. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism

PubMed Central

Matsuda, Fumio; Nakabayashi, Ryo; Yang, Zhigang; Okazaki, Yozo; Yonemaru, Jun-ichi; Ebana, Kaworu; Yano, Masahiro; Saito, Kazuki

2015-01-01

Plants produce structurally diverse secondary (specialized) metabolites to increase their fitness for survival under adverse environments. Several bioactive compounds for new drugs have been identified through screening of plant extracts. In this study, genome-wide association studies (GWAS) were conducted to investigate the genetic architecture behind the natural variation of rice secondary metabolites. GWAS using the metabolome data of 175 rice accessions successfully identified 323 associations among 143 single nucleotide polymorphisms (SNPs) and 89 metabolites. The data analysis highlighted that levels of many metabolites are tightly associated with a small number of strong quantitative trait loci (QTLs). The tight association may be a mechanism generating strains with distinct metabolic composition through the crossing of two different strains. The results indicate that one plant species produces more diverse phytochemicals than previously expected, and plants still contain many useful compounds for human applications. PMID:25267402

Fast Modeling of Binding Affinities by Means of Superposing Significant Interaction Rules (SSIR) Method

PubMed Central

Besalú, Emili

2016-01-01

The Superposing Significant Interaction Rules (SSIR) method is described. It is a general combinatorial and symbolic procedure able to rank compounds belonging to combinatorial analogue series. The procedure generates structure-activity relationship (SAR) models and also serves as an inverse SAR tool. The method is fast and can deal with large databases. SSIR operates from statistical significances calculated from the available library of compounds and according to the previously attached molecular labels of interest or non-interest. The required symbolic codification allows dealing with almost any combinatorial data set, even in a confidential manner, if desired. The application example categorizes molecules as binding or non-binding, and consensus ranking SAR models are generated from training and two distinct cross-validation methods: leave-one-out and balanced leave-two-out (BL2O), the latter being suited for the treatment of binary properties. PMID:27240346

Artefacts in geometric phase analysis of compound materials.

PubMed

Peters, Jonathan J P; Beanland, Richard; Alexe, Marin; Cockburn, John W; Revin, Dmitry G; Zhang, Shiyong Y; Sanchez, Ana M

2015-10-01

The geometric phase analysis (GPA) algorithm is known as a robust and straightforward technique that can be used to measure lattice strains in high resolution transmission electron microscope (TEM) images. It is also attractive for analysis of aberration-corrected scanning TEM (ac-STEM) images that resolve every atom column, since it uses Fourier transforms and does not require real-space peak detection and assignment to appropriate sublattices. Here it is demonstrated that, in ac-STEM images of compound materials with compositionally distinct atom columns, an additional geometric phase is present in the Fourier transform. If the structure changes from one area to another in the image (e.g. across an interface), the change in this additional phase will appear as a strain in conventional GPA, even if there is no lattice strain. Strategies to avoid this pitfall are outlined. Copyright © 2015 Elsevier B.V. All rights reserved.

Humic Acids as Therapeutic Compounds in Lead Intoxication.

PubMed

Krempaská, Klára; Vaško, Ladislav; Vašková, Janka

2016-01-01

The toxicity of lead and its compounds is well known, causing anemia by inhibiting the synthesis of porphyrins. The neurotoxic effects, particularly in the young, alter the structure of cell membranes and DNA. Chronic exposure to lead has adverse effects on the body by disrupting the mechanisms of energy production and tissue damage, in particular in its links with thiol groups and competition for binding sites with zinc. This review is therefore a description of the mechanism of lead toxicity as well as of possible interventions for the detoxification of the body. Part of the clinical intervention is the provision of chelates that form insoluble complexes with lead and eliminate the load in tissues. Most of these chelating agents have a number of side effects. It is therefore not surprising that active compounds with distinctive antioxidant and chelating properties are being sought after. The possibility of administering lower amounts, and the corresponding decrease in side effects, would be important for clinical practice. Both prospective studies and our initial studies on humic acids have highlighted positive effects based on their antioxidant and chelating properties.

Secondary metabolites from three Florida sponges with antidepressant activity.

PubMed

Kochanowska, Anna J; Rao, Karumanchi V; Childress, Suzanne; El-Alfy, Abir; Matsumoto, Rae R; Kelly, Michelle; Stewart, Gina S; Sufka, Kenneth J; Hamann, Mark T

2008-02-01

Brominated indole alkaloids are a common class of metabolites reported from sponges of the order Verongida. Herein we report the isolation, structure determination, and activity of metabolites from three Florida sponges, namely, Verongula rigida (order Verongida, family Aplysinidae), Smenospongia aurea, and S. cerebriformis (order Dictyoceratida, family Thorectidae). All three species were investigated chemically, revealing similarities in secondary metabolites. Brominated compounds, as well as sesquiterpene quinones and hydroquinones, were identified from both V. rigida and S. aurea despite their apparent taxonomic differences at the ordinal level. Similar metabolites found in these distinct sponge species of two different genera provide evidence for a microbial origin of the metabolites. Isolated compounds were evaluated in the Porsolt forced swim test (FST) and the chick anxiety-depression continuum model. Among the isolated compounds, 5,6-dibromo- N,N-dimethyltryptamine ( 1) exhibited significant antidepressant-like action in the rodent FST model, while 5-bromo- N,N-dimethyltryptamine ( 2) caused significant reduction of locomotor activity indicative of a potential sedative action. The current study provides ample evidence that marine natural products with the diversity of brominated marine alkaloids will provide potential leads for antidepressant and anxiolytic drugs.

Crystal field effects in the intermetallic R Ni3Ga9 (R =Tb , Dy, Ho, and Er) compounds

NASA Astrophysics Data System (ADS)

Silva, L. S.; Mercena, S. G.; Garcia, D. J.; Bittar, E. M.; Jesus, C. B. R.; Pagliuso, P. G.; Lora-Serrano, R.; Meneses, C. T.; Duque, J. G. S.

2017-04-01

In this paper, we report temperature-dependent magnetic susceptibility, electrical resistivity, and heat-capacity experiments in the family of intermetallic compounds R Ni3Ga9 (R = Tb, Dy, Ho, and Er). Single-crystalline samples were grown using Ga self-flux method. These materials crystallize in a trigonal ErNi3Al9 -type structure with space group R 32 . They all order antiferromagnetically with TN<20 K . The anisotropic magnetic susceptibility presents large values of the ratio χeasy/χhard indicating strong crystalline electric-field (CEF) effects. The evolution of the crystal-field scheme for each R was analyzed in detail by using a spin model including anisotropic nearest-neighbor Ruderman-Kittel-Kasuya-Yosida interaction and the trigonal CEF Hamiltonian. Our analysis allows one to understand the distinct direction of the ordered moments along the series—the Tb-, Dy-, and Ho-based compounds have the ordered magnetic moments in the easy ab plane and the Er sample magnetization easy axis is along the c ̂ direction.

Phenolic Lipids Affect the Activity and Conformation of Acetylcholinesterase from Electrophorus electricus (Electric eel)

PubMed Central

Stasiuk, Maria; Janiszewska, Alicja; Kozubek, Arkadiusz

2014-01-01

Phenolic lipids were isolated from rye grains, cashew nutshell liquid (CNSL) from Anacardium occidentale, and fruit bodies of Merrulius tremellosus, and their effects on the electric eel acetylcholinesterase activity and conformation were studied. The observed effect distinctly depended on the chemical structure of the phenolic lipids that were available for interaction with the enzyme. All of the tested compounds reduced the activity of acetylcholinesterase. The degree of inhibition varied, showing a correlation with changes in the conformation of the enzyme tested by the intrinsic fluorescence of the Trp residues of the protein. PMID:24787269

Perception and Bias in the Processing of Compound versus Phrasal Stress: Evidence from Event-Related Brain Potentials

ERIC Educational Resources Information Center

McCauley, Stewart M; Hestvik, Arild; Vogel, Irene

2013-01-01

Previous research using picture/word matching tasks has demonstrated a tendency to incorrectly interpret phrasally stressed strings as compounds. Using event-related potentials, we sought to determine whether this pattern stems from poor perceptual sensitivity to the compound/phrasal stress distinction, or from a post-perceptual bias in behavioral…

A series of new copper iodobismuthates: structural relationships, optical band gaps affected by dimensionality, and distinct thermal stabilities.

PubMed

Chai, Wen-Xiang; Wu, Li-Ming; Li, Jun-Qian; Chen, Ling

2007-10-15

Three new copper iodobismuthates, red tetranuclear [n-Bu(4)N][Cu(2)(CH(3)CN)(2)Bi(2)I(10)] (1), dark-red infinite linear [Et(4)N](2n)[Cu(2)Bi(2)I(10)](n) (2), and black polymeric ladderlike [Cu(CH(3)CN)(4)](2n)[Cu(2)Bi(2)I(10)](n) (3), crystallize from solutions of BiI3 and CuI in the presence of different cations. A regular structural relationship from 0-D (1) to 1-D linear anion chains (2) to 1-D ladderlike anion chains (3) is observed. The self-assembly of the basic building unit Cu(2)Bi(2)I(10) as altered by different cations is proposed to be the driving force for their formation. The optical band gaps exhibit a structure-related decrease from 1 to 2/3, in agreement with their color changes and the density functional theory (DFT) calculation results. The electronic structures and the relationship with corresponding monobismuth analogues and the Ag-Bi isotypes are discussed on the basis of DFT calculations. In spite of their structural similarities, the compounds are distinctive thermally: 2 is stable to 230 degrees C, 1 undergoes a solvent loss at 85 degrees C to form a new phase that is thermally stable to 230 degrees C, and 3 releases a solvent molecule and decomposes at 80 degrees C into BiI(3) and CuI. The essential reasons for these differences are discussed.

3D chiral and 2D achiral cobalt(ii) compounds constructed from a 4-(benzimidazole-1-yl)benzoic ligand exhibiting field-induced single-ion-magnet-type slow magnetic relaxation.

PubMed

Wang, Yu-Ling; Chen, Lin; Liu, Cai-Ming; Du, Zi-Yi; Chen, Li-Li; Liu, Qing-Yan

2016-05-04

Organizing magnetically isolated 3d transition metal ions, which behave as single-ion magnet (SIM) units, in a coordination network is a promising approach to design novel single-molecule magnets (SMMs). Herein 3D chiral and 2D achiral cobalt(ii) coordination compounds based on single metal nodes with a 4-(benzimidazole-1-yl)benzoic acid (Hbmzbc) ligand, namely, [Co(bmzbc)2(1,2-etdio)]n () (1,2-etdio = 1,2-ethanediol) and [Co(bmzbc)2(Hbmzbc)]n (), have been synthesized and structurally characterized. The 3D chiral structure with 2-fold interpenetrating qtz topological nets consisting of totally achiral components was obtained via spontaneous resolution, while the achiral structure is a 2D (4,4) net. In both structures, individual cobalt(ii) ions are spatially well separated by the long organic ligands in the well-defined networks. Magnetic measurements on and showed field-induced slow magnetic relaxation resulting from single-ion anisotropy of the individual Co(ii) ions. Analysis of the dynamic ac susceptibilities with the Arrhenius law afforded an anisotropy energy barrier of 16.8(3) and 31.3(2) K under a 2 kOe static magnetic field for and , respectively. The distinct coordination environments of the Co(ii) ions in and lead to the different anisotropic energy barriers.

Structural and optical properties of Tb and Na-Tb co-doped Ca3V2O8 phosphors prepared by sol-gel process

NASA Astrophysics Data System (ADS)

Parab, Shambhu S.; Salker, A. V.

2018-01-01

A malic acid assisted sol-gel route was successfully employed to prepare two distinct series of green emitting Ca3V2O8 phosphors. In the first series, Tb was solely doped whereas in the second series Na and Tb were doped simultaneously in the Ca3V2O8 crystal lattice. X-ray diffraction studies proved the utility of adopted preparative method by confirming the monophasic formation of all compounds from both the series. Spectral analysis like Raman spectroscopy, UV-DRS were undertaken to analyse the local structure, crystallinity and absorptive characteristics. XPS validated the presence of desired oxidation states of all the elements present. Finally, photoluminescence studies were done to elucidate the scope of prepared compounds as green emitting phosphors and also to understand the effect of both doping schemes on the luminescence. Intense green emission was observed in both the cases. Tb concentration of 0.08 was found to be optimum in case of Tb singly doped compounds whereas Tb = 0.12 showed highest intensity among the Na-Tb co-doped samples. Moreover, a red shift in the excitation wavelength was observed after Na doping signifying a change in the local electronic environment which in turn has affected the luminescence pattern. Local crystallinity and vacancy concentrations were found to have a major say on the emission intensities.

A UV resonance Raman (UVRR) spectroscopic study on the extractable compounds in Scots pine (Pinus sylvestris) wood. Part II. Hydrophilic compounds.

PubMed

Nuopponen, M; Willför, S; Jääskeläinen, A-S; Vuorinen, T

2004-11-01

Hydrophilic extracts of Scots pine (Pinus sylvestris) heartwood and sapwood and a solid Scots pine knotwood sample were studied by UV resonance Raman spectroscopy (UVRRS). In addition, UVRR spectra of two hydrophilic model compounds (pinosylvin and chrysin) were analysed. UV Raman spectra were collected using 244 and 257 nm excitation wavelengths. The chemical composition of the acetone:water (95:5 v/v) extracts were also determined by gas chromatography. The aromatic and oleophilic structures of pinosylvin and chrysin showed three intense resonance enhanced bands in the spectral region of 1649-1548 cm(-1). Pinosylvin showed also a relatively intense band in the aromatic substitution region at 996 cm(-1). The spectra of the heartwood acetone:water extract showed many bands typical of pinosylvin. In addition, the extract included bands distinctive for resin and fatty acids. The sapwood acetone:water extract showed bands due to oleophilic structures at 1655-1650 cm(-1). The extract probably also contained oligomeric lignans because the UVRR spectra were in parts similar to that of guaiacyl lignin. The characteristic band of pinosylvin (996 cm(-1)) was detected in the UVRR spectrum of the resin rich knotwood. In addition, several other bands typical for wood resin were observed, which indicated that the wood resin in the knotwood was resonance enhanced even more than lignin.

A UV resonance Raman (UVRR) spectroscopic study on the extractable compounds in Scots pine ( Pinus sylvestris) wood . Part II. Hydrophilic compounds

NASA Astrophysics Data System (ADS)

Nuopponen, M.; Willför, S.; Jääskeläinen, A.-S.; Vuorinen, T.

2004-11-01

Hydrophilic extracts of Scots pine ( Pinus sylvestris) heartwood and sapwood and a solid Scots pine knotwood sample were studied by UV resonance Raman spectroscopy (UVRRS). In addition, UVRR spectra of two hydrophilic model compounds (pinosylvin and chrysin) were analysed. UV Raman spectra were collected using 244 and 257 nm excitation wavelengths. The chemical composition of the acetone:water (95:5 v/v) extracts were also determined by gas chromatography. The aromatic and oleophilic structures of pinosylvin and chrysin showed three intense resonance enhanced bands in the spectral region of 1649-1548 cm -1. Pinosylvin showed also a relatively intense band in the aromatic substitution region at 996 cm -1. The spectra of the heartwood acetone:water extract showed many bands typical of pinosylvin. In addition, the extract included bands distinctive for resin and fatty acids. The sapwood acetone:water extract showed bands due to oleophilic structures at 1655-1650 cm -1. The extract probably also contained oligomeric lignans because the UVRR spectra were in parts similar to that of guaiacyl lignin. The characteristic band of pinosylvin (996 cm -1) was detected in the UVRR spectrum of the resin rich knotwood. In addition, several other bands typical for wood resin were observed, which indicated that the wood resin in the knotwood was resonance enhanced even more than lignin.

Pharmaceutically active secondary metabolites of marine actinobacteria.

PubMed

Manivasagan, Panchanathan; Venkatesan, Jayachandran; Sivakumar, Kannan; Kim, Se-Kwon

2014-04-01

Marine actinobacteria are one of the most efficient groups of secondary metabolite producers and are very important from an industrial point of view. Many representatives of the order Actinomycetales are prolific producers of thousands of biologically active secondary metabolites. Actinobacteria from terrestrial sources have been studied and screened since the 1950s, for many important antibiotics, anticancer, antitumor and immunosuppressive agents. However, frequent rediscovery of the same compounds from the terrestrial actinobacteria has made them less attractive for screening programs in the recent years. At the same time, actinobacteria isolated from the marine environment have currently received considerable attention due to the structural diversity and unique biological activities of their secondary metabolites. They are efficient producers of new secondary metabolites that show a range of biological activities including antibacterial, antifungal, anticancer, antitumor, cytotoxic, cytostatic, anti-inflammatory, anti-parasitic, anti-malaria, antiviral, antioxidant, anti-angiogenesis, etc. In this review, an evaluation is made on the current status of research on marine actinobacteria yielding pharmaceutically active secondary metabolites. Bioactive compounds from marine actinobacteria possess distinct chemical structures that may form the basis for synthesis of new drugs that could be used to combat resistant pathogens. With the increasing advancement in science and technology, there would be a greater demand for new bioactive compounds synthesized by actinobacteria from various marine sources in future. Copyright © 2013 Elsevier GmbH. All rights reserved.

X-ray structure of the ternary MTX·NADPH complex of the anthrax dihydrofolate reductase: A pharmacophore for dual-site inhibitor design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bennett, Brad C.; Wan, Qun; Ahmad, Md Faiz

2009-11-18

For reasons of bioterrorism and drug resistance, it is imperative to identify and develop new molecular points of intervention against anthrax. Dihydrofolate reductase (DHFR) is a highly conserved enzyme and an established target in a number of species for a variety of chemotherapeutic programs. Recently, the crystal structure of B. anthracis DHFR (baDHFR) in complex with methotrexate (MTX) was determined and, based on the structure, proposals were made for drug design strategies directed against the substrate binding site. However, little is gleaned about the binding site for NADPH, the cofactor responsible for hydride transfer in the catalytic mechanism. In themore » present study, X-ray crystallography at 100 K was used to determine the structure of baDHFR in complex with MTX and NADPH. Although the NADPH binding mode is nearly identical to that seen in other DHFR ternary complex structures, the adenine moiety adopts an off-plane tilt of nearly 90 deg. and this orientation is stabilized by hydrogen bonds to functionally conserved Arg residues. A comparison of the binding site, focusing on this region, between baDHFR and the human enzyme is discussed, with an aim at designing species-selective therapeutics. Indeed, the ternary model, refined to 2.3{angstrom} resolution, provides an accurate template for testing the feasibility of identifying dual-site inhibitors, compounds that target both the substrate and cofactor binding site. With the ternary model in hand, using in silico methods, several compounds were identified which could potentially form key bonding contacts in the substrate and cofactor binding sites. Ultimately, two structurally distinct compounds were verified that inhibit baDHFR at low {mu}M concentrations. The apparent K{sub d} for one of these, (2-(3-(2-(hydroxyimino)-2-(pyridine-4-yl)-6,7-dimethylquinoxalin-2-yl)-1-(pyridine-4-yl)ethanone oxime), was measured by fluorescence spectroscopy to be 5.3 {mu}M.« less

Temperature Responses of Soil Organic Matter Components With Varying Recalcitrance

NASA Astrophysics Data System (ADS)

Simpson, M. J.; Feng, X.

2007-12-01

The response of soil organic matter (SOM) to global warming remains unclear partly due to the chemical heterogeneity of SOM composition. In this study, the decomposition of SOM from two grassland soils was investigated in a one-year laboratory incubation at six different temperatures. SOM was separated into solvent- extractable compounds, suberin- and cutin-derived compounds, and lignin monomers by solvent extraction, base hydrolysis, and CuO oxidation, respectively. These SOM components had distinct chemical structures and recalcitrance, and their decomposition was fitted by a two-pool exponential decay model. The stability of SOM components was assessed using geochemical parameters and kinetic parameters derived from model fitting. Lignin monomers exhibited much lower decay rates than solvent-extractable compounds and a relatively low percentage of lignin monomers partitioned into the labile SOM pool, which confirmed the generally accepted recalcitrance of lignin compounds. Suberin- and cutin-derived compounds had a poor fitting for the exponential decay model, and their recalcitrance was shown by the geochemical degradation parameter which stabilized during the incubation. The aliphatic components of suberin degraded faster than cutin-derived compounds, suggesting that cutin-derived compounds in the soil may be at a higher stage of degradation than suberin- derived compounds. The temperature sensitivity of decomposition, expressed as Q10, was derived from the relationship between temperature and SOM decay rates. SOM components exhibited varying temperature responses and the decomposition of the recalcitrant lignin monomers had much higher Q10 values than soil respiration or the solvent-extractable compounds decomposition. Our study shows that the decomposition of recalcitrant SOM is highly sensitive to temperature, more so than bulk soil mineralization. This observation suggests a potential acceleration in the degradation of the recalcitrant SOM pool with global warming.

Wood degradation under UV irradiation: A lignin characterization.

PubMed

Cogulet, Antoine; Blanchet, Pierre; Landry, Véronic

2016-05-01

The photodegradation of white spruce by artificial ageing was studied by several techniques: colourimetry, FTIR-ATR and FT-Raman spectroscopy. Samples were exposed at a xenon lamp for 2000h. Two distinct colour changes were found by colourimetric analysis, yellowing and silvering. These colour modifications indicate the formation of chromophoric structures which supports previous FTIR-ATR experiments. The degradation of lignin to generate the first chromophoric group for yellowing and then the appearance of surface layer cellulose. New carbonyl compounds conjugated with double bond at 1615cm(-1) are probably the second chromophoric group. The crystallinity index was also calculated and showed an increase of cellulose crystallinity by prior degradation of amorphous cellulose. The FT-Raman analysis confirms the wood sensitivity to photodegradation but the most remarkable results is the increase of fluorescence as a function of time. In softwood lignin, the compound able to produce fluorescence is a free rotating 5-5' linkage of one biphenyl structure. At native state these linkages are not free rotating, this phenomenon means the release of 5-5' linkage of lignin structure by cleavage of both α carbon linkages (Norrish type I reaction). These data confirm also the photosensitivity of α and β carbon in lignin and the resistance of 5-5' linkages. Copyright © 2016 Elsevier B.V. All rights reserved.

Structure and thermodynamic stability of UTa 3O 10, aU(v)-bearing compound

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Xiaofeng; Lipp, Christian; Tiferet, Eitan

Heating a mixture of uranyl (VI) nitrate and tantalum (V) oxide in the molar ratio of 2 : 3 to 1400 °C resulted in the formation of a new compound, UTa 3O 10. The honey colored to yellow brown crystals of UTa 3O 10 crystallize in an orthorhombic structure with the space group Fddd (no. 70), lattice parameters a = 7.3947(1), b = 12.7599(2), c = 15.8156(2) Å, and Z = 8. Vertex sharing [TaO 6] 7– octahedra of two crystallographically distinct Ta cations form a three dimensional tantalate framework. Within this framework, six membered rings of [TaO 6] 7–more » octahedra are formed within the (001) plane. The center of these rings is occupied by the uranyl cations [UO 2]+, with an oxidation state of +5 for uranium. The pentavalence of U and Ta was confirmed by X-ray photoelectron spectroscopy and X-ray adsorption spectroscopy. The enthalpy of formation of UTa 3O 10 from Ta 2O 5, β-U 3O 7, and U3O8 has been determined to be 13.1 ± 18.1 kJ mol–1 using high temperature oxide melt solution calorimetry with sodium molybdate as the solvent at 700 °C. As a result, the close to zero enthalpy of formation of UTa 3O 10 can be explained by closely balanced structural stabilizing and destabilizing factors, which may also apply to other UM 3O 10 compounds.« less

Structure and thermodynamic stability of UTa 3O 10, aU(v)-bearing compound

DOE PAGES

Guo, Xiaofeng; Lipp, Christian; Tiferet, Eitan; ...

2016-09-09

Heating a mixture of uranyl (VI) nitrate and tantalum (V) oxide in the molar ratio of 2 : 3 to 1400 °C resulted in the formation of a new compound, UTa 3O 10. The honey colored to yellow brown crystals of UTa 3O 10 crystallize in an orthorhombic structure with the space group Fddd (no. 70), lattice parameters a = 7.3947(1), b = 12.7599(2), c = 15.8156(2) Å, and Z = 8. Vertex sharing [TaO 6] 7– octahedra of two crystallographically distinct Ta cations form a three dimensional tantalate framework. Within this framework, six membered rings of [TaO 6] 7–more » octahedra are formed within the (001) plane. The center of these rings is occupied by the uranyl cations [UO 2]+, with an oxidation state of +5 for uranium. The pentavalence of U and Ta was confirmed by X-ray photoelectron spectroscopy and X-ray adsorption spectroscopy. The enthalpy of formation of UTa 3O 10 from Ta 2O 5, β-U 3O 7, and U3O8 has been determined to be 13.1 ± 18.1 kJ mol–1 using high temperature oxide melt solution calorimetry with sodium molybdate as the solvent at 700 °C. As a result, the close to zero enthalpy of formation of UTa 3O 10 can be explained by closely balanced structural stabilizing and destabilizing factors, which may also apply to other UM 3O 10 compounds.« less

The R2R3MYB VvMYBPA1 from grape reprograms the phenylpropanoid pathway in tobacco flowers.

PubMed

Passeri, Valentina; Martens, Stefan; Carvalho, Elisabete; Bianchet, Chantal; Damiani, Francesco; Paolocci, Francesco

2017-08-01

This work shows that, in tobacco, the ectopic expression of VvMYBPA1 , a grape regulator of proanthocyanidin biosynthesis, up- or down-regulates different branches of the phenylproanoid pathway, in a structure-specific fashion. Proanthocyanidins are flavonoids of paramount importance for animal and human diet. Research interest increasingly tilts towards generating crops enriched with these health-promoting compounds. Flavonoids synthesis is regulated by the MBW transcriptional complex, made of R2R3MYB, bHLH and WD40 proteins, with the MYB components liable for channeling the complex towards specific branches of the pathway. Hence, using tobacco as a model, here, we tested if the ectopic expression of the proanthocyanidin regulator VvMYBPA1 from grape induces the biosynthesis of these compounds in not-naturally committed cells. Here, we show, via targeted transcriptomic and metabolic analyses of primary transgenic lines and their progeny, that VvMYBPA1 alters the phenylpropanoid pathway in tobacco floral organs, in a structure-specific fashion. We also report that a modest VvMYBPA1 expression is sufficient to induce the expression of both proanthocyanidin-specific and early genes of the phenylpropanoid pathway. Consequently, proanthocyanidins and chlorogenic acids are induced or de novo synthetised in floral limbs, tubes and stamens. Other phenylpropanoid branches are conversely induced or depleted according to the floral structure. Our study documents a novel and distinct function of VvMYBPA1 with respect to other MYBs regulating proanthocyanidins. Present findings may have major implications in designing strategies for enriching crops with health-promoting compounds.

Performance of the strongly constrained and appropriately normed density functional for solid-state materials

DOE PAGES

Isaacs, Eric B.; Wolverton, Chris

2018-06-22

Constructed to satisfy 17 known exact constraints for a semilocal density functional, the strongly constrained and appropriately normed (SCAN) meta-generalized-gradient-approximation functional has shown early promise for accurately describing the electronic structure of molecules and solids. One open question is how well SCAN predicts the formation energy, a key quantity for describing the thermodynamic stability of solid-state compounds. To answer this question, we perform an extensive benchmark of SCAN by computing the formation energies for a diverse group of nearly 1000 crystalline compounds for which experimental values are known. Due to an enhanced exchange interaction in the covalent bonding regime, SCANmore » substantially decreases the formation energy errors for strongly bound compounds, by approximately 50% to 110 meV/atom, as compared to the generalized gradient approximation of Perdew, Burke, and Ernzerhof (PBE). However, for intermetallic compounds, SCAN performs moderately worse than PBE with an increase in formation energy error of approximately 20%, stemming from SCAN's distinct behavior in the weak bonding regime. The formation energy errors can be further reduced via elemental chemical potential fitting. We find that SCAN leads to significantly more accurate predicted crystal volumes, moderately enhanced magnetism, and mildly improved band gaps as compared to PBE. Altogether, SCAN represents a significant improvement in accurately describing the thermodynamics of strongly bound compounds.« less

Performance of the strongly constrained and appropriately normed density functional for solid-state materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Isaacs, Eric B.; Wolverton, Chris

Constructed to satisfy 17 known exact constraints for a semilocal density functional, the strongly constrained and appropriately normed (SCAN) meta-generalized-gradient-approximation functional has shown early promise for accurately describing the electronic structure of molecules and solids. One open question is how well SCAN predicts the formation energy, a key quantity for describing the thermodynamic stability of solid-state compounds. To answer this question, we perform an extensive benchmark of SCAN by computing the formation energies for a diverse group of nearly 1000 crystalline compounds for which experimental values are known. Due to an enhanced exchange interaction in the covalent bonding regime, SCANmore » substantially decreases the formation energy errors for strongly bound compounds, by approximately 50% to 110 meV/atom, as compared to the generalized gradient approximation of Perdew, Burke, and Ernzerhof (PBE). However, for intermetallic compounds, SCAN performs moderately worse than PBE with an increase in formation energy error of approximately 20%, stemming from SCAN's distinct behavior in the weak bonding regime. The formation energy errors can be further reduced via elemental chemical potential fitting. We find that SCAN leads to significantly more accurate predicted crystal volumes, moderately enhanced magnetism, and mildly improved band gaps as compared to PBE. Altogether, SCAN represents a significant improvement in accurately describing the thermodynamics of strongly bound compounds.« less

Temperature responses of individual soil organic matter components

NASA Astrophysics Data System (ADS)

Feng, Xiaojuan; Simpson, Myrna J.

2008-09-01

Temperature responses of soil organic matter (SOM) remain unclear partly due to its chemical and compositional heterogeneity. In this study, the decomposition of SOM from two grassland soils was investigated in a 1-year laboratory incubation at six different temperatures. SOM was separated into solvent extractable compounds, suberin- and cutin-derived compounds, and lignin-derived monomers by solvent extraction, base hydrolysis, and CuO oxidation, respectively. These SOM components have distinct chemical structures and stabilities and their decomposition patterns over the course of the experiment were fitted with a two-pool exponential decay model. The stability of SOM components was also assessed using geochemical parameters and kinetic parameters derived from model fitting. Compared with the solvent extractable compounds, a low percentage of lignin monomers partitioned into the labile SOM pool. Suberin- and cutin-derived compounds were poorly fitted by the decay model, and their recalcitrance was shown by the geochemical degradation parameter (ω - C16/∑C16), which was observed to stabilize during the incubation. The temperature sensitivity of decomposition, expressed as Q10, was derived from the relationship between temperature and SOM decay rates. SOM components exhibited varying temperature responses and the decomposition of lignin monomers exhibited higher Q10 values than the decomposition of solvent extractable compounds. Our study shows that Q10 values derived from soil respiration measurements may not be reliable indicators of temperature responses of individual SOM components.

Structure symmetry determination and magnetic evolution in Sr 2Ir 1–xRh xO 4

DOE PAGES

Ye, Feng; Wang, Xiaoping; Hoffmann, Christina; ...

2015-11-23

We use single-crystal neutron diffraction to determine the crystal structure symmetry and to study the magnetic evolution in the rhodium doped iridates Sr 2Ir 1–xRh xO 4 (0 ≤ x ≤ 0.16). Throughout this doping range, the crystal structure retains a tetragonal symmetry (space group I4 1/a) with two distinct magnetic Ir sites in the unit cell forming staggered IrO 6 rotation. Upon Rh doping, the magnetic order is suppressed and the magnetic moment of Ir4+ is reduced from 0.21 μ B/Ir for x = 0 to 0.18 μ B/Ir for x = 0.12. As a result, the magnetic structuremore » at x = 0.12 is different from that of the parent compound while the moments remain in the basal plane.« less

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

DOE PAGES

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe; ...

2014-06-16

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less

A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase.

PubMed

Edwards, Marcus J; Flatman, Ruth H; Mitchenall, Lesley A; Stevenson, Clare E M; Le, Tung B K; Clarke, Thomas A; McKay, Adam R; Fiedler, Hans-Peter; Buttner, Mark J; Lawson, David M; Maxwell, Anthony

2009-12-04

Simocyclinones are bifunctional antibiotics that inhibit bacterial DNA gyrase by preventing DNA binding to the enzyme. We report the crystal structure of the complex formed between the N-terminal domain of the Escherichia coli gyrase A subunit and simocyclinone D8, revealing two binding pockets that separately accommodate the aminocoumarin and polyketide moieties of the antibiotic. These are close to, but distinct from, the quinolone-binding site, consistent with our observations that several mutations in this region confer resistance to both agents. Biochemical studies show that the individual moieties of simocyclinone D8 are comparatively weak inhibitors of gyrase relative to the parent compound, but their combination generates a more potent inhibitor. Our results should facilitate the design of drug molecules that target these unexploited binding pockets.

Innovative computer-aided methods for the discovery of new kinase ligands.

PubMed

Abuhammad, Areej; Taha, Mutasem

2016-04-01

Recent evidence points to significant roles played by protein kinases in cell signaling and cellular proliferation. Faulty protein kinases are involved in cancer, diabetes and chronic inflammation. Efforts are continuously carried out to discover new inhibitors for selected protein kinases. In this review, we discuss two new computer-aided methodologies we developed to mine virtual databases for new bioactive compounds. One method is ligand-based exploration of the pharmacophoric space of inhibitors of any particular biotarget followed by quantitative structure-activity relationship-based selection of the best pharmacophore(s). The second approach is structure-based assuming that potent ligands come into contact with binding site spots distinct from those contacted by weakly potent ligands. Both approaches yield pharmacophores useful as 3D search queries for the discovery of new bioactive (kinase) inhibitors.

Characterization of Two Distinct Structural Classes of Selective Aldehyde Dehydrogenase 1A1 Inhibitors

DOE PAGES

Morgan, Cynthia A.; Hurley, Thomas D.

2015-01-29

Aldehyde dehydrogenases (ALDH) catalyze the irreversible oxidation of aldehydes to their corresponding carboxylic acid. Alterations in ALDH1A1 activity are associated with such diverse diseases as cancer, Parkinson’s disease, obesity, and cataracts. Inhibitors of ALDH1A1 could aid in illuminating the role of this enzyme in disease processes. However, there are no commercially available selective inhibitors for ALDH1A1. Here we characterize two distinct chemical classes of inhibitors that are selective for human ALDH1A1 compared to eight other ALDH isoenzymes. The prototypical members of each structural class, CM026 and CM037, exhibit sub-micromolar inhibition constants, but have different mechanisms of inhibition. The crystal structuresmore » of these compounds bound to ALDH1A1 demonstrate that they bind within the aldehyde binding pocket of ALDH1A1 and exploit the presence of a unique Glycine residue to achieve their selectivity. Lastly, these two novel and selective ALDH1A1 inhibitors may serve as chemical tools to better understand the contributions of ALDH1A1 to normal biology and to disease states.« less

Effects of triclosan on bacterial community composition and ...

EPA Pesticide Factsheets

Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for selection through antimicrobial resistance. In particular, Vibrio, a marine bacterial genus that includes several human pathogens, displays resistance to the ubiquitous antimicrobial compound triclosan. Here we demonstrated through use of natural seawater microcosms that triclosan (at a concentration of ~5 ppm) can induce a significant Vibrio growth response (68–1,700 fold increases) in comparison with no treatment controls for three distinct coastal ecosystems: Looe Key Reef (Florida Keys National Marine Sanctuary), Doctors Arm Canal (Big Pine Key, FL), and Clam Bank Landing (North Inlet Estuary, Georgetown, SC). Additionally, microbial community analysis by 16 S rRNA gene sequencing for Looe Key Reef showed distinct changes in microbial community structure with exposure to 5 ppm triclosan, with increases observed in the relative abundance of Vibrionaceae (17-fold), Pseudoalteromonadaceae (65-fold), Alteromonadaceae (108-fold), Colwelliaceae (430-fold), and Oceanospirillaceae (1,494-fold). While the triclosan doses tested were above concentrations typically observed in coastal surface waters, results identify bacterial families that are potentially resistant to triclosan and/or adapted to u

Metal alkyls programmed to generate metal alkylidenes by α-H abstraction: prognosis from NMR chemical shift† †Electronic supplementary information (ESI) available: Experimental and computational details, NMR spectra, results of NMR calculations and NCS analysis, graphical representation of shielding tensors, molecular orbital diagrams of selected compounds, optimized structures for all calculated species. See DOI: 10.1039/c7sc05039a

PubMed Central

Gordon, Christopher P.; Yamamoto, Keishi; Searles, Keith; Shirase, Satoru

2018-01-01

Metal alkylidenes, which are key organometallic intermediates in reactions such as olefination or alkene and alkane metathesis, are typically generated from metal dialkyl compounds [M](CH2R)2 that show distinctively deshielded chemical shifts for their α-carbons. Experimental solid-state NMR measurements combined with DFT/ZORA calculations and a chemical shift tensor analysis reveal that this remarkable deshielding originates from an empty metal d-orbital oriented in the M–Cα–Cα′ plane, interacting with the Cα p-orbital lying in the same plane. This π-type interaction inscribes some alkylidene character into Cα that favors alkylidene generation via α-H abstraction. The extent of the deshielding and the anisotropy of the alkyl chemical shift tensors distinguishes [M](CH2R)2 compounds that form alkylidenes from those that do not, relating the reactivity to molecular orbitals of the respective molecules. The α-carbon chemical shifts and tensor orientations thus predict the reactivity of metal alkyl compounds towards alkylidene generation. PMID:29675237

Investigation of the interaction of iron(III) complexes with dAMP by ESI-MS, MALDI-MS and potentiometric titration: insights into synthetic nuclease behavior.

PubMed

Fernandes, Christiane; Oliveira Moreira, Rafaela; Lube, Leonardo M; Horn, Adolfo; Szpoganicz, Bruno; Sherrod, Stacy; Russell, David H

2010-06-07

We report herein the characterization by electrospray ionization (ESI) mass spectrometry (MS), matrix assisted laser desorption ionization (MALDI-MS) and potentiometric titration of three iron(III) compounds: [Fe(III)(HPClNOL)Cl2]·NO3 (1), [Cl(HPClNOL)Fe(III)-(μ-O)-Fe(III)(HPClNOL)Cl]·Cl2·H2O (2) and [(SO4)(HPClNOL)Fe(III)-(μ-O)-Fe(III)(HPClNOL)(SO4)]·6H2O (3), where HPClNOL= 1-(bis-pyridin-2-ylmethyl-amino)-3-chloropropan-2-ol). Despite the fact that the compounds have distinct structures in solid state and non-buffered solution, all compounds present similar ESI and MALDI mass spectra in a buffered medium (pH 7.0). At this pH, the species [(PClNOL)Fe(III)-(μ-O)-Fe(III)(PClNOL)](2+) (m/z 354) was observed for all the compounds under investigation. Potentiometric titration confirms a similar behavior for all compounds, indicating that the dihydroxo form [(OH)(HPClNOL)Fe(III)-(μ-O)-Fe(III)(HPClNOL)(OH)](2+) is the major species at pH 7.0, for all the compounds. The products of the interaction between compounds (1), (2) and (3) and dAMP (2'-deoxyadenosine-5'-monophosphate) in a buffered medium (pH 7.0) were identified by MALDI-MS/MS. The fragmentation data obtained by MS/MS allow one to identify the nature of the interaction between the iron(III) compounds and dAMP, revealing the direct interaction between the iron center and phosphate groups.

Integrative “omic” analysis reveals distinctive cold responses in leaves and roots of strawberry, Fragaria × ananassa ‘Korona’

PubMed Central

Koehler, Gage; Rohloff, Jens; Wilson, Robert C.; Kopka, Joachim; Erban, Alexander; Winge, Per; Bones, Atle M.; Davik, Jahn; Alsheikh, Muath K.; Randall, Stephen K.

2015-01-01

To assess underlying metabolic processes and regulatory mechanisms during cold exposure of strawberry, integrative “omic” approaches were applied to Fragaria × ananassa Duch. ‘Korona.’ Both root and leaf tissues were examined for responses to the cold acclimation processes. Levels of metabolites, proteins, and transcripts in tissues from plants grown at 18°C were compared to those following 1–10 days of cold (2°C) exposure. When leaves and roots were subjected to GC/TOF-MS-based metabolite profiling, about 160 compounds comprising mostly structurally annotated primary and secondary metabolites, were found. Overall, ‘Korona’ showed a modest increase of protective metabolites such as amino acids (aspartic acid, leucine, isoleucine, and valine), pentoses, phosphorylated and non-phosphorylated hexoses, and distinct compounds of the raffinose pathway (galactinol and raffinose). Distinctive responses were observed in roots and leaves. By 2DE proteomics a total of 845 spots were observed in leaves; 4.6% changed significantly in response to cold. Twenty-one proteins were identified, many of which were associated with general metabolism or photosynthesis. Transcript levels in leaves were determined by microarray, where dozens of cold associated transcripts were quantitatively characterized, and levels of several potential key contributors (e.g., the dehydrin COR47 and GADb) to cold tolerance were confirmed by qRT-PCR. Cold responses are placed within the existing knowledge base of low temperature-induced changes in plants, allowing an evaluation of the uniqueness or generality of Fragaria responses in photosynthetic tissues. Overall, the cold response characteristics of ‘Korona’ are consistent with a moderately cold tolerant plant. PMID:26528299

Lack of Influence of Substrate on Ligand Interaction with the Human Multidrug and Toxin Extruder, MATE1

PubMed Central

Martínez-Guerrero, Lucy J.; Morales, Mark; Ekins, Sean

2016-01-01

Multidrug and toxin extruder (MATE) 1 plays a central role in mediating renal secretion of organic cations, a structurally diverse collection of compounds that includes ∼40% of prescribed drugs. Because inhibition of transport activity of other multidrug transporters, including the organic cation transporter (OCT) 2, is influenced by the structure of the transported substrate, the present study screened over 400 drugs as inhibitors of the MATE1-mediated transport of four structurally distinct organic cation substrates: the commonly used drugs: 1) metformin and 2) cimetidine; and two prototypic cationic substrates, 3) 1-methyl-4-phenylpyridinium (MPP), and 4) the novel fluorescent probe, N,N,N-trimethyl-2-[methyl(7-nitrobenzo[c][1,2,5]oxadiazol-4-yl)amino]ethanaminium iodide. Transport was measured in Chinese hamster ovary cells that stably expressed the human ortholog of MATE1. Comparison of the resulting inhibition profiles revealed no systematic influence of substrate structure on inhibitory efficacy. Similarly, IC50 values for 26 structurally diverse compounds revealed no significant influence of substrate structure on the kinetic interaction of inhibitor with MATE1. The IC50 data were used to generate three-dimensional quantitative pharmacophores that identified hydrophobic regions, H-bond acceptor sites, and an ionizable (cationic) feature as key determinants for ligand binding to MATE1. In summary, in contrast to the behavior observed with some other multidrug transporters, including OCT2, the results suggest that substrate identity exerts comparatively little influence on ligand interaction with MATE1. PMID:27418674

Selective photoswitching of the binuclear spin crossover compound {[Fe(bt)(NCS)2]2(bpm)} into two distinct macroscopic phases.

PubMed

Moussa, N Ould; Molnár, G; Bonhommeau, S; Zwick, A; Mouri, S; Tanaka, K; Real, J A; Bousseksou, A

2005-03-18

The low-spin (LS-LS, S = 0) diamagnetic form of the binuclear spin crossover complex {[Fe(bt)(NCS)(2)](2)(bpm)} was selectively photoconverted into two distinct macroscopic phases at different excitation wavelengths (1342 or 647.1 nm). These long-lived metastable phases have been identified, respectively, as the symmetry-broken paramagnetic form (HS-LS, S = 2) and the antiferromagnetically coupled (HS-HS, S = 0) high-spin form of the compound. The selectivity may be explained by the strong coupling of the primary excited states to the paramagnetic state.

Novel Electronically Conducting Tellurium Oxides

NASA Astrophysics Data System (ADS)

Subramanian, Mas; Siritanon, Theerunan; Sleight, Arthur

2010-03-01

Tellurium oxides seldom show measurable electronic conductivity. Tellurium oxides that appear to have Te^5+ contain Te^4+ and Te^6+ in two distinct crystallographic sites and are electronic insulators. Here we report on the synthesis and characterization of several new tellurium rich oxides of the general formula, CsMxTe2-xO6, crystallizing in modified pyrochlore structure. Most of the compounds reported here are black in color with some exhibiting good electronic conductivities (2 S/cm) and Seebeck measurements indicate all are n-type. The observation of high electronic conductivities in compounds like CsGe0.5Te1.5O6, CsAl0.33Te1.67O6 confirms that observed conductivity is arising from doping of electrons into the empty 5s orbitals of Te^6+. This reduction is apparently accompanied with some small deviation from the ideal formula: oxygen content and/or ratio of cations on octahedral sites. This is in consistent with single-crystal X-ray as well as powder neutron diffraction structure refinements and the observed sign of the Seebeck coefficient. To our knowledge, this is a first observance of high electrical conductivity in mixed valent tellurium oxides.

A General Model of Sensitized Luminescence in Lanthanide-Based Coordination Polymers and Metal-Organic Framework Materials.

PubMed

Einkauf, Jeffrey D; Clark, Jessica M; Paulive, Alec; Tanner, Garrett P; de Lill, Daniel T

2017-05-15

Luminescent lanthanides containing coordination polymers and metal-organic frameworks hold great potential in many applications due to their distinctive spectroscopic properties. While the ability to design coordination polymers for specific functions is often mentioned as a major benefit bestowed on these compounds, the lack of a meaningful understanding of the luminescence in lanthanide coordination polymers remains a significant challenge toward functional design. Currently, the study of these compounds is based on the antenna effect as derived from molecular systems, where organic antennae are used to facilitate lanthanide-centered luminescence. This molecular-based approach does not take into account the unique features of extended network solids, particularly the formation of band structure. While guidelines for the antenna effect are well established, they require modification before being applied to coordination polymers. A series of nine coordination polymers with varying topologies and organic linkers were studied to investigate the accuracy of the antenna effect in coordination polymer systems. By comparing a molecular-based approach to a band-based one, it was determined that the band structure that occurs in aggregated organic solids needs to be considered when evaluating the luminescence of lanthanide coordination polymers.

Crystallization of toxic glycol solvates of rifampin from glycerin and propylene glycol contaminated with ethylene glycol or diethylene glycol.

PubMed

de Villiers, Melgardt M; Caira, Mino R; Li, Jinjing; Strydom, Schalk J; Bourne, Susan A; Liebenberg, Wilna

2011-06-06

This study was initiated when it was suspected that syringe blockage experienced upon administration of a compounded rifampin suspension was caused by the recrystallization of toxic glycol solvates of the drug. Single crystal X-ray structure analysis, powder X-ray diffraction, thermal analysis and gas chromatography were used to identify the ethylene glycol in the solvate crystals recovered from the suspension. Controlled crystallization and solubility studies were used to determine the ease with which toxic glycol solvates crystallized from glycerin and propylene glycol contaminated with either ethylene or diethylene glycol. The single crystal structures of two distinct ethylene glycol solvates of rifampin were solved while thermal analysis, GC analysis and solubility studies confirmed that diethylene glycol solvates of the drug also crystallized. Controlled crystallization studies showed that crystallization of the rifampin solvates from glycerin and propylene glycol depended on the level of contamination and changes in the solubility of the drug in the contaminated solvents. Although the exact source of the ethylene glycol found in the compounded rifampin suspension is not known, the results of this study show how important it is to ensure that the drug and excipients comply with pharmacopeial or FDA standards.

Electronic structures and population dynamics of excited states of xanthione and its derivatives

NASA Astrophysics Data System (ADS)

Fedunov, Roman G.; Rogozina, Marina V.; Khokhlova, Svetlana S.; Ivanov, Anatoly I.; Tikhomirov, Sergei A.; Bondarev, Stanislav L.; Raichenok, Tamara F.; Buganov, Oleg V.; Olkhovik, Vyacheslav K.; Vasilevskii, Dmitrii A.

2017-09-01

A new compound, 1,3-dimethoxy xanthione (DXT), has been synthesized and its absorption (stationary and transient) and luminescence spectra have been measured in n-hexane and compared with xanthione (XT) spectra. The pronounced broadening of xanthione vibronic absorption band related to the electronic transition to the second singlet excited state has been observed. Distinctions between the spectra of xanthione and its methoxy derivatives are discussed. Quantum chemical calculations of these compounds in the ground and excited electronic states have been accomplished to clarify the nature of electronic spectra changes due to modification of xanthione by methoxy groups. Appearance of a new absorption band of DXT caused by symmetry changes has been discussed. Calculations of the second excited state structure of xanthione and its methoxy derivatives confirm noticeable charge transfer (about 0.1 of the charge of an electron) from the methoxy group to thiocarbonyl group. Fitting of the transient spectra of XT and DXT has been fulfilled and the time constants of internal conversion S2 →S1 and intersystem crossing S1 →T1 have been determined. A considerable difference between the time constants of internal conversion S2 →S1 in XT and DXT is uncovered.

Distinct brain metabolic patterns separately associated with cognition, motor function, and aging in Parkinson's disease dementia.

PubMed

Ko, Ji Hyun; Katako, Audrey; Aljuaid, Maram; Goertzen, Andrew L; Borys, Andrew; Hobson, Douglas E; Kim, Seok Min; Lee, Chong Sik

2017-12-01

We explored whether patients with Parkinson's disease dementia (PDD) show a distinct spatial metabolic pattern that characterizes cognitive deficits in addition to motor dysfunction. Eighteen patients with PDD underwent 3 separate positron emission tomography sessions with [ 18 F]fluorodeoxyglucose (for glucose metabolism), fluorinated N-3-fluoropropyl-2-beta-carboxymethoxy-3-beta-(4-iodophenyl) nortropane (for dopamine transporter density) and Pittsburgh compound-B (for beta-amyloid load). We confirmed in PDD versus normal controls, overall hypometabolism in the posterior and prefrontal brain regions accompanied with hypermetabolism in subcortical structures and the cerebellar vermis. A multivariate network analysis then revealed 3 metabolic patterns that are separately associated with cognitive performance (p = 0.042), age (p = 0.042), and motor symptom severity (p = 0.039). The age-related pattern's association with aging was replicated in healthy controls (p = 0.047) and patients with Alzheimer's disease (p = 0.002). The cognition-related pattern's association with cognitive performance was observed, with a trend-level of correlation, in patients with dementia with Lewy bodies (p = 0.084) but not in patients with Alzheimer's disease (p = 0.974). We found no association with fluorinated N-3-fluoropropyl-2-beta-carboxymethoxy-3-beta-(4-iodophenyl) nortropane and Pittsburgh compound-B positron emission tomography with patients' cognitive performance. Copyright © 2017 Elsevier Inc. All rights reserved.

Common and Distant Structural Characteristics of Feruloyl Esterase Families from Aspergillus oryzae

PubMed Central

Udatha, D. B. R. K. Gupta; Mapelli, Valeria; Panagiotou, Gianni; Olsson, Lisbeth

2012-01-01

Background Feruloyl esterases (FAEs) are important biomass degrading accessory enzymes due to their capability of cleaving the ester links between hemicellulose and pectin to aromatic compounds of lignin, thus enhancing the accessibility of plant tissues to cellulolytic and hemicellulolytic enzymes. FAEs have gained increased attention in the area of biocatalytic transformations for the synthesis of value added compounds with medicinal and nutritional applications. Following the increasing attention on these enzymes, a novel descriptor based classification system has been proposed for FAEs resulting into 12 distinct families and pharmacophore models for three FAE sub-families have been developed. Methodology/Principal Findings The feruloylome of Aspergillus oryzae contains 13 predicted FAEs belonging to six sub-families based on our recently developed descriptor-based classification system. The three-dimensional structures of the 13 FAEs were modeled for structural analysis of the feruloylome. The three genes coding for three enzymes, viz., A.O.2, A.O.8 and A.O.10 from the feruloylome of A. oryzae, representing sub-families with unknown functional features, were heterologously expressed in Pichia pastoris, characterized for substrate specificity and structural characterization through CD spectroscopy. Common feature-based pharamacophore models were developed according to substrate specificity characteristics of the three enzymes. The active site residues were identified for the three expressed FAEs by determining the titration curves of amino acid residues as a function of the pH by applying molecular simulations. Conclusions/Significance Our findings on the structure-function relationships and substrate specificity of the FAEs of A. oryzae will be instrumental for further understanding of the FAE families in the novel classification system. The developed pharmacophore models could be applied for virtual screening of compound databases for short listing the putative substrates prior to docking studies or for post-processing docking results to remove false positives. Our study exemplifies how computational predictions can complement to the information obtained through experimental methods. PMID:22745763

Common and distant structural characteristics of feruloyl esterase families from Aspergillus oryzae.

PubMed

Udatha, D B R K Gupta; Mapelli, Valeria; Panagiotou, Gianni; Olsson, Lisbeth

2012-01-01

Feruloyl esterases (FAEs) are important biomass degrading accessory enzymes due to their capability of cleaving the ester links between hemicellulose and pectin to aromatic compounds of lignin, thus enhancing the accessibility of plant tissues to cellulolytic and hemicellulolytic enzymes. FAEs have gained increased attention in the area of biocatalytic transformations for the synthesis of value added compounds with medicinal and nutritional applications. Following the increasing attention on these enzymes, a novel descriptor based classification system has been proposed for FAEs resulting into 12 distinct families and pharmacophore models for three FAE sub-families have been developed. The feruloylome of Aspergillus oryzae contains 13 predicted FAEs belonging to six sub-families based on our recently developed descriptor-based classification system. The three-dimensional structures of the 13 FAEs were modeled for structural analysis of the feruloylome. The three genes coding for three enzymes, viz., A.O.2, A.O.8 and A.O.10 from the feruloylome of A. oryzae, representing sub-families with unknown functional features, were heterologously expressed in Pichia pastoris, characterized for substrate specificity and structural characterization through CD spectroscopy. Common feature-based pharamacophore models were developed according to substrate specificity characteristics of the three enzymes. The active site residues were identified for the three expressed FAEs by determining the titration curves of amino acid residues as a function of the pH by applying molecular simulations. Our findings on the structure-function relationships and substrate specificity of the FAEs of A. oryzae will be instrumental for further understanding of the FAE families in the novel classification system. The developed pharmacophore models could be applied for virtual screening of compound databases for short listing the putative substrates prior to docking studies or for post-processing docking results to remove false positives. Our study exemplifies how computational predictions can complement to the information obtained through experimental methods.

SOD activity of carboxyfullerenes predicts their neuroprotective efficacy: A structure-activity study

PubMed Central

Ali, Sameh Saad; Hardt, Joshua I.; Dugan, Laura L.

2008-01-01

Superoxide radical anion is a biologically important oxidant that has been linked to tissue injury and inflammation in several diseases. Here we carried out a structure-activity study on 6 different carboxyfullerene superoxide dismutase (SOD) mimetics with distinct electronic and biophysical characteristics. Neurotoxicity via NMDA receptors, which involves intracellular superoxide, was used as a model to evaluate structure-activity relationships between reactivity towards superoxide and neuronal rescue by these drugs. A significant correlation between neuroprotection by carboxyfullerenes and their ki towards superoxide radical was observed. Computer-assistant molecular modeling demonstrated that the reactivity towards superoxide is sensitive to changes in dipole moment which are dictated not only by the number of carboxyl groups, but also by their distribution on the fullerene ball. These results indicate that the SOD activity of these cell-permeable compounds predicts neuroprotection, and establishes a structure-activity relationship to aid in future studies on the biology of superoxide across disciplines. PMID:18656425

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Huixian; Wacker, Daniel; Mileni, Mauro

Opioid receptors mediate the actions of endogenous and exogenous opioids on many physiological processes, including the regulation of pain, respiratory drive, mood, and - in the case of {kappa}-opioid receptor ({kappa}-OR) - dysphoria and psychotomimesis. Here we report the crystal structure of the human {kappa}-OR in complex with the selective antagonist JDTic, arranged in parallel dimers, at 2.9 {angstrom} resolution. The structure reveals important features of the ligand-binding pocket that contribute to the high affinity and subtype selectivity of JDTic for the human {kappa}-OR. Modelling of other important {kappa}-OR-selective ligands, including the morphinan-derived antagonists norbinaltorphimine and 5'-guanidinonaltrindole, and the diterpenemore » agonist salvinorin A analogue RB-64, reveals both common and distinct features for binding these diverse chemotypes. Analysis of site-directed mutagenesis and ligand structure-activity relationships confirms the interactions observed in the crystal structure, thereby providing a molecular explanation for {kappa}-OR subtype selectivity, and essential insights for the design of compounds with new pharmacological properties targeting the human {kappa}-OR.« less

Combinatorial selection of molecular conformations and supramolecular synthons in quercetin cocrystal landscapes: a route to ternary solids

PubMed Central

Dubey, Ritesh; Desiraju, Gautam R.

2015-01-01

The crystallization of 28 binary and ternary cocrystals of quercetin with dibasic coformers is analyzed in terms of a combinatorial selection from a solution of preferred molecular conformations and supramolecular synthons. The crystal structures are characterized by distinctive O—H⋯N and O—H⋯O based synthons and are classified as nonporous, porous and helical. Variability in molecular conformation and synthon structure led to an increase in the energetic and structural space around the crystallization event. This space is the crystal structure landscape of the compound and is explored by fine-tuning the experimental conditions of crystallization. In the landscape context, we develop a strategy for the isolation of ternary cocrystals with the use of auxiliary template molecules to reduce the molecular and supramolecular ‘confusion’ that is inherent in a molecule like quercetin. The absence of concomitant polymorphism in this study highlights the selectivity in conformation and synthon choice from the virtual combinatorial library in solution. PMID:26175900

The Enzymatic and Structural Basis for Inhibition of Echinococcus granulosus Thioredoxin Glutathione Reductase by Gold(I).

PubMed

Salinas, Gustavo; Gao, Wei; Wang, Yang; Bonilla, Mariana; Yu, Long; Novikov, Andrey; Virginio, Veridiana G; Ferreira, Henrique B; Vieites, Marisol; Gladyshev, Vadim N; Gambino, Dinorah; Dai, Shaodong

2017-12-20

New drugs are needed to treat flatworm infections that cause severe human diseases such as schistosomiasis. The unique flatworm enzyme thioredoxin glutathione reductase (TGR), structurally different from the human enzyme, is a key drug target. Structural studies of the flatworm Echinococcus granulosus TGR, free and complexed with Au I -MPO, a novel gold inhibitor, together with inhibition assays were performed. Au I -MPO is a potent TGR inhibitor that achieves 75% inhibition at a 1:1 TGR:Au ratio and efficiently kills E. granulosus in vitro. The structures revealed salient insights: (i) unique monomer-monomer interactions, (ii) distinct binding sites for thioredoxin and the glutaredoxin (Grx) domain, (iii) a single glutathione disulfide reduction site in the Grx domain, (iv) rotation of the Grx domain toward the Sec-containing redox active site, and (v) a single gold atom bound to Cys 519 and Cys 573 in the Au I -TGR complex. Structural modeling suggests that these residues are involved in the stabilization of the Sec-containing C-terminus. Consistently, Cys→Ser mutations in these residues decreased TGR activities. Mass spectroscopy confirmed these cysteines are the primary binding site. The identification of a primary site for gold binding and the structural model provide a basis for gold compound optimization through scaffold adjustments. The structural study revealed that TGR functions are achieved not only through a mobile Sec-containing redox center but also by rotation of the Grx domain and distinct binding sites for Grx domain and thioredoxin. The conserved Cys 519 and Cys 573 residues targeted by gold assist catalysis through stabilization of the Sec-containing redox center. Antioxid. Redox Signal. 27, 1491-1504.

The Enzymatic and Structural Basis for Inhibition of Echinococcus granulosus Thioredoxin Glutathione Reductase by Gold(I)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salinas, Gustavo; Gao, Wei; Wang, Yang

Aims: New drugs are needed to treat flatworm infections that cause severe human diseases such as schistosomiasis. The unique flatworm enzyme thioredoxin glutathione reductase (TGR), structurally different from the human enzyme, is a key drug target. Structural studies of the flatworm Echinococcus granulosus TGR, free and complexed with AuI-MPO, a novel gold inhibitor, together with inhibition assays were performed. Results: AuI-MPO is a potent TGR inhibitor that achieves 75% inhibition at a 1:1 TGR:Au ratio and efficiently kills E. granulosus in vitro. The structures revealed salient insights: (i) unique monomer–monomer interactions, (ii) distinct binding sites for thioredoxin and the glutaredoxinmore » (Grx) domain, (iii) a single glutathione disulfide reduction site in the Grx domain, (iv) rotation of the Grx domain toward the Sec-containing redox active site, and (v) a single gold atom bound to Cys519 and Cys573 in the AuI-TGR complex. Structural modeling suggests that these residues are involved in the stabilization of the Sec-containing C-terminus. Consistently, Cys→Ser mutations in these residues decreased TGR activities. Mass spectroscopy confirmed these cysteines are the primary binding site. Innovation: The identification of a primary site for gold binding and the structural model provide a basis for gold compound optimization through scaffold adjustments. Conclusions: The structural study revealed that TGR functions are achieved not only through a mobile Sec-containing redox center but also by rotation of the Grx domain and distinct binding sites for Grx domain and thioredoxin. The conserved Cys519 and Cys573 residues targeted by gold assist catalysis through stabilization of the Sec-containing redox center. Antioxid. Redox Signal. 27, 1491–1504.« less

Closer insight into the reactivity of TMP-dialkyl zincates in directed ortho-zincation of anisole: experimental evidence of amido basicity and structural elucidation of key reaction intermediates.

PubMed

Clegg, William; Conway, Ben; Hevia, Eva; McCall, Matthew D; Russo, Luca; Mulvey, Robert E

2009-02-18

The new dialkyl(aryl) lithium zincates [(THF)(2)Li(C(6)H(4)-OMe)MeZnMe] (4), [(TMEDA)Li(C(6)H(4)-OMe)MeZnMe] (6), [(THF)(3)Li(C(6)H(4)-OMe)(t)BuZn(t)Bu] (7), and [(PMDETA)Li(C(6)H(4)-OMe)(t)BuZn(t)Bu] (8) have been prepared by co-complexation reactions of lithiated anisole with the relevant dialkylzinc compound and the relevant Lewis base. These new heterobimetallic compounds have been characterized in solution using (1)H, (13)C{H}, and (7)Li NMR spectroscopy, and the molecular structures of 6 and 8 have been elucidated by X-ray crystallography. In 6 the distinct metals are connected through the anisole ligand which binds in an ambidentate fashion (through carbon-zinc and oxygen-lithium contacts) and also through one of the methyl groups, to close a [LiOCCZnC] six-membered ring; whereas 8 displays an open structure where anisole connects the two metals (in the same mode as in 6) but with the tert-butyl groups exclusively bonded terminally to zinc. Reactivity studies of zincates 4 and 7 with the amine TMP(H) supply experimental evidence that these heterobimetallic compounds are intermediates in the two-step deprotonation reaction of anisole by TMP-dialkyl zincates and show the relevance of the alkyl groups in the efficiency of TMP-dialkyl zincate bases. In addition, important solvent effects have also been evaluated. When hexane is added to THF solutions of compounds 4 or 7, the homoleptic tetraorganozincate [(THF)(2)Li(2)Zn(C(6)H(4)-OMe)(4)] (5) is obtained as the result of a disproportionation process. This lithium-rich zincate has also been spectroscopically and crystallographically characterized.

Tautomerism and isomerism in some antitrichinellosis active benzimidazoles: Morphological study in polarized light, quantum chemical computations

NASA Astrophysics Data System (ADS)

Anichina, Kameliya; Mavrova, Anelia; Yancheva, Denitsa; Tsenov, Jordan; Dimitrov, Rasho

2017-12-01

The morphology of the crystal structure of some antitrichinellosis active benzimidazole derivatives including (1H-benzimidazol-2-ylthio)acetic acids, [1,3]thiazolo[3,2-a]benzimidazol-3(2H)-ones, 1H-benzimidazol-2-ylthioacetylpiperazines and starting 2-mercapto benzimidazoles, was studied by the use of Polarized Light Microscopy (PLM). Characterization of the crystal phase was complimented by Differential scanning calorimetry analysis (DSC) and spectroscopic data. DFT computations were performed in order to investigate the prototropic tautomerism and the geometry of the molecule of the synthesized compounds. One distinct type of crystal structure for each one of 5 or 6-methyl-(1H-benzimidazol-2-ylthio)acetic acid 6 was observed by PLM - dendritic and needle-shaped formations. Compound 14, containing a methyl substituent in the benzimidazole ring crystallized also into two phases; while for the unsubstituted compound 13 a separation of phases does not take place. The influence of the both solvents - chloroform and ethanol on the phase separation and the formation of the crystalline structure of compound 14 was investigated. The morphological study showed that the cyclization of 6 in the presence of acetic anhydride in pyridine medium led to a mixture of 6-methyl-[1,3]tiazolo[3,2-a]benzimidazol-3(2H)-one (10a) and 7-methyl-[1,3]thiazolo[3,2-a]-benzimidazole-3(2H)-one (10b), which crystallized in the form of fibrils and spherulites respectively. It was found that a difference in the crystal structures of substituted and unsubstituted benzimidazol-2-thiones, respectively benzimidazol-2-thiol derivatives exists, which may be due not only to the thiol-thione tautomerism but to the prototropic properties of the hydrogen atom in first position of the ring. The calculation results indicated that the thione form is more stable than the thiol tautomer by 51-55 kJ mol-1. But at the same time ΔG for the two thiol tautomers is below 0.5 kJ mol-1. In solid phase the 5(6)-substituted-1H-benzimidazol-2-thiols crystallized in two different crystal structures while the unsubstituted 1H-benzimidazol-2-thiol possess one type of crystal structure.

CoAs: The line of 3 d demarcation

NASA Astrophysics Data System (ADS)

Campbell, Daniel J.; Wang, Limin; Eckberg, Chris; Graf, Dave; Hodovanets, Halyna; Paglione, Johnpierre

2018-05-01

Transition metal-pnictide compounds have received attention for their tendency to combine magnetism and unconventional superconductivity. Binary CoAs lies on the border of paramagnetism and the more complex behavior seen in isostructural CrAs, MnP, FeAs, and FeP. Here we report the properties of CoAs single crystals grown with two distinct techniques along with density functional theory calculations of its electronic structure and magnetic ground state. While all indications are that CoAs is paramagnetic, both experiment and theory suggest proximity to a ferromagnetic instability. Quantum oscillations are seen in torque measurements up to 31.5 T and support the calculated paramagnetic Fermiology.

Semiconductor quantum dots: synthesis and water-solubilization for biomedical applications.

PubMed

Yu, William W

2008-10-01

Quantum dots (QDs) are generally nanosized inorganic particles. They have distinctive size-dependent optical properties due to their very small size (mostly < 10 nm). QDs are regarded as promising new fluorescent materials for biological labeling and imaging because of their superior properties compared with traditional organic molecular dyes. These properties include high quantum efficiency, long-term photostability and very narrow emission but broad absorption spectra. Recent developments in synthesizing high quality semiconductor QDs (mainly metal-chalcogenide compounds) and forming biocompatible structures for biomedical applications are discussed in this paper. This information may facilitate the research to create new materials/technologies for future clinical applications.

Mechanically controlling the reversible phase transformation from zinc blende to wurtzite in AlN

DOE PAGES

Li, Zhen; Yadav, Satyesh; Chen, Youxing; ...

2017-04-10

III–V and other binary octet semiconductors often take two phase forms—wurtzite (wz) and zinc blende (zb) crystal structures—with distinct functional performance at room temperature. Here, we investigate how to control the synthesized phase structure to either wz or zb phase by tuning the interfacial strain by taking AlN as a representative III–V compound. Furthermore, by applying in situ mechanical tests at atomic scale in a transmission electron microscope, we observed the reversible phase transformation from zb to wz, and characterized the transition path—the collective glide of Shockley partials on every two {111} planes of the zb AlN.

Structures of a Na+-coupled, substrate-bound MATE multidrug transporter

PubMed Central

Lu, Min; Symersky, Jindrich; Radchenko, Martha; Koide, Akiko; Guo, Yi; Nie, Rongxin; Koide, Shohei

2013-01-01

Multidrug transporters belonging to the multidrug and toxic compound extrusion (MATE) family expel dissimilar lipophilic and cationic drugs across cell membranes by dissipating a preexisting Na+ or H+ gradient. Despite its clinical relevance, the transport mechanism of MATE proteins remains poorly understood, largely owing to a lack of structural information on the substrate-bound transporter. Here we report crystal structures of a Na+-coupled MATE transporter NorM from Neisseria gonorrheae in complexes with three distinct translocation substrates (ethidium, rhodamine 6G, and tetraphenylphosphonium), as well as Cs+ (a Na+ congener), all captured in extracellular-facing and drug-bound states. The structures revealed a multidrug-binding cavity festooned with four negatively charged amino acids and surprisingly limited hydrophobic moieties, in stark contrast to the general belief that aromatic amino acids play a prominent role in multidrug recognition. Furthermore, we discovered an uncommon cation–π interaction in the Na+-binding site located outside the drug-binding cavity and validated the biological relevance of both the substrate- and cation-binding sites by conducting drug resistance and transport assays. Additionally, we uncovered potential rearrangement of at least two transmembrane helices upon Na+-induced drug export. Based on our structural and functional analyses, we suggest that Na+ triggers multidrug extrusion by inducing protein conformational changes rather than by directly competing for the substrate-binding amino acids. This scenario is distinct from the canonical antiport mechanism, in which both substrate and counterion compete for a shared binding site in the transporter. Collectively, our findings provide an important step toward a detailed and mechanistic understanding of multidrug transport. PMID:23341609

Differential cytokine modulation and T cell activation by two distinct classes of thalidomide analogues that are potent inhibitors of TNF-alpha.

PubMed

Corral, L G; Haslett, P A; Muller, G W; Chen, R; Wong, L M; Ocampo, C J; Patterson, R T; Stirling, D I; Kaplan, G

1999-07-01

TNF-alpha mediates both protective and detrimental manifestations of the host immune response. Our previous work has shown thalidomide to be a relatively selective inhibitor of TNF-alpha production in vivo and in vitro. Additionally, we have recently reported that thalidomide exerts a costimulatory effect on T cell responses. To develop thalidomide analogues with increased anti-TNF-alpha activity and reduced or absent toxicities, novel TNF-alpha inhibitors were designed and synthesized. When a selected group of these compounds was examined for their immunomodulatory activities, different patterns of cytokine modulation were revealed. The tested compounds segregated into two distinct classes: one class of compounds, shown to be potent phosphodiesterase 4 inhibitors, inhibited TNF-alpha production, increased IL-10 production by LPS-induced PBMC, and had little effect on T cell activation; the other class of compounds, similar to thalidomide, were not phosphodiesterase 4 inhibitors and markedly stimulated T cell proliferation and IL-2 and IFN-gamma production. These compounds inhibited TNF-alpha, IL-1beta, and IL-6 and greatly increased IL-10 production by LPS-induced PBMC. Similar to thalidomide, the effect of these agents on IL-12 production was dichotomous; IL-12 was inhibited when PBMC were stimulated with LPS but increased when cells were stimulated by cross-linking the TCR. The latter effect was associated with increased T cell CD40 ligand expression. The distinct immunomodulatory activities of these classes of thalidomide analogues may potentially allow them to be used in the clinic for the treatment of different immunopathological disorders.

Investigation of Classical Organic and Ionic Liquid Cosolvents for Early-Stage Screening in Fragment-Based Inhibitor Design with Unrelated Bacterial and Human Dihydrofolate Reductases.

PubMed

Toulouse, Jacynthe L; Abraham, Sarah M J; Kadnikova, Natalia; Bastien, Dominic; Gauchot, Vincent; Schmitzer, Andreea R; Pelletier, Joelle N

Drug design by methods such as fragment screening requires effective solubilization of millimolar concentrations of small organic compounds while maintaining the properties of the biological target. We investigate four organic solvents and three 1-butyl-3-methylimidazolium (BMIm)-based ionic liquids (ILs) as cosolvents to establish conditions for screening two structurally unrelated dihydrofolate reductases (DHFRs) that are prime drug targets. Moderate concentrations (10%-15%) of cosolvents had little effect on inhibition of the microbial type II R67 DHFR and of human DHFR (hDHFR), while higher concentrations of organic cosolvents generally decreased activity of both DHFRs. In contrast, a specific IL conserved the activity of one DHFR, while severely reducing the activity of the other, and vice versa, illustrating the differing effect of ILs on distinct protein folds. Most of the cosolvents investigated preserved the fold of R67 DHFR and had little effect on binding of the cofactor NADPH, but reduced the productive affinity for its substrate. In contrast, cosolvents resulted in modest structural destabilization of hDHFR with little effect on productive affinity. We conclude that the organic cosolvents, methanol, dimethylformamide, and dimethylsulfoxide, offer the most balanced conditions for early-stage compound screening as they maintain sufficient biological activity of both DHFRs while allowing for compound dissolution in the millimolar range. However, IL cosolvents showed poor capacity to solubilize organic compounds at millimolar concentrations, mitigating their utility in early-stage screening. Nonetheless, ILs could provide an alternative to classical organic cosolvents when low concentrations of inhibitors are used, as when characterizing higher affinity inhibitors.

The selectivity and promiscuity of brain-neuroregenerative inhibitors between ROCK1 and ROCK2 isoforms: An integration of SB-QSSR modelling, QM/MM analysis and in vitro kinase assay.

PubMed

Zhu, L; Yang, Y; Lu, X

2016-01-01

The Rho-associated kinases (ROCKs) have long been recognized as an attractive therapeutic target for various neurological diseases; selective inhibition of ROCK1 and ROCK2 isoforms would result in distinct biological effects on neurogenesis, neuroplasticity and neuroregeneration after brain surgery and traumatic brain injury. However, the discovery and design of isoform-selective inhibitors remain a great challenge due to the high conservation and similarity between the kinase domains of ROCK1 and ROCK2. Here, a structure-based quantitative structure-selectivity relationship (SB-QSSR) approach was used to correlate experimentally measured selectivity with the difference in inhibitor binding to the two kinase isoforms. The resulting regression models were examined rigorously through both internal cross-validation and external blind validation; a nonlinear predictor was found to have high fitting stability and strong generalization ability, which was then employed to perform virtual screening against a structurally diverse, drug-like compound library. Consequently, five and seven hits were identified as promising candidates of 1-o-2 and 2-o-1 selective inhibitors, respectively, from which seven purchasable compounds were tested in vitro using a standard kinase assay protocol to determine their inhibitory activity against and selectivity between ROCK1 and ROCK2. The structural basis, energetic property and biological implication underlying inhibitor selectivity and promiscuity were also investigated systematically using a hybrid quantum mechanics/molecular mechanics (QM/MM) scheme.

Small structural changes on a hydroquinone scaffold determine the complex I inhibition or uncoupling of tumoral oxidative phosphorylation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Urra, Félix A., E-mail: felix.urra@qf.uchile.cl; Córdova-Delgado, Miguel; Lapier, Michel

2016-01-15

Mitochondria participate in several distinctiveness of cancer cell, being a promising target for the design of anti-cancer compounds. Previously, we described that ortho-carbonyl hydroquinone scaffold 14 inhibits the complex I-dependent respiration with selective anti-proliferative effect on mouse mammary adenocarcinoma TA3/Ha cancer cells; however, the structural requirements of this hydroquinone scaffold to affect the oxidative phosphorylation (OXPHOS) of cancer cells have not been studied in detail. Here, we characterize the mitochondrial metabolism of TA3/Ha cancer cells, which exhibit a high oxidative metabolism, and evaluate the effect of small structural changes of the hydroquinone scaffold 14 on the respiration of this cellmore » line. Our results indicate that these structural changes modify the effect on OXPHOS, obtaining compounds with three alternative actions: inhibitors of complex I-dependent respiration, uncoupler of OXPHOS and compounds with both actions. To confirm this, the effect of a bicyclic hydroquinone (9) was evaluated in isolated mitochondria. Hydroquinone 9 increased mitochondrial respiration in state 4o without effects on the ADP-stimulated respiration (state 3{sub ADP}), decreasing the complexes I and II-dependent respiratory control ratio. The effect on mitochondrial respiration was reversed by 6-ketocholestanol addition, indicating that this hydroquinone is a protonophoric uncoupling agent. In intact TA3/Ha cells, hydroquinone 9 caused mitochondrial depolarization, decreasing intracellular ATP and NAD(P)H levels and GSH/GSSG ratio, and slightly increasing the ROS levels. Moreover, it exhibited selective NAD(P)H availability-dependent anti-proliferative effect on cancer cells. Therefore, our results indicate that the ortho-carbonyl hydroquinone scaffold offers the possibility to design compounds with specific actions on OXPHOS of cancer cells. - Highlights: • Small changes on a hydroquinone scaffold modify the action on OXPHOS of cancer cells. • Complex I Inhibitors, uncoupler of OXPHOS and agents with dual action are described. • Cpd. 9 is an uncoupler agent of OXPHOS with selective anti-proliferative effects. • Useful information to design agents with a selective mechanism on OXPHOS is provided.« less

Investigating the effect of emetic compounds on chemotaxis in Dictyostelium identifies a non-sentient model for bitter and hot tastant research.

PubMed

Robery, Steven; Mukanowa, Janina; Percie du Sert, Nathalie; Andrews, Paul L R; Williams, Robin S B

2011-01-01

Novel chemical entities (NCEs) may be investigated for emetic liability in a range of unpleasant experiments involving retching, vomiting or conditioned taste aversion/food avoidance in sentient animals. We have used a range of compounds with known emetic /aversive properties to examine the possibility of using the social amoeba, Dictyostelium discoideum, for research into identifying and understanding emetic liability, and hence reduce adverse animal experimentation in this area. Twenty eight emetic or taste aversive compounds were employed to investigate the acute (10 min) effect of compounds on Dictyostelium cell behaviour (shape, speed and direction of movement) in a shallow chemotaxic gradient (Dunn chamber). Compound concentrations were chosen based on those previously reported to be emetic or aversive in in vivo studies and results were recorded and quantified by automated image analysis. Dictyostelium cell motility was rapidly and strongly inhibited by four structurally distinct tastants (three bitter tasting compounds--denatonium benzoate, quinine hydrochloride, phenylthiourea, and the pungent constituent of chilli peppers--capsaicin). In addition, stomach irritants (copper chloride and copper sulphate), and a phosphodiesterase IV inhibitor also rapidly blocked movement. A concentration-dependant relationship was established for five of these compounds, showing potency of inhibition as capsaicin (IC(50) = 11.9 ± 4.0 µM) > quinine hydrochloride (IC(50) = 44.3 ± 6.8 µM) > denatonium benzoate (IC(50) = 129 ± 4 µM) > phenylthiourea (IC(50) = 366 ± 5 µM) > copper sulphate (IC(50) = 1433 ± 3 µM). In contrast, 21 compounds within the cytotoxic and receptor agonist/antagonist classes did not affect cell behaviour. Further analysis of bitter and pungent compounds showed that the effect on cell behaviour was reversible and not cytotoxic, suggesting an uncharacterised molecular mechanism of action for these compounds. These results therefore demonstrate that Dictyostelium has potential as a non-sentient model in the analysis of the molecular effects of tastants, although it has limited utility in identification of emetic agents in general.

pH-specific hydrothermal assembly of binary and ternary Pb(II)-(O,N-carboxylic acid) metal organic framework compounds: correlation of aqueous solution speciation with variable dimensionality solid-state lattice architecture and spectroscopic signatures.

PubMed

Gabriel, C; Perikli, M; Raptopoulou, C P; Terzis, A; Psycharis, V; Mateescu, C; Jakusch, T; Kiss, T; Bertmer, M; Salifoglou, A

2012-09-03

Hydrothermal pH-specific reactivity in the binary/ternary systems of Pb(II) with the carboxylic acids N-hydroxyethyl-iminodiacetic acid (Heida), 1,3-diamino-2-hydroxypropane-N,N,N',N'-tetraacetic acid (Dpot), and 1,10-phenanthroline (Phen) afforded the new well-defined crystalline compounds [Pb(Heida)](n)·nH(2)O(1), [Pb(Phen)(Heida)]·4H(2)O(2), and [Pb(3)(NO(3))(Dpot)](n)(3). All compounds were characterized by elemental analysis, FT-IR, solution or/and solid-state NMR, and single-crystal X-ray diffraction. The structures in 1-2 reveal the presence of a Pb(II) center coordinated to one Heida ligand, with 1 exhibiting a two-dimensional (2D) lattice extending to a three-dimensional (3D) one through H-bonding interactions. The concurrent aqueous speciation study of the binary Pb(II)-Heida system projects species complementing the synthetic efforts, thereby lending credence to a global structural speciation strategy in investigating binary/ternary Pb(II)-Heida/Phen systems. The involvement of Phen in 2 projects the significance of nature and reactivity potential of N-aromatic chelators, disrupting the binary lattice in 1 and influencing the nature of the ultimately arising ternary 3D lattice. 3 is a ternary coordination polymer, where Pb(II)-Dpot coordination leads to a 2D metal-organic-framework material with unique architecture. The collective physicochemical properties of 1-3 formulate the salient features of variable dimensionality metal-organic-framework lattices in binary/ternary Pb(II)-(hydroxy-carboxylate) structures, based on which new Pb(II) materials with distinct architecture and spectroscopic signature can be rationally designed and pursued synthetically.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Kuo; Hu, Yufei; Wang, Yingxia, E-mail: Wangyx@pku.edu.cn

Isostructural compounds RE{sub 3}Sb{sub 3}Co{sub 2}O{sub 14} (RE=La, Pr, Nd, Sm–Ho) with an ordered pyrochlore structure were synthesized. The structure of La{sub 3}Sb{sub 3}Co{sub 2}O{sub 14} was solved ab initio based on powder XRD data, and refined by combining with high resolution neutron diffraction data. La{sub 3}Sb{sub 3}Co{sub 2}O{sub 14} crystallizes in the space group R-3m with the unit cell parameters a=7.52954(2) Å and c=17.59983(6) Å. The structures of other members in this family are confirmed by Rietveld refinement using powder X-ray diffraction data. The cations (RE, Sb and Co) in RE{sub 3}Sb{sub 3}Co{sub 2}O{sub 14} are orderly distributed, presentingmore » as [RE{sub 3}Co][Sb{sub 3}Co]O{sub 14} formula, and giving rise to two distinctive Kagome lattices constructed by RE{sup 3+} and Sb{sup 5+}, respectively. Co{sup 2+} occupies 8-coordinated and 6-coordinated environments, showing low spin (S=1/2) and high spin (S=3/2) states respectively. The magnetic susceptibility and UV–visual spectroscopy supports the magnetic observation. TDDFT calculation was performed to interpret the electronic states. The compounds [RE{sub 3}Co][Sb{sub 3}Co]O{sub 14} provide a profound example in which the ideal 2D Kagome lattice is derived from the 3D pyrochlore-type structure by an ordered distribution of the metal cations. - Graphical abstract: La{sub 3}Sb{sub 3}Co{sub 2}O{sub 14} crystallizes in a pyrochlore related structure with an ordered distribution of cations, giving rise to two sets of ideal 2D Kagome lattices formed by La{sup 3+} or Sb{sup 5+} respectively. This rhombohedral pyrochlore is a tolerant structure for stable compounds composed by many light rare-earth and d-transition elements. Substituting Zn{sup 2+} or Mg{sup 2+} for Co{sup 2+} will provide a series of compounds useful for studying magnetic interactions in the rare-earth Kagome lattices. - Highlights: • Pyrochlore-type La{sub 3}Sb{sub 3}Co{sub 2}O{sub 14} shows an ordered distribution of cations in its structure. • It presents two sets of ideal 2D Kagome lattices formed by La{sup 3+} or Sb{sup 5+}, respectively. • A family of isostructural compounds RE{sub 3}Sb{sub 3}Co{sub 2}O{sub 14} (RE=Pr, Nd, Sm–Ho) were realized. • Co{sup 2+} presents two spin states with S=1/2, 3/2 due to two coordinated environments.« less

Identification and Metabolite Profiling of Chemical Activators of Lipid Accumulation in Green Algae1[OPEN

PubMed Central

2017-01-01

Microalgae are proposed as feedstock organisms useful for producing biofuels and coproducts. However, several limitations must be overcome before algae-based production is economically feasible. Among these is the ability to induce lipid accumulation and storage without affecting biomass yield. To overcome this barrier, a chemical genetics approach was employed in which 43,783 compounds were screened against Chlamydomonas reinhardtii, and 243 compounds were identified that increase triacylglyceride (TAG) accumulation without terminating growth. Identified compounds were classified by structural similarity, and 15 were selected for secondary analyses addressing impacts on growth fitness, photosynthetic pigments, and total cellular protein and starch concentrations. TAG accumulation was verified using gas chromatography-mass spectrometry quantification of total fatty acids, and targeted TAG and galactolipid measurements were performed using liquid chromatography-multiple reaction monitoring/mass spectrometry. These results demonstrated that TAG accumulation does not necessarily proceed at the expense of galactolipid. Untargeted metabolite profiling provided important insights into pathway shifts due to five different compound treatments and verified the anabolic state of the cells with regard to the oxidative pentose phosphate pathway, Calvin cycle, tricarboxylic acid cycle, and amino acid biosynthetic pathways. Metabolite patterns were distinct from nitrogen starvation and other abiotic stresses commonly used to induce oil accumulation in algae. The efficacy of these compounds also was demonstrated in three other algal species. These lipid-inducing compounds offer a valuable set of tools for delving into the biochemical mechanisms of lipid accumulation in algae and a direct means to improve algal oil content independent of the severe growth limitations associated with nutrient deprivation. PMID:28652262

Discovery of a Potent BTK Inhibitor with a Novel Binding Mode by Using Parallel Selections with a DNA-Encoded Chemical Library.

PubMed

Cuozzo, John W; Centrella, Paolo A; Gikunju, Diana; Habeshian, Sevan; Hupp, Christopher D; Keefe, Anthony D; Sigel, Eric A; Soutter, Holly H; Thomson, Heather A; Zhang, Ying; Clark, Matthew A

2017-05-04

We have identified and characterized novel potent inhibitors of Bruton's tyrosine kinase (BTK) from a single DNA-encoded library of over 110 million compounds by using multiple parallel selection conditions, including variation in target concentration and addition of known binders to provide competition information. Distinct binding profiles were observed by comparing enrichments of library building block combinations under these conditions; one enriched only at high concentrations of BTK and was competitive with ATP, and another enriched at both high and low concentrations of BTK and was not competitive with ATP. A compound representing the latter profile showed low nanomolar potency in biochemical and cellular BTK assays. Results from kinetic mechanism of action studies were consistent with the selection profiles. Analysis of the co-crystal structure of the most potent compound demonstrated a novel binding mode that revealed a new pocket in BTK. Our results demonstrate that profile-based selection strategies using DNA-encoded libraries form the basis of a new methodology to rapidly identify small molecule inhibitors with novel binding modes to clinically relevant targets. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Secondary Metabolites from Three Florida Sponges with Antidepressant Activity

PubMed Central

Kochanowska, Anna J.; Rao, Karumanchi V.; Childress, Suzanne; El-Alfy, Abir; Matsumoto, Rae R.; Kelly, Michelle; Stewart, Gina S.; Sufka, Kenneth J.; Hamann, Mark T.

2016-01-01

Brominated indole alkaloids are a common class of metabolites reported from sponges of the order Verongida. Herein we report the isolation, structure determination, and activity of metabolites from three Florida sponges, namely, Verongula rigida (order Verongida, family Aplysinidae), Smenospongia aurea, and S. cerebriformis (order Dictyoceratida, family Thorectidae). All three species were investigated chemically, revealing similarities in secondary metabolites. Brominated compounds, as well as sesquiterpene quinones and hydroquinones, were identified from both V. rigida and S. aurea despite their apparent taxonomic differences at the ordinal level. Similar metabolites found in these distinct sponge species of two different genera provide evidence for a microbial origin of the metabolites. Isolated compounds were evaluated in the Porsolt forced swim test (FST) and the chick anxiety–depression continuum model. Among the isolated compounds, 5,6-dibromo-N,N-dimethyltryptamine (1) exhibited significant antidepressant-like action in the rodent FST model, while 5-bromo-N,N-dimethyltryptamine (2) caused significant reduction of locomotor activity indicative of a potential sedative action. The current study provides ample evidence that marine natural products with the diversity of brominated marine alkaloids will provide potential leads for antidepressant and anxiolytic drugs. PMID:18217716

Conformationally-restricted bicarbazoles with phenylene bridges displaying deep-blue emission and high triplet energies: systematic structure-property relationships.

PubMed

Wright, Iain A; Al-Attar, Hameed A; Batsanov, Andrei S; Monkman, Andrew P; Bryce, Martin R

2018-05-07

The synthesis is reported of twelve new symmetrical carbazole dimers in which the carbazole units are linked via 1,4-phenylene spacers. There are two distinct series of compounds based on the position on the carbazole ring where the phenylene spacer is attached: this is either at carbazole C(3) (series 1a-1f) or at C(2) (series 2a-2f). The central phenylene ring is substituted with either two methyl, two methoxy or two cyano substituents which impart an intramolecular torsional angle between the phenylene and carbazole rings, thereby limiting the extent of π-conjugation between the carbazole units, and raising the triplet energies of the molecules to E T 2.6-3.0 eV, as determined from their phosphorescence spectra at 80 K. Structure-property relationships were studied by UV-vis and fluorescence spectroscopy, cyclic voltammetry and theoretical calculations. A notable observation is that substitution at the 2-position of carbazole (linear conjugation) exerts control over the position of the HOMO, while substitution at the 3-position of carbazole (meta conjugation) allows greater control over the LUMO. X-ray crystal structures are reported for two of the bicarbazoles. Compound 2d is shown to be a suitable host for the sky-blue emitter FIrpic in PhOLEDs, with improved device performance compared to CBP as host.

Structure-Activity Relationship and Pharmacokinetic Studies of 1,5-Diheteroarylpenta-1,4-dien-3-ones: A Class of Promising Curcumin-Based Anticancer Agents.

PubMed

Wang, Rubing; Chen, Chengsheng; Zhang, Xiaojie; Zhang, Changde; Zhong, Qiu; Chen, Guanglin; Zhang, Qiang; Zheng, Shilong; Wang, Guangdi; Chen, Qiao-Hong

2015-06-11

Forty-three 1,5-diheteroaryl-1,4-pentadien-3-ones were designed as potential curcumin mimics, structurally featuring a central five-carbon dienone linker and two identical nitrogen-containing aromatic rings. They were synthesized using a Horner-Wadsworth-Emmons reaction as the critical step and evaluated for their cytotoxicity and antiproliferative activities toward both androgen-insensitive and androgen-sensitive prostate cancer cell lines and an aggressive cervical cancer cell line. Most of the synthesized compounds showed distinctly better in vitro potency than curcumin in the four cancer cell lines. The structure-activity data acquired from the study validated (1E,4E)-1,5-dihereroaryl-1,4-pentadien-3-ones as an excellent scaffold for in-depth development for clinical treatment of prostate and cervical cancers. 1-Alkyl-1H-imidazol-2-yl, ortho pyridyl, 1-alkyl-1H-benzo[d]imidazole-2-yl, 4-bromo-1-methyl-1H-pyrazol-3-yl, thiazol-2-yl, and 2-methyl-4-(trifluoromethyl)thiazol-5-yl were identified as optimal heteroaromatic rings for the promising in vitro potency. (1E,4E)-1,5-Bis(2-methyl-4-(trifluoromethyl)thiazol-5-yl)penta-1,4-dien-3-one, featuring thiazole rings and trifluoromethyl groups, was established as the optimal lead compound because of its good in vitro potency and attractive in vivo pharmacokinetic profiles.

Topological phase diagram and saddle point singularity in a tunable topological crystalline insulator

DOE PAGES

Neupane, Madhab; Xu, Su-Yang; Sankar, R.; ...

2015-08-20

Here we report the evolution of the surface electronic structure and surface material properties of a topological crystalline insulator (TCI), Pb 1more » $${-}$$xSnxSe, as a function of various material parameters including composition x, temperature T , and crystal structure. Our spectroscopic data demonstrate the electronic ground-state condition for the saddle point singularity, the tunability of surface chemical potential, and the surface states’ response to circularly polarized light. Our results show that each material parameter can tune the system between the trivial and topological phase in a distinct way, unlike that seen in Bi 2Se 3 and related compounds, leading to a rich topological phase diagram. Our systematic studies of the TCI Pb 1$${-}$$xSnxSe are a valuable materials guide to realize new topological phenomena.« less

Fractionation of secondary metabolites of orange (Citrus sinensis L.) leaves by fast centrifugal partition chromatography

USDA-ARS?s Scientific Manuscript database

Conventional HPLC provides ready detection of the major phenolic compounds in methanol extracts of orange leaves, yet conventional HPLC also shows the presence of many more compounds, to an extent where extensive peak overlap prevents distinct peak detection and reliable quantitation. A more complet...

Electronegativity and the Bond Triangle

ERIC Educational Resources Information Center

Meek, Terry L.; Garner, Leah D.

2005-01-01

The usefulness of the bond triangle for categorizing compounds of the main-group elements may be extended by the use of weighted average electronegativities to allow distinction between compounds of the same elements with different stoichiometries. In such cases a higher valency for the central atom leads to greater covalent character and the…

Optimization of Aryl Amides that Extend Survival in Prion-Infected Mice.

PubMed

Giles, Kurt; Berry, David B; Condello, Carlo; Dugger, Brittany N; Li, Zhe; Oehler, Abby; Bhardwaj, Sumita; Elepano, Manuel; Guan, Shenheng; Silber, B Michael; Olson, Steven H; Prusiner, Stanley B

2016-09-01

Developing therapeutics for neurodegenerative diseases (NDs) prevalent in the aging population remains a daunting challenge. With the growing understanding that many NDs progress by conformational self-templating of specific proteins, the prototypical prion diseases offer a platform for ND drug discovery. We evaluated high-throughput screening hits with the aryl amide scaffold and explored the structure-activity relationships around three series differing in their N-aryl core: benzoxazole, benzothiazole, and cyano. Potent anti-prion compounds were advanced to pharmacokinetic studies, and the resulting brain-penetrant leads from each series, together with a related N-aryl piperazine lead, were escalated to long-term dosing and efficacy studies. Compounds from each of the four series doubled the survival of mice infected with a mouse-passaged prion strain. Treatment with aryl amides altered prion strain properties, as evidenced by the distinct patterns of neuropathological deposition of prion protein and associated astrocytic gliosis in the brain; however, none of the aryl amide compounds resulted in drug-resistant prion strains, in contrast to previous studies on compounds with the 2-aminothiazole (2-AMT) scaffold. As seen with 2-AMTs and other effective anti-prion compounds reported to date, the novel aryl amides reported here were ineffective in prolonging the survival of transgenic mice infected with human prions. Most encouraging is our discovery that aryl amides show that the development of drug resistance is not an inevitable consequence of efficacious anti-prion therapeutics. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.

Inhibition of protein synthesis and malaria parasite development by drug targeting of methionyl-tRNA synthetases.

PubMed

Hussain, Tahir; Yogavel, Manickam; Sharma, Amit

2015-04-01

Aminoacyl-tRNA synthetases (aaRSs) are housekeeping enzymes that couple cognate tRNAs with amino acids to transmit genomic information for protein translation. The Plasmodium falciparum nuclear genome encodes two P. falciparum methionyl-tRNA synthetases (PfMRS), termed PfMRS(cyt) and PfMRS(api). Phylogenetic analyses revealed that the two proteins are of primitive origin and are related to heterokonts (PfMRS(cyt)) or proteobacteria/primitive bacteria (PfMRS(api)). We show that PfMRS(cyt) localizes in parasite cytoplasm, while PfMRS(api) localizes to apicoplasts in asexual stages of malaria parasites. Two known bacterial MRS inhibitors, REP3123 and REP8839, hampered Plasmodium growth very effectively in the early and late stages of parasite development. Small-molecule drug-like libraries were screened against modeled PfMRS structures, and several "hit" compounds showed significant effects on parasite growth. We then tested the effects of the hit compounds on protein translation by labeling nascent proteins with (35)S-labeled cysteine and methionine. Three of the tested compounds reduced protein synthesis and also blocked parasite growth progression from the ring stage to the trophozoite stage. Drug docking studies suggested distinct modes of binding for the three compounds, compared with the enzyme product methionyl adenylate. Therefore, this study provides new targets (PfMRSs) and hit compounds that can be explored for development as antimalarial drugs. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Two-photon absorption spectra of carotenoids compounds

NASA Astrophysics Data System (ADS)

Vivas, Marcelo Gonçalves; Silva, Daniel Luiz; Boni, Leonardo de; Zalesny, Robert; Bartkowiak, Wojciech; Mendonca, Cleber Renato

2011-05-01

Carotenoids are biosynthetic organic pigments that constitute an important class of one-dimensional π-conjugated organic molecules with enormous potential for application in biophotonic devices. In this context, we studied the degenerate two-photon absorption (2PA) cross-section spectra of two carotenoid compounds (β-carotene and β-apo-8'-carotenal) employing the conventional and white-light-continuum Z-scan techniques and quantum chemistry calculations. Because carotenoids coexist at room temperature as a mixture of isomers, the 2PA spectra reported here are due to samples containing a distribution of isomers, presenting distinct conjugation length and conformation. We show that these compounds present a defined structure on the 2PA spectra, that peaks at 650 nm with an absorption cross-section of approximately 5000 GM, for both compounds. In addition, we observed a 2PA band at 990 nm for β-apo-8'-carotenal, which was attributed to a overlapping of 11Bu+-like and 21Ag--like states, which are strongly one- and two-photon allowed, respectively. Spectroscopic parameters of the electronic transitions to singlet-excited states, which are directly related to photophysical properties of these compounds, were obtained by fitting the 2PA spectra using the sum-over-states approach. The analysis and interpretations of the 2PA spectra of the investigated carotenoids were supported by theoretical predictions of one- and two-photon transitions carried out using the response functions formalism within the density functional theory framework, using the long-range corrected CAM-B3LYP functional.

Three new europium(III) methanetriacetate metal-organic frameworks: the influence of synthesis on the product topology.

PubMed

Cañadillas-Delgado, Laura; Fabelo, Oscar; Pasán, Jorge; Déniz, Mariadel; Martínez-Benito, Carla; Díaz-Gallifa, Pau; Martín, Tomás; Ruiz-Pérez, Catalina

2014-02-01

Three new metal-organic framework structures containing Eu(III) and the little explored methanetriacetate (C7H7O6(3-), mta(3-)) ligand have been synthesized. Gel synthesis yields a two-dimensional framework with the formula [Eu(mta)(H2O)3]n·2nH2O, (I), while two polymorphs of the three-dimensional framework material [Eu(mta)(H2O)]n·nH2O, (II) and (III), are obtained through hydrothermal synthesis at either 423 or 443 K. Compounds (I) and (II) are isomorphous with previously reported Gd(III) compounds, but compound (III) constitutes a new phase. Compound (I) can be described in terms of dinuclear [Eu2(H2O)4](6+) units bonded through mta(3-) ligands to form a two-dimensional framework with topology corresponding to a (6,3)-connected binodal (4(3))(4(6)6(6)8(3))-kgd net, where the dinuclear [Eu2(H2O)4](6+) units are considered as a single node. Compounds (II) and (III) have distinct three-dimensional topologies, namely a (4(12)6(3))(4(9)6(6))-nia net for (II) and a (4(10)6(5))(4(11)6(4))-K2O2; 36641 net for (III). The crystal density of (III) is greater than that of (II), consistent with the increase of temperature, and thereby autogeneous pressure, in the hydrothermal synthesis.

Comparative analysis of native and permethylated human milk oligosaccharides by liquid chromatography coupled to high resolution mass spectrometry.

PubMed

Oursel, Stéphanie; Cholet, Sophie; Junot, Christophe; Fenaille, François

2017-12-15

Human milk oligosaccharides (HMOs) represent the third most abundant components of milk after lactose and lipids. HMOs are indigestible by the suckling infant but can act as prebiotics and have significant biological functions regarding the organism defense against pathogens (such as bacteria or viruses) by preventing interactions with their receptors. Although constituted of only five distinct monosaccharide building blocks, HMOs are highly structurally diverse compounds with many co-existing structural isomers. Here we report the development and comparison of two distinct glycomic platforms based on liquid chromatography coupled to high resolution mass spectrometry (LC-MS) for analyzing HMOs. We have implemented and thoroughly compared the LC-MS of permethylated and native HMOs on reversed phase (RP) and porous graphitic carbon (PGC) columns for their ability to resolve the natural heterogeneity of milk oligosaccharides at the highest sensitivity. Our data essentially underlines the usefulness of analyzing HMOs as permethylated derivatives especially for getting more precise structural information at high sensitivity. For instance, permethylation annihilates gas-phase fucose migration during MS/MS experiments, thus facilitating spectra interpretation and giving access to relevant information regarding oligosaccharide branching and isomer distinction. At the opposite, LC-MS profiling of native HMOs (using PGC) in milk performed best in terms of detected species, while also being much faster in terms of sample preparation. Although less efficient than PGC chromatography, RPLC proved successful for separating pairs of permethylated isomeric HMOs. A key advantage of RP over PGC liquid chromatography is that retention times can be correlated to molecular weights, which can greatly facilitate further HMO identification using retention time prediction. Altogether these data lead us to think that LC-MS analysis of native HMOs (using PGC) can be used as first-line profiling approach while permethylation can be performed afterwards for facilitating structural characterization. Copyright © 2017 Elsevier B.V. All rights reserved.

Extensive structural change of the envelope protein of dengue virus induced by a tuned ionic strength: conformational and energetic analyses

NASA Astrophysics Data System (ADS)

Degrève, Léo; Fuzo, Carlos A.; Caliri, Antonio

2012-12-01

The Dengue has become a global public health threat, with over 100 million infections annually; to date there is no specific vaccine or any antiviral drug. The structures of the envelope (E) proteins of the four known serotype of the dengue virus (DENV) are already known, but there are insufficient molecular details of their structural behavior in solution in the distinct environmental conditions in which the DENVs are submitted, from the digestive tract of the mosquito up to its replication inside the host cell. Such detailed knowledge becomes important because of the multifunctional character of the E protein: it mediates the early events in cell entry, via receptor endocytosis and, as a class II protein, participates determinately in the process of membrane fusion. The proposed infection mechanism asserts that once in the endosome, at low pH, the E homodimers dissociate and insert into the endosomal lipid membrane, after an extensive conformational change, mainly on the relative arrangement of its three domains. In this work we employ all-atom explicit solvent Molecular Dynamics simulations to specify the thermodynamic conditions in that the E proteins are induced to experience extensive structural changes, such as during the process of reducing pH. We study the structural behavior of the E protein monomer at acid pH solution of distinct ionic strength. Extensive simulations are carried out with all the histidine residues in its full protonated form at four distinct ionic strengths. The results are analyzed in detail from structural and energetic perspectives, and the virtual protein movements are described by means of the principal component analyses. As the main result, we found that at acid pH and physiological ionic strength, the E protein suffers a major structural change; for lower or higher ionic strengths, the crystal structure is essentially maintained along of all extensive simulations. On the other hand, at basic pH, when all histidine residues are in the unprotonated form, the protein structure is very stable for ionic strengths ranging from 0 to 225 mM. Therefore, our findings support the hypothesis that the histidines constitute the hot points that induce configurational changes of E protein in acid pH, and give extra motivation to the development of new ideas for antivirus compound design.

How to Achieve Better Results Using Pass-Based Virtual Screening: Case Study for Kinase Inhibitors

NASA Astrophysics Data System (ADS)

Pogodin, Pavel V.; Lagunin, Alexey A.; Rudik, Anastasia V.; Filimonov, Dmitry A.; Druzhilovskiy, Dmitry S.; Nicklaus, Mark C.; Poroikov, Vladimir V.

2018-04-01

Discovery of new pharmaceutical substances is currently boosted by the possibility of utilization of the Synthetically Accessible Virtual Inventory (SAVI) library, which includes about 283 million molecules, each annotated with a proposed synthetic one-step route from commercially available starting materials. The SAVI database is well-suited for ligand-based methods of virtual screening to select molecules for experimental testing. In this study, we compare the performance of three approaches for the analysis of structure-activity relationships that differ in their criteria for selecting of “active” and “inactive” compounds included in the training sets. PASS (Prediction of Activity Spectra for Substances), which is based on a modified Naïve Bayes algorithm, was applied since it had been shown to be robust and to provide good predictions of many biological activities based on just the structural formula of a compound even if the information in the training set is incomplete. We used different subsets of kinase inhibitors for this case study because many data are currently available on this important class of drug-like molecules. Based on the subsets of kinase inhibitors extracted from the ChEMBL 20 database we performed the PASS training, and then applied the model to ChEMBL 23 compounds not yet present in ChEMBL 20 to identify novel kinase inhibitors. As one may expect, the best prediction accuracy was obtained if only the experimentally confirmed active and inactive compounds for distinct kinases in the training procedure were used. However, for some kinases, reasonable results were obtained even if we used merged training sets, in which we designated as inactives the compounds not tested against the particular kinase. Thus, depending on the availability of data for a particular biological activity, one may choose the first or the second approach for creating ligand-based computational tools to achieve the best possible results in virtual screening.

Structure-Based Virtual Screening and Biochemical Evaluation for the Identification of Novel Trypanosoma Brucei Aldolase Inhibitors.

PubMed

Ferreira, Leonardo L G; Ferreira, Rafaela S; Palomino, David L; Andricopulo, Adriano D

2018-04-27

The glycolytic enzyme fructose-1,6-bisphosphate aldolase is a validated molecular target in human African trypanosomiasis (HAT) drug discovery, a neglected tropical disease (NTD) caused by the protozoan Trypanosoma brucei. Herein, a structure-based virtual screening (SBVS) approach to the identification of novel T. brucei aldolase inhibitors is described. Distinct molecular docking algorithms were used to screen more than 500,000 compounds against the X-ray structure of the enzyme. This SBVS strategy led to the selection of a series of molecules which were evaluated for their activity on recombinant T. brucei aldolase. The effort led to the discovery of structurally new ligands able to inhibit the catalytic activity the enzyme. The predicted binding conformations were additionally investigated in molecular dynamics simulations, which provided useful insights into the enzyme-inhibitor intermolecular interactions. The molecular modeling results along with the enzyme inhibition data generated practical knowledge to be explored in further structure-based drug design efforts in HAT drug discovery. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Insights into Cullin-RING E3 ubiquitin ligase recruitment: structure of the VHL-EloBC-Cul2 complex.

PubMed

Nguyen, Henry C; Yang, Haitao; Fribourgh, Jennifer L; Wolfe, Leslie S; Xiong, Yong

2015-03-03

The von Hippel-Lindau tumor suppressor protein (VHL) recruits a Cullin 2 (Cul2) E3 ubiquitin ligase to downregulate HIF-1α, an essential transcription factor for the hypoxia response. Mutations in VHL lead to VHL disease and renal cell carcinomas. Inhibition of this pathway to upregulate erythropoietin production is a promising new therapy to treat ischemia and chronic anemia. Here, we report the crystal structure of VHL bound to a Cul2 N-terminal domain, Elongin B, and Elongin C (EloC). Cul2 interacts with both the VHL BC box and cullin box and a novel EloC site. Comparison with other cullin E3 ligase structures shows that there is a conserved, yet flexible, cullin recognition module and that cullin selectivity is influenced by distinct electrostatic interactions. Our structure provides a structural basis for the study of the pathogenesis of VHL disease and rationale for the design of novel compounds that may modulate cullin-substrate receptor interactions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structuralism, Post-Structuralism, and Neo-Liberalism: Assessing Foucault's Legacy.

ERIC Educational Resources Information Center

Olssen, Mark

2003-01-01

Traces Foucault's distinctive commitment to "post-structuralism." Argues that under the influence of Nietzsche, Foucault's approach marks a distinct break with structuralism in several crucial aspects. What results is a materialist post-structuralism that is also distinctively different from the post-structuralism of Derrida, Lyotard,…

Bio-prospecting of soil Streptomyces and its bioassay-guided isolation of microbial derived auxin with antifungal properties.

PubMed

Saravana Kumar, P; Yuvaraj, P; Gabrial Paulraj, M; Ignacimuthu, S; Abdullah Al-Dhabi, N

2018-06-05

The present study was aimed to isolate bioactive actinomycetes with antifungal properties. Twenty-seven distinct soil derived actinomycetes were investigated for their antifungal activities. Among these, one isolate exhibited significant antifungal activity. Phenotypic and 16s rRNA gene sequence analysis strongly suggested that the active isolate BG4 belonged to the genus Streptomyces. Further, the chemical investigation of the active extract resulted in the isolation of a major compound and it was structurally elucidated as phenyl acetic acid (PAA). PAA exhibited promising antifungal activity with 100% inhibition, ranging from 31.25 to 25μg/mL. It is to be noted that PAA is naturally occurring and biologically active auxin. In addition, it has also been hypothesized that phytohormone endorsing the source of soil-symbionts has similar pathways for synthesizing compounds and its congeners of host due to horizontal gene transfer. These findings demonstrate that microbially derived phytohormone can be used to treat fungal infections. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

A new glucosidic phthalide from Helichrysum microphyllum subsp. tyrrhenicum from La Maddalena Island (Sardinia, Italy).

PubMed

Venditti, Alessandro; Lattanzi, Claudia; Ornano, Luigi; Maggi, Filippo; Sanna, Cinzia; Ballero, Mauro; Alvino, Antonello; Serafini, Mauro; Bianco, Armandodoriano

2016-01-01

In this study, we reported the analysis of the medium polarity fraction obtained from an accession of Helichrysum microphyllum subsp. tyrrhenicum from La Maddalena Island. Besides several compounds already evidenced in this species and related genera, i.e. micropyrone (1), arzanol (2), helipyrone (3), acetyl-bitalin derivatives (4, 5), gnaphaliol (6), caffeic acid (7), ursolic acid (8), 7-O-β-(D-glucopyranosyl)-5-methoxy-1(3H)-isobenzofuranone (9), gnaphaliol-9-O-β-D-glucopyranoside (11) and gnaphaliol-3-O-β-D-glucopyranoside (12), the presence of a new glycosidic phthalide, 6-O-β-(D-glucopyranosyl)-4-methoxy-1(3H)-benzofuranone (10), was evidenced for the first time, which resulted in a structural isomer of compound (9). The occurrence of this new benzofuranone derivative is an additional evidence of the deep intraspecific variability expressed by this species, which was also stated for the non-volatile components, and may be a distinctive trait of the population growing on La Maddalena Island.

Comparative study of perovskite-type scintillator materials CsCaI3 and KCaI3 via first-principles calculations

NASA Astrophysics Data System (ADS)

Kang, Byungkyun; Feng, Qingguo; Biswas, Koushik

2018-02-01

Several members of a large family of perovskite-like halides with a common chemical formula, ABX3 (A  =  monovalent, B  =  divalent, and X  =  halogen ion), are being investigated for their interesting properties and potential technological applications. CsCaI3 and KCaI3 are two such ionic compounds who are of interest in the quest for superior and cost-effective alternatives to NaI or CsI based scintillators. They are the subject of this first-principles based computational study. Both are wide-gap materials having primarily I 5p and Ca 3d characters near the valence and conduction band edges, respectively. Although built from [CaI6] octahedral motifs, structural differences between the two compounds is reflected in anisotropic electron effective mass and distinctive formation and migration of self-trapped holes. We discuss these properties as they relate to scintillation decay and proportional light yield.

Diffuse Scattering as an Aid to the Understanding of Polymorphism in Pharmaceuticals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Welberry, T.R.; Chan, E.J.; Goossens, D.J.

Polymorphism occurs when the same molecular compound can crystallize in more than one distinct crystal structure. Its study is a field of great interest and activity. This is largely driven by its importance in the pharmaceutical industry, but polymorphism is also an issue in the pigments, dyes, and explosives industries. The polymorph formed by a compound generally exerts a strong influence on its solid-state properties. The polymorphic form of a drug molecule may affect the ease of manufacture and processing, shelf life, and most significantly the rate of uptake of the molecule by the human body. They can even varymore » in toxicity; one polymorph may be safe, while a second may be toxic. In this review of recently published work, we show how diffuse scattering experiments coupled with Monte Carlo (MC) computer modeling can aid in the understanding of polymorphism. Examples of the two common pharmaceuticals, benzocaine and aspirin, both of which are bimorphic, at ambient temperatures, are discussed.« less

Diffuse Scattering as an Aid to the Understanding of Polymorphism in Pharmaceuticals

NASA Astrophysics Data System (ADS)

Welberry, T. R.; Chan, E. J.; Goossens, D. J.; Heerdegen, A. P.

2012-05-01

Polymorphism occurs when the same molecular compound can crystallize in more than one distinct crystal structure. Its study is a field of great interest and activity. This is largely driven by its importance in the pharmaceutical industry, but polymorphism is also an issue in the pigments, dyes, and explosives industries. The polymorph formed by a compound generally exerts a strong influence on its solid-state properties. The polymorphic form of a drug molecule may affect the ease of manufacture and processing, shelf life, and most significantly the rate of uptake of the molecule by the human body. They can even vary in toxicity; one polymorph may be safe, while a second may be toxic. In this review of recently published work, we show how diffuse scattering experiments coupled with Monte Carlo (MC) computer modeling can aid in the understanding of polymorphism. Examples of the two common pharmaceuticals, benzocaine and aspirin, both of which are bimorphic, at ambient temperatures, are discussed.

Chemical assessment and in vitro antioxidant capacity of Ficus carica latex.

PubMed

Oliveira, Andreia P; Silva, Luís R; Ferreres, Federico; Guedes de Pinho, Paula; Valentão, Patrícia; Silva, Branca M; Pereira, José A; Andrade, Paula B

2010-03-24

Ficus species possess latex-like material within their vasculatures, affording protection and self-healing from physical attacks. In this work, metabolite profiling was performed on Ficus carica latex. Volatiles profile was determined by HS-SPME/GC-IT-MS, with 34 compounds being identified, distributed by distinct chemical classes: 5 aldehydes, 7 alcohols, 1 ketone, 9 monoterpenes, 9 sesquiterpenes and 3 other compounds. Sesquiterpenes constituted the most abundant class in latex (ca. 91% of total identified compounds). Organic acids composition was also characterized, by HPLC-UV, and oxalic, citric, malic, quinic, shikimic and fumaric acids were determined. Malic and shikimic acids were present in higher amounts (ca. 26%, each). The antioxidant potential of this material was checked by distinct in vitro chemical assays. A concentration-dependent activity was noticed against DPPH, nitric oxide and superoxide radicals. Additionally, acetylcholinesterase inhibitory capacity was evaluated, but a weak effect was found.

Caenorhabditis elegans as Model System in Pharmacology and Toxicology: Effects of Flavonoids on Redox-Sensitive Signalling Pathways and Ageing

PubMed Central

Koch, Karoline; Havermann, Susannah; Büchter, Christian

2014-01-01

Flavonoids are secondary plant compounds that mediate diverse biological activities, for example, by scavenging free radicals and modulating intracellular signalling pathways. It has been shown in various studies that distinct flavonoid compounds enhance stress resistance and even prolong the life span of organisms. In the last years the model organism C. elegans has gained increasing importance in pharmacological and toxicological sciences due to the availability of various genetically modified nematode strains, the simplicity of modulating genes by RNAi, and the relatively short life span. Several studies have been performed demonstrating that secondary plant compounds influence ageing, stress resistance, and distinct signalling pathways in the nematode. Here we present an overview of the modulating effects of different flavonoids on oxidative stress, redox-sensitive signalling pathways, and life span in C. elegans introducing the usability of this model system for pharmacological and toxicological research. PMID:24895670

Identification and Optimization of Classifier Genes from Multi-Class Earthworm Microarray Dataset

DTIC Science & Technology

2010-10-28

rapid and accurate diagnostic assays. A variety of toxicological effects have been associated with explosive compounds TNT and RDX. One important goal of...analyze toxicological mechanisms for two military- unique explosive compounds 2,4,6-trinitrotolune (TNT) and 1,3,5- trinitro-1,3,5-triazacyclohexane...also known as Royal Demolition eXplosive or RDX) [7,8]. These two compounds exhibit distinctive toxicological properties that are accompanied by

Organic matter in extraterrestrial water-bearing salt crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chan, Queenie H. S.; Zolensky, Michael E.; Kebukawa, Yoko

Direct evidence of complex prebiotic chemistry from a water-rich world in the outer solar system is provided by the 4.5-billion-year-old halite crystals hosted in the Zag and Monahans (1998) meteorites. This study offers the first comprehensive organic analysis of the soluble and insoluble organic compounds found in the millimeter-sized halite crystals containing brine inclusions and sheds light on the nature and activity of aqueous fluids on a primitive parent body. Associated with these trapped brines are organic compounds exhibiting wide chemical variations representing organic precursors, intermediates, and reaction products that make up life’s precursor molecules such as amino acids. Themore » organic compounds also contain a mixture of C-, O-, and N-bearing macromolecular carbon materials exhibiting a wide range of structural order, as well as aromatic, ketone, imine, and/or imidazole compounds. The enrichment in 15N is comparable to the organic matter in pristine Renazzo-type carbonaceous chondrites, which reflects the sources of interstellar 15N, such as ammonia and amino acids. The amino acid content of the Zag halite deviates from the meteorite matrix, supporting an exogenic origin of the halite, and therefore, the Zag meteorite contains organics synthesized on two distinct parent bodies. Lastly, our study suggests that the asteroidal parent body where the halite precipitated, potentially asteroid 1 Ceres, shows evidence for a complex combination of biologically and prebiologically relevant molecules.« less

Flavonoids from acai (Euterpe oleracea Mart.) pulp and their antioxidant and anti-inflammatory activities.

PubMed

Kang, Jie; Xie, Chenghui; Li, Zhimin; Nagarajan, Shanmugam; Schauss, Alexander G; Wu, Tong; Wu, Xianli

2011-09-01

Five flavonoids, (2S,3S)-dihyrokaempferol 3-O-β-d-glucoside (1) and its isomer (2R,3R)-dihydrokaempferol 3-O-β-d-glucoside (2) , isovitexin (3), velutin (4) and 5,4'-dihydroxy-7,3',5'-trimethoxyflavone (5), were isolated from acai (Euterpe oleracea Mart.) pulp. The structures of these compounds were elucidated based upon spectroscopic and chemical analyses. To our knowledge, compounds 1, 2, 4 and 5 were identified from acai pulp for the first time. The in vitro antioxidant activities of these compounds were evaluated by the oxygen radial absorbance capacity (ORAC) assay. The ORAC values varied distinctly (4458.0-22404.5μmol Trolox equivalent (TE)/g) from 5,4'-dihydroxy-7,3',5'-trimethoxyflavone (5) to isovitexin (3) and were affected by the numbers/positions of hydroxyl groups, substitute groups, as well as stereo configuration. The anti-inflammatory effects of these compounds were screened by the secreted embryonic alkaline phosphatase (SEAP) reporter assay, which is designed to measure NF-κB activation. Velutin (4) was found to dose-dependently inhibit SEAP secretion in RAW-blue cells induced by LPS, with an IC50 value of 2.0μM. Velutin (4) also inhibited SEAP secretion induced by oxidised LDL, indicating potential athero-protective effects. Copyright © 2011 Elsevier Ltd. All rights reserved.

Organic matter in extraterrestrial water-bearing salt crystals

PubMed Central

Chan, Queenie H. S.; Zolensky, Michael E.; Kebukawa, Yoko; Fries, Marc; Ito, Motoo; Steele, Andrew; Rahman, Zia; Nakato, Aiko; Kilcoyne, A. L. David; Suga, Hiroki; Takahashi, Yoshio; Takeichi, Yasuo; Mase, Kazuhiko

2018-01-01

Direct evidence of complex prebiotic chemistry from a water-rich world in the outer solar system is provided by the 4.5-billion-year-old halite crystals hosted in the Zag and Monahans (1998) meteorites. This study offers the first comprehensive organic analysis of the soluble and insoluble organic compounds found in the millimeter-sized halite crystals containing brine inclusions and sheds light on the nature and activity of aqueous fluids on a primitive parent body. Associated with these trapped brines are organic compounds exhibiting wide chemical variations representing organic precursors, intermediates, and reaction products that make up life’s precursor molecules such as amino acids. The organic compounds also contain a mixture of C-, O-, and N-bearing macromolecular carbon materials exhibiting a wide range of structural order, as well as aromatic, ketone, imine, and/or imidazole compounds. The enrichment in 15N is comparable to the organic matter in pristine Renazzo-type carbonaceous chondrites, which reflects the sources of interstellar 15N, such as ammonia and amino acids. The amino acid content of the Zag halite deviates from the meteorite matrix, supporting an exogenic origin of the halite, and therefore, the Zag meteorite contains organics synthesized on two distinct parent bodies. Our study suggests that the asteroidal parent body where the halite precipitated, potentially asteroid 1 Ceres, shows evidence for a complex combination of biologically and prebiologically relevant molecules. PMID:29349297

Organic matter in extraterrestrial water-bearing salt crystals

DOE PAGES

Chan, Queenie H. S.; Zolensky, Michael E.; Kebukawa, Yoko; ...

2018-01-10

Direct evidence of complex prebiotic chemistry from a water-rich world in the outer solar system is provided by the 4.5-billion-year-old halite crystals hosted in the Zag and Monahans (1998) meteorites. This study offers the first comprehensive organic analysis of the soluble and insoluble organic compounds found in the millimeter-sized halite crystals containing brine inclusions and sheds light on the nature and activity of aqueous fluids on a primitive parent body. Associated with these trapped brines are organic compounds exhibiting wide chemical variations representing organic precursors, intermediates, and reaction products that make up life’s precursor molecules such as amino acids. Themore » organic compounds also contain a mixture of C-, O-, and N-bearing macromolecular carbon materials exhibiting a wide range of structural order, as well as aromatic, ketone, imine, and/or imidazole compounds. The enrichment in 15N is comparable to the organic matter in pristine Renazzo-type carbonaceous chondrites, which reflects the sources of interstellar 15N, such as ammonia and amino acids. The amino acid content of the Zag halite deviates from the meteorite matrix, supporting an exogenic origin of the halite, and therefore, the Zag meteorite contains organics synthesized on two distinct parent bodies. Lastly, our study suggests that the asteroidal parent body where the halite precipitated, potentially asteroid 1 Ceres, shows evidence for a complex combination of biologically and prebiologically relevant molecules.« less

Organic matter in extraterrestrial water-bearing salt crystals.

PubMed

Chan, Queenie H S; Zolensky, Michael E; Kebukawa, Yoko; Fries, Marc; Ito, Motoo; Steele, Andrew; Rahman, Zia; Nakato, Aiko; Kilcoyne, A L David; Suga, Hiroki; Takahashi, Yoshio; Takeichi, Yasuo; Mase, Kazuhiko

2018-01-01

Direct evidence of complex prebiotic chemistry from a water-rich world in the outer solar system is provided by the 4.5-billion-year-old halite crystals hosted in the Zag and Monahans (1998) meteorites. This study offers the first comprehensive organic analysis of the soluble and insoluble organic compounds found in the millimeter-sized halite crystals containing brine inclusions and sheds light on the nature and activity of aqueous fluids on a primitive parent body. Associated with these trapped brines are organic compounds exhibiting wide chemical variations representing organic precursors, intermediates, and reaction products that make up life's precursor molecules such as amino acids. The organic compounds also contain a mixture of C-, O-, and N-bearing macromolecular carbon materials exhibiting a wide range of structural order, as well as aromatic, ketone, imine, and/or imidazole compounds. The enrichment in 15 N is comparable to the organic matter in pristine Renazzo-type carbonaceous chondrites, which reflects the sources of interstellar 15 N, such as ammonia and amino acids. The amino acid content of the Zag halite deviates from the meteorite matrix, supporting an exogenic origin of the halite, and therefore, the Zag meteorite contains organics synthesized on two distinct parent bodies. Our study suggests that the asteroidal parent body where the halite precipitated, potentially asteroid 1 Ceres, shows evidence for a complex combination of biologically and prebiologically relevant molecules.

Halogen bonds in some dihalogenated phenols: applications to crystal engineering.

PubMed

Mukherjee, Arijit; Desiraju, Gautam R

2014-01-01

3,4-Dichlorophenol (1) crystallizes in the tetragonal space group I41/a with a short axis of 3.7926 (9) Å. The structure is unique in that both type I and type II Cl⋯Cl interactions are present, these contact types being distinguished by the angle ranges of the respective C-Cl⋯Cl angles. The present study shows that these two types of contacts are utterly different. The crystal structures of 4-bromo-3-chlorophenol (2) and 3-bromo-4-chlorophenol (3) have been determined. The crystal structure of (2) is isomorphous to that of (1) with the Br atom in the 4-position participating in a type II interaction. However, the monoclinic P21/c packing of compound (3) is different; while the structure still has O-H⋯O hydrogen bonds, the tetramer O-H⋯O synthon seen in (1) and (2) is not seen. Rather than a type I Br⋯Br interaction which would have been mandated if (3) were isomorphous to (1) and (2), Br forms a Br⋯O contact wherein its electrophilic character is clearly evident. Crystal structures of the related compounds 4-chloro-3-iodophenol (4) and 3,5-dibromophenol (5) were also determined. A computational survey of the structural landscape was undertaken for (1), (2) and (3), using a crystal structure prediction protocol in space groups P21/c and I41/a with the COMPASS26 force field. While both tetragonal and monoclinic structures are energetically reasonable for all compounds, the fact that (3) takes the latter structure indicates that Br prefers type II over type I contacts. In order to differentiate further between type I and type II halogen contacts, which being chemically distinct are expected to have different distance fall-off properties, a variable-temperature crystallography study was performed on compounds (1), (2) and (4). Length variations with temperature are greater for type II contacts compared with type I. The type II Br⋯Br interaction in (2) is stronger than the corresponding type II Cl⋯Cl interaction in (1), leading to elastic bending of the former upon application of mechanical stress, which contrasts with the plastic deformation of (1). The observation of elastic deformation in (2) is noteworthy; in that it finds an explanation based on the strengths of the respective halogen bonds, it could also be taken as a good starting model for future property design. Cl/Br isostructurality is studied with the Cambridge Structural Database and it is indicated that this isostructurality is based on shape and size similarity of Cl and Br, rather than arising from any chemical resemblance.

Using C. elegans Forward and Reverse Genetics to Identify New Compounds with Anthelmintic Activity

PubMed Central

Mathew, Mark D.; Mathew, Neal D.; Miller, Angela; Simpson, Mike; Au, Vinci; Garland, Stephanie; Gestin, Marie; Edgley, Mark L.; Flibotte, Stephane; Balgi, Aruna; Chiang, Jennifer; Giaever, Guri; Dean, Pamela; Tung, Audrey; Roberge, Michel; Roskelley, Calvin; Forge, Tom; Nislow, Corey; Moerman, Donald

2016-01-01

Background The lack of new anthelmintic agents is of growing concern because it affects human health and our food supply, as both livestock and plants are affected. Two principal factors contribute to this problem. First, nematode resistance to anthelmintic drugs is increasing worldwide and second, many effective nematicides pose environmental hazards. In this paper we address this problem by deploying a high throughput screening platform for anthelmintic drug discovery using the nematode Caenorhabditis elegans as a surrogate for infectious nematodes. This method offers the possibility of identifying new anthelmintics in a cost-effective and timely manner. Methods/Principal findings Using our high throughput screening platform we have identified 14 new potential anthelmintics by screening more than 26,000 compounds from the Chembridge and Maybridge chemical libraries. Using phylogenetic profiling we identified a subset of the 14 compounds as potential anthelmintics based on the relative sensitivity of C. elegans when compared to yeast and mammalian cells in culture. We showed that a subset of these compounds might employ mechanisms distinct from currently used anthelmintics by testing diverse drug resistant strains of C. elegans. One of these newly identified compounds targets mitochondrial complex II, and we used structural analysis of the target to suggest how differential binding of this compound may account for its different effects in nematodes versus mammalian cells. Conclusions/Significance The challenge of anthelmintic drug discovery is exacerbated by several factors; including, 1) the biochemical similarity between host and parasite genomes, 2) the geographic location of parasitic nematodes and 3) the rapid development of resistance. Accordingly, an approach that can screen large compound collections rapidly is required. C. elegans as a surrogate parasite offers the ability to screen compounds rapidly and, equally importantly, with specificity, thus reducing the potential toxicity of these compounds to the host and the environment. We believe this approach will help to replenish the pipeline of potential nematicides. PMID:27755544

Isotopic and molecular distributions of biochemicals from fresh and buried Rhizophora mangle leaves†

PubMed Central

Smallwood, Barbara J; Wooller, Matthew J; Jacobson, Myrna E; Fogel, Marilyn L

2003-01-01

Rhizophora mangle L. (red mangrove) is the dominant species of mangrove in the Americas. At Twin Cays, Belize (BZ) red mangroves are present in a variety of stand structures (tall >5 m in height, transition ~2–4 m and dwarf ~1–1.5 m). These height differences are coupled with very different stable carbon and nitrogen isotopic values[1] (mean tall δ13C = -28.3‰, δ15N = 0‰; mean tall δ13C = -25.3‰, δ15N = -10‰). To determine the utility of using these distinct isotopic compositions as 'biomarkers' for paleoenvironmental reconstruction of mangrove ecosystems and nutrient availability, we investigated the distribution and isotopic (δ13C and δ15N) composition of different biochemical fractions (water soluble compounds, free lipids, acid hydrolysable compounds, individual amino acids, and the residual un-extractable compounds) in fresh and preserved red mangrove leaves from dwarf and tall trees. The distribution of biochemicals are similar in dwarf and tall red mangrove leaves, suggesting that, regardless of stand structure, red mangroves use nutrients for biosynthesis and metabolism in a similar manner. However, the δ13C and δ15N of the bulk leaf, the biochemical fractions, and seven amino acids can be used to distinguish dwarf and tall trees at Twin Cays, BZ. The data support the theory that the fractionation of carbon and nitrogen occurs prior to or during uptake in dwarf and tall red mangrove trees. Stable carbon and nitrogen isotopes could, therefore, be powerful tools for predicting levels of nutrient limitation at Twin Cays. The δ13C and δ15N of biochemical fractions within preserved leaves, reflect sedimentary cycling and nitrogen immobilization. The δ15N of the immobilized fraction reveals the overlying stand structure at the time of leaf deposition. The isotopic composition of preserved mangrove leaves could yield significant information about changes in ecosystem dynamics, nutrient limitation and past stand structure in mangrove paleoecosystems.

Structure-based Design and In-Parallel Synthesis of Inhibitors of AmpC b-lactamase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tondi, D.; Powers, R.A.; Negri, M.C.

2010-03-08

Group I {beta}-lactamases are a major cause of antibiotic resistance to {beta}-lactams such as penicillins and cephalosporins. These enzymes are only modestly affected by classic {beta}-lactam-based inhibitors, such as clavulanic acid. Conversely, small arylboronic acids inhibit these enzymes at sub-micromolar concentrations. Structural studies suggest these inhibitors bind to a well-defined cleft in the group I {beta}-lactamase AmpC; this cleft binds the ubiquitous R1 side chain of {beta}-lactams. Intriguingly, much of this cleft is left unoccupied by the small arylboronic acids. To investigate if larger boronic acids might take advantage of this cleft, structure-guided in-parallel synthesis was used to explore newmore » inhibitors of AmpC. Twenty-eight derivatives of the lead compound, 3-aminophenylboronic acid, led to an inhibitor with 80-fold better binding (2; K{sub i} 83 nM). Molecular docking suggested orientations for this compound in the R1 cleft. Based on the docking results, 12 derivatives of 2 were synthesized, leading to inhibitors with K{sub i} values of 60 nM and with improved solubility. Several of these inhibitors reversed the resistance of nosocomial Gram-positive bacteria, though they showed little activity against Gram-negative bacteria. The X-ray crystal structure of compound 2 in complex with AmpC was subsequently determined to 2.1 {angstrom} resolution. The placement of the proximal two-thirds of the inhibitor in the experimental structure corresponds with the docked structure, but a bond rotation leads to a distinctly different placement of the distal part of the inhibitor. In the experimental structure, the inhibitor interacts with conserved residues in the R1 cleft whose role in recognition has not been previously explored. Combining structure-based design with in-parallel synthesis allowed for the rapid exploration of inhibitor functionality in the R1 cleft of AmpC. The resulting inhibitors differ considerably from {beta}-lactams but nevertheless inhibit the enzyme well. The crystal structure of 2 (K{sub i} 83 nM) in complex with AmpC may guide exploration of a highly conserved, largely unexplored cleft, providing a template for further design against AmpC {beta}-lactamase.« less

Harnessing Insect-Microbe Chemical Communications To Control Insect Pests of Agricultural Systems.

PubMed

Beck, John J; Vannette, Rachel L

2017-01-11

Insect pests cause serious economic, yield, and food safety problems to managed crops worldwide. Compounding these problems, insect pests often vector pathogenic or toxigenic microbes to plants. Previous work has considered plant-insect and plant-microbe interactions separately. Although insects are well-understood to use plant volatiles to locate hosts, microorganisms can produce distinct and abundant volatile compounds that in some cases strongly attract insects. In this paper, we focus on the microbial contribution to plant volatile blends, highlighting the compounds emitted and the potential for variation in microbial emission. We suggest that these aspects of microbial volatile emission may make these compounds ideal for use in agricultural applications, as they may be more specific or enhance methods currently used in insect control or monitoring. Our survey of microbial volatiles in insect-plant interactions suggests that these emissions not only signal host suitability but may indicate a distinctive time frame for optimal conditions for both insect and microbe. Exploitation of these host-specific microbe semiochemicals may provide important microbe- and host-based attractants and a basis for future plant-insect-microbe chemical ecology investigations.

Early-Time Excited-State Relaxation Dynamics of Iridium Compounds: Distinct Roles of Electron and Hole Transfer.

PubMed

Liu, Xiang-Yang; Zhang, Ya-Hui; Fang, Wei-Hai; Cui, Ganglong

2018-06-28

Excited-state and photophysical properties of Ir-containing complexes have been extensively studied because of their potential applications as organic light-emitting diode emitting materials. However, their early time excited-state relaxation dynamics are less explored computationally. Herein we have employed our recently implemented TDDFT-based generalized surface-hopping dynamics method to simulate excited-state relaxation dynamics of three Ir(III) compounds having distinct ligands. According to our multistate dynamics simulations including five excited singlet states i.e., S n ( n = 1-5) and ten excited triplet states, i.e., T n ( n = 1-10), we have found that the intersystem crossing (ISC) processes from the S n to T n are very efficient and ultrafast in these three Ir(III) compounds. The corresponding ISC rates are estimated to be 65, 81, and 140 fs, which are reasonably close to the experimentally measured ca. 80, 80, and 110 fs. In addition, the internal conversion (IC) processes within respective singlet and triplet manifolds are also ultrafast. These ultrafast IC and ISC processes are caused by large nonadiabatic and spin-orbit couplings, respectively, as well as small energy gaps. Importantly, although these Ir(III) complexes share similar macroscopic phenomena, i.e., ultrafast IC and ISC, their microscopic excited-state relaxation mechanism and dynamics are qualitatively distinct. Specifically, the dynamical behaviors of electron and hole and their roles are variational in modulating the excited-state relaxation dynamics of these Ir(III) compounds. In other words, the electronic properties of the ligands that are coordinated with the central Ir(III) atom play important roles in regulating the microscopic excited-state relaxation dynamics. These gained insights could be useful for rationally designing Ir(III) compounds with excellent photoluminescence.

Overlapping and Divergent Actions of Structurally Distinct Histone Deacetylase Inhibitors in Cardiac Fibroblasts

PubMed Central

Schuetze, Katherine B.; Stratton, Matthew S.; Blakeslee, Weston W.; Wempe, Michael F.; Wagner, Florence F.; Holson, Edward B.; Kuo, Yin-Ming; Andrews, Andrew J.; Gilbert, Tonya M.; Hooker, Jacob M.

2017-01-01

Inhibitors of zinc-dependent histone deacetylases (HDACs) profoundly affect cellular function by altering gene expression via changes in nucleosomal histone tail acetylation. Historically, investigators have employed pan-HDAC inhibitors, such as the hydroxamate trichostatin A (TSA), which simultaneously targets members of each of the three zinc-dependent HDAC classes (classes I, II, and IV). More recently, class- and isoform-selective HDAC inhibitors have been developed, providing invaluable chemical biology probes for dissecting the roles of distinct HDACs in the control of various physiologic and pathophysiological processes. For example, the benzamide class I HDAC-selective inhibitor, MGCD0103 [N-(2-aminophenyl)-4-[[(4-pyridin-3-ylpyrimidin-2-yl)amino]methyl] benzamide], was shown to block cardiac fibrosis, a process involving excess extracellular matrix deposition, which often results in heart dysfunction. Here, we compare the mechanisms of action of structurally distinct HDAC inhibitors in isolated primary cardiac fibroblasts, which are the major extracellular matrix–producing cells of the heart. TSA, MGCD0103, and the cyclic peptide class I HDAC inhibitor, apicidin, exhibited a common ability to enhance histone acetylation, and all potently blocked cardiac fibroblast cell cycle progression. In contrast, MGCD0103, but not TSA or apicidin, paradoxically increased expression of a subset of fibrosis-associated genes. Using the cellular thermal shift assay, we provide evidence that the divergent effects of HDAC inhibitors on cardiac fibroblast gene expression relate to differential engagement of HDAC1- and HDAC2-containing complexes. These findings illustrate the importance of employing multiple compounds when pharmacologically assessing HDAC function in a cellular context and during HDAC inhibitor drug development. PMID:28174211

Effects of Grammatical Structure of Compound Words on Word Recognition in Chinese

PubMed Central

Cui, Lei; Cong, Fengjiao; Wang, Jue; Zhang, Wenxin; Zheng, Yuwei; Hyönä, Jukka

2018-01-01

Two lexical priming experiments were conducted to examine effects of grammatical structure of Chinese two-constituent compounds on their recognition. The target compound words conformed to two types of grammatical structure: subordinate and coordinative compounds. Subordinate compounds follow a structure where the first constituent modifies the second constituent (e.g., , meaning snowball); here the meaning of the second constituent (head) is modified by the first constituent (modifier). On the other hand, in coordinative compounds both constituents contribute equally to the word meaning (e.g., , wind and rain, meaning storm where the two constituent equally contribute to the word meaning). In Experiment 1 that was a replication attempt of Liu and McBride-Chang (2010), possible priming effects of word structure and semantic relatedness were examined. In lexical decision latencies only a semantic priming effect was observed. In Experiment 2, compound word structure and individual constituents were primed by the prime and target sharing either the first or second constituent. A structure priming effect was obtained in lexical decision times for subordinate compounds when the prime and target compound shared the same constituent. This suggests that a compound word constituent (either the modifier or the head) has to be simultaneously active with the structure information in order for the structure information to exert an effect on compound word recognition in Chinese. For the coordinative compounds the structure priming effect was non-significant. When the meaning of the whole word was primed (Experiment 1), no structure effect was observable. The pattern of results suggests that effects of structure priming are constituent-specific and no general structure priming was observable. PMID:29593594

μ Opioid receptor: novel antagonists and structural modeling

NASA Astrophysics Data System (ADS)

Kaserer, Teresa; Lantero, Aquilino; Schmidhammer, Helmut; Spetea, Mariana; Schuster, Daniela

2016-02-01

The μ opioid receptor (MOR) is a prominent member of the G protein-coupled receptor family and the molecular target of morphine and other opioid drugs. Despite the long tradition of MOR-targeting drugs, still little is known about the ligand-receptor interactions and structure-function relationships underlying the distinct biological effects upon receptor activation or inhibition. With the resolved crystal structure of the β-funaltrexamine-MOR complex, we aimed at the discovery of novel agonists and antagonists using virtual screening tools, i.e. docking, pharmacophore- and shape-based modeling. We suggest important molecular interactions, which active molecules share and distinguish agonists and antagonists. These results allowed for the generation of theoretically validated in silico workflows that were employed for prospective virtual screening. Out of 18 virtual hits evaluated in in vitro pharmacological assays, three displayed antagonist activity and the most active compound significantly inhibited morphine-induced antinociception. The new identified chemotypes hold promise for further development into neurochemical tools for studying the MOR or as potential therapeutic lead candidates.

Structural basis for subtype-specific inhibition of the P2X7 receptor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karasawa, Akira; Kawate, Toshimitsu

The P2X7 receptor is a non-selective cation channel activated by extracellular adenosine triphosphate (ATP). Chronic activation of P2X7 underlies many health problems such as pathologic pain, yet we lack effective antagonists due to poorly understood mechanisms of inhibition. Here we present crystal structures of a mammalian P2X7 receptor complexed with five structurally-unrelated antagonists. Unexpectedly, these drugs all bind to an allosteric site distinct from the ATP-binding pocket in a groove formed between two neighboring subunits. This novel drug-binding pocket accommodates a diversity of small molecules mainly through hydrophobic interactions. Functional assays propose that these compounds allosterically prevent narrowing of themore » drug-binding pocket and the turret-like architecture during channel opening, which is consistent with a site of action distal to the ATP-binding pocket. These novel mechanistic insights will facilitate the development of P2X7-specific drugs for treating human diseases.« less

Structure-Activity Relationships of a Novel Pyranopyridine Series of Gram-negative Bacterial Efflux Pump Inhibitors

PubMed Central

Nguyen, Son T.; Kwasny, Steven M.; Ding, Xiaoyuan; Cardinale, Steven C.; McCarthy, Courtney T.; Kim, Hong-Suk; Nikaido, Hiroshi; Peet, Norton P.; Williams, John D.; Bowlin, Terry L.; Opperman, Timothy J.

2015-01-01

Recently we described a novel pyranopyridine inhibitor (MBX2319) of RND-type efflux pumps of the Enterobacteriaceae. MBX2319 (3,3-dimethyl-5-cyano-8-morpholino-6-(phenethylthio)-3,4-dihydro-1H-pyrano[3,4-c]pyridine) is structurally distinct from other known Gram-negative efflux pump inhibitors (EPIs), such as 1-(1-naphthylmethyl)-piperazine (NMP), phenylalanylarginine-β-naphthylamide (PAβN), D13-9001, and the pyridopyrimidine derivatives. Here, we report the synthesis and biological evaluation of 60 new analogs of MBX2319 that were designed to probe the structure activity relationships (SARs) of the pyranopyridine scaffold. The results of these studies produced a molecular activity map of the scaffold, which identifies regions that are critical to efflux inhibitory activities and those that can be modified to improve potency, metabolic stability and solubility. Several compounds, such as 22d–f, 22i and 22k, are significantly more effective than MBX2319 at potentiating the antibacterial activity of levofloxacin and piperacillin against Escherichia coli. PMID:25818767

A ligand-directed divergent catalytic approach to establish structural and functional scaffold diversity

NASA Astrophysics Data System (ADS)

Lee, Yen-Chun; Patil, Sumersing; Golz, Christopher; Strohmann, Carsten; Ziegler, Slava; Kumar, Kamal; Waldmann, Herbert

2017-02-01

The selective transformation of different starting materials by different metal catalysts under individually optimized reaction conditions to structurally different intermediates and products is a powerful approach to generate diverse molecular scaffolds. In a more unified albeit synthetically challenging strategy, common starting materials would be exposed to a common metal catalysis, leading to a common intermediate and giving rise to different scaffolds by tuning the reactivity of the metal catalyst through different ligands. Herein we present a ligand-directed synthesis approach for the gold(I)-catalysed cycloisomerization of oxindole-derived 1,6-enynes that affords distinct molecular scaffolds following different catalytic reaction pathways. Varying electronic properties and the steric demand of the gold(I) ligands steers the fate of a common intermediary gold carbene to selectively form spirooxindoles, quinolones or df-oxindoles. Investigation of a synthesized compound collection in cell-based assays delivers structurally novel, selective modulators of the Hedgehog and Wnt signalling pathways, autophagy and of cellular proliferation.

Structural Diversity, Biological Properties and Applications of Natural Products from Cyanobacteria. A Review †

PubMed Central

Shah, Sayed Asmat Ali; Akhter, Najeeb; Auckloo, Bibi Nazia; Khan, Ishrat; Lu, Yanbin; Wang, Kuiwu; Wu, Bin

2017-01-01

Nowadays, various drugs on the market are becoming more and more resistant to numerous diseases, thus declining their efficacy for treatment purposes in human beings. Antibiotic resistance is one among the top listed threat around the world which eventually urged the discovery of new potent drugs followed by an increase in the number of deaths caused by cancer due to chemotherapy resistance as well. Accordingly, marine cyanobacteria, being the oldest prokaryotic microorganisms belonging to a monophyletic group, have proven themselves as being able to generate pharmaceutically important natural products. They have long been known to produce distinct and structurally complex secondary metabolites including peptides, polyketides, alkaloids, lipids, and terpenes with potent biological properties and applications. As such, this review will focus on recently published novel compounds isolated from marine cyanobacteria along with their potential bioactivities such as antibacterial, antifungal, anticancer, anti-tuberculosis, immunosuppressive and anti-inflammatory capacities. Moreover, various structural classes, as well as their technological uses will also be discussed. PMID:29125580

Crude oil degradation by bacterial consortia under four different redox and temperature conditions.

PubMed

Xiong, Shunzi; Li, Xia; Chen, Jianfa; Zhao, Liping; Zhang, Hui; Zhang, Xiaojun

2015-02-01

There is emerging interest in the anaerobic degradation of crude oil. However, there is limited knowledge about the geochemical effects and microbiological activities for it. A mixture of anaerobic sludge and the production water from an oil well was used as an inoculum to construct four consortia, which were incubated under sulfate-reducing or methanogenic conditions at either mesophilic or thermophilic temperatures. Significant degradation of saturated and aromatic hydrocarbons and the changing quantities of some marker compounds, such as pristane, phytane, hopane and norhopane, and their relative quantities, suggested the activity of microorganisms in the consortia. Notably, the redox conditions and temperature strongly affected the diversity and structure of the enriched microbial communities and the oil degradation. Although some specific biomarker showed larger change under methanogenic condition, the degradation efficiencies for total aromatic and saturated hydrocarbon were higher under sulfate-reducing condition. After the 540-day incubation, bacteria of unknown classifications were dominant in the thermophilic methanogenic consortia, whereas Clostridium dominated the mesophilic methanogenic consortia. With the exception of the dominant phylotypes that were shared with the methanogenic consortia, the sulfate-reducing consortia were predominantly composed of Thermotogae, Deltaproteobacteria, Spirochaeta, and Synergistetes phyla. In conclusion, results in this study demonstrated that the different groups of degraders were responsible for degradation in the four constructed crude oil degrading consortia and consequently led to the existence of different amount of marker compounds under these distinct conditions. There might be distinct metabolic mechanism for degrading crude oil under sulfate-reducing and methanogenic conditions.

Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize.

PubMed

Riedelsheimer, Christian; Lisec, Jan; Czedik-Eysenberg, Angelika; Sulpice, Ronan; Flis, Anna; Grieder, Christoph; Altmann, Thomas; Stitt, Mark; Willmitzer, Lothar; Melchinger, Albrecht E

2012-06-05

The diversity of metabolites found in plants is by far greater than in most other organisms. Metabolic profiling techniques, which measure many of these compounds simultaneously, enabled investigating the regulation of metabolic networks and proved to be useful for predicting important agronomic traits. However, little is known about the genetic basis of metabolites in crops such as maize. Here, a set of 289 diverse maize inbred lines was genotyped with 56,110 SNPs and assayed for 118 biochemical compounds in the leaves of young plants, as well as for agronomic traits of mature plants in field trials. Metabolite concentrations had on average a repeatability of 0.73 and showed a correlation pattern that largely reflected their functional grouping. Genome-wide association mapping with correction for population structure and cryptic relatedness identified for 26 distinct metabolites strong associations with SNPs, explaining up to 32.0% of the observed genetic variance. On nine chromosomes, we detected 15 distinct SNP-metabolite associations, each of which explained more then 15% of the genetic variance. For lignin precursors, including p-coumaric acid and caffeic acid, we found strong associations (P values to ) with a region on chromosome 9 harboring cinnamoyl-CoA reductase, a key enzyme in monolignol synthesis and a target for improving the quality of lignocellulosic biomass by genetic engineering approaches. Moreover, lignin precursors correlated significantly with lignin content, plant height, and dry matter yield, suggesting that metabolites represent promising connecting links for narrowing the genotype-phenotype gap of complex agronomic traits.

Binding mechanism investigations guiding the synthesis of novel condensed 1,4-dihydropyridine derivatives with L-/T-type calcium channel blocking activity.

PubMed

Schaller, David; Gündüz, Miyase Gözde; Zhang, Fang Xiong; Zamponi, Gerald W; Wolber, Gerhard

2018-05-23

Nifedipine and isradipine are prominent examples of calcium channel blockers with a 1,4-dihydropyridine (DHP) scaffold. Although successfully used in clinics since decades for the treatment of hypertension, the binding mechanism to their target, the L-type voltage-gated calcium channel Cav1.2, is still incompletely understood. Recently, novel DHP derivatives with a condensed ring system have been discovered that show distinct selectivity profiles to different calcium channel subtypes. This property renders this DHP class as a promising tool to achieve selectivity towards distinct calcium channel subtypes. In this study, we identified a common binding mode for prominent DHPs nifedipine and isradipine using docking and pharmacophore analysis that is also able to explain the structure-activity relationship of a small subseries of DHP derivatives with a condensed ring system. These findings were used to guide the synthesis of twenty-two novel DHPs. An extensive characterization using 1 H NMR, 13 C NMR, mass spectra and elemental analysis was followed by whole cell patch clamp assays for analyzing activity at Cav1.2 and Cav3.2. Two compounds were identified with significant activity against Cav1.2. Additionally, we identified four compounds active against Cav3.2 of which three were selective over Cav1.2. Novel binding modes were analyzed using docking and pharmacophore analysis as well as molecular dynamics simulations. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Fragmentation of mercury compounds under ultraviolet light irradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kokkonen, E.; Hautala, L.; Jänkälä, K.

2015-08-21

Ultraviolet light induced photofragmentation of mercury compounds is studied experimentally with electron energy resolved photoelectron-photoion coincidence techniques and theoretically with computational quantum chemical methods. A high resolution photoelectron spectrum using synchrotron radiation is presented. Fragmentation of the molecule is studied subsequent to ionization to the atomic-mercury-like d orbitals. State dependent fragmentation behaviour is presented and specific reactions for dissociation pathways are given. The fragmentation is found to differ distinctly in similar orbitals of different mercury compounds.

N-(L-2-aminopentanoyl)-L-phenylalanine dihydrate, a hydrophobic dipeptide with a nonproteinogenic residue.

PubMed

Görbitz, Carl Henrik; Yadav, Vitthal N

2013-09-01

The title dipeptide, better known as L-norvalyl-L-phenylalanine {systematic name: (S)-2-[(S)-2-aminopentanamido]-3-phenylpropanoic acid dihydrate}, C14H20N2O3·2H2O, has a nonproteinogenic N-terminal residue. In the solid state, it takes on a molecular conformation typical for one of the three classes of nanoporous dipeptides, but like two related compounds with a hydrophobic N-terminal residue and a C-terminal L-phenylalanine, it fails to form channels or pores. Instead, the crystal structure is divided into distinct hydrophobic and hydrophilic layers, the latter encompassing cocrystallized water molecules connecting the charged N- and C-terminal groups.

Erythropoietin and engineered innate repair activators.

PubMed

Brines, Michael; Cerami, Anthony

2013-01-01

Erythropoietin (EPO) is a pleiotropic type I cytokine that has been identified as a major endogenous tissue protective molecule. In response to injury, EPO and a distinct receptor are expressed with a characteristic temporal and spatial expression pattern. Together, these serve to limit injury and to initiate repair. Administration of EPO in the setting of injury has been shown to be beneficial in a multitude of preclinical models. However, translation into the clinic has been hampered by EPO's adverse effects, including promotion of thrombosis. Recently, engineered molecules based on EPO's structure-activity relationships have been developed that are devoid of hematopoietic effects. These compounds are promising candidates for treatment of a wide variety of acute and chronic diseases.

Structure-activity relationships and colorimetric properties of specific probes for the putative cancer biomarker human arylamine N-acetyltransferase 1.

PubMed

Egleton, James E; Thinnes, Cyrille C; Seden, Peter T; Laurieri, Nicola; Lee, Siu Po; Hadavizadeh, Kate S; Measures, Angelina R; Jones, Alan M; Thompson, Sam; Varney, Amy; Wynne, Graham M; Ryan, Ali; Sim, Edith; Russell, Angela J

2014-06-01

A naphthoquinone inhibitor of human arylamine N-acetyltransferase 1 (hNAT1), a potential cancer biomarker and therapeutic target, has been reported which undergoes a distinctive concomitant color change from red to blue upon binding to the enzyme. Here we describe the use of in silico modeling alongside structure-activity relationship studies to advance the hit compound towards a potential probe to quantify hNAT1 levels in tissues. Derivatives with both a fifty-fold higher potency against hNAT1 and a two-fold greater absorption coefficient compared to the initial hit have been synthesized; these compounds retain specificity for hNAT1 and its murine homologue mNat2 over the isoenzyme hNAT2. A relationship between pKa, inhibitor potency and colorimetric properties has also been uncovered. The high potency of representative examples against hNAT1 in ZR-75-1 cell extracts also paves the way for the development of inhibitors with improved intrinsic sensitivity which could enable detection of hNAT1 in tissue samples and potentially act as tools for elucidating the unknown role hNAT1 plays in ER+ breast cancer; this could in turn lead to a therapeutic use for such inhibitors. Copyright © 2014. Published by Elsevier Ltd.

An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides.

PubMed

Plummer, Chelsea E; Stover, Michele L; Bokatzian, Samantha S; Davis, John T M; Dixon, David A; Cassady, Carolyn J

2015-07-30

Using proton-transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and correlated molecular orbital theory at the G3(MP2) level, gas-phase acidities (GAs) and the associated structures for amides corresponding to the common amino acids have been determined for the first time. These values are important because amino acid amides are models for residues in peptides and proteins. For compounds whose most acidic site is the C-terminal amide nitrogen, two ions populations were observed experimentally with GAs that differ by 4-7 kcal/mol. The lower energy, more acidic structure accounts for the majority of the ions formed by electrospray ionization. G3(MP2) calculations predict that the lowest energy anionic conformer has a cis-like orientation of the [-C(═O)NH](-) group whereas the higher energy, less acidic conformer has a trans-like orientation of this group. These two distinct conformers were predicted for compounds with aliphatic, amide, basic, hydroxyl, and thioether side chains. For the most acidic amino acid amides (tyrosine, cysteine, tryptophan, histidine, aspartic acid, and glutamic acid amides) only one conformer was observed experimentally, and its experimental GA correlates with the theoretical GA related to side chain deprotonation.

Aspherical-atom modeling of coordination compounds by single-crystal X-ray diffraction allows the correct metal atom to be identified.

PubMed

Dittrich, Birger; Wandtke, Claudia M; Meents, Alke; Pröpper, Kevin; Mondal, Kartik Chandra; Samuel, Prinson P; Amin Sk, Nurul; Singh, Amit Pratap; Roesky, Herbert W; Sidhu, Navdeep

2015-02-02

Single-crystal X-ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid-state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical-atom least-squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld-atom refinement (Acta Crystallogr. Sect. A- 2008, 64, 383-393; IUCrJ. 2014, 1,61-79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B- 2013, 69, 91-104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear-coordinate 3d metal complexes, for which the wrong element is found if standard independent-atom model scattering factors are relied upon, are studied, and it is shown that only aspherical-atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tunable Weyl and Dirac states in the nonsymmorphic compound CeSbTe.

PubMed

Schoop, Leslie M; Topp, Andreas; Lippmann, Judith; Orlandi, Fabio; Müchler, Lukas; Vergniory, Maia G; Sun, Yan; Rost, Andreas W; Duppel, Viola; Krivenkov, Maxim; Sheoran, Shweta; Manuel, Pascal; Varykhalov, Andrei; Yan, Binghai; Kremer, Reinhard K; Ast, Christian R; Lotsch, Bettina V

2018-02-01

Recent interest in topological semimetals has led to the proposal of many new topological phases that can be realized in real materials. Next to Dirac and Weyl systems, these include more exotic phases based on manifold band degeneracies in the bulk electronic structure. The exotic states in topological semimetals are usually protected by some sort of crystal symmetry, and the introduction of magnetic order can influence these states by breaking time-reversal symmetry. We show that we can realize a rich variety of different topological semimetal states in a single material, CeSbTe. This compound can exhibit different types of magnetic order that can be accessed easily by applying a small field. Therefore, it allows for tuning the electronic structure and can drive it through a manifold of topologically distinct phases, such as the first nonsymmorphic magnetic topological phase with an eightfold band crossing at a high-symmetry point. Our experimental results are backed by a full magnetic group theory analysis and ab initio calculations. This discovery introduces a realistic and promising platform for studying the interplay of magnetism and topology. We also show that we can generally expand the numbers of space groups that allow for high-order band degeneracies by introducing antiferromagnetic order.

Assessing the biological contribution to microbialite growth and morphogenesis utilizing lipid biomarkers

NASA Astrophysics Data System (ADS)

Beeler, S. R.; Gomez, F. J.; Bradley, A. S.

2016-12-01

Microbialites are sedimentary structures that arise from the interaction of microbial, geochemical, and physical processes. These structures are among the oldest evidence for life on Earth, and are abundant through much of the Proterozoic before declining in the Phanerozoic. Microbialites are of great importance geobiologically as they provide a record of microbial life and its interaction with the environment throughout Earth history. Yet, our capacity to use microbialites to reconstruct biological processes on ancient Earth is complicated by our lack of understanding of the mechanisms controlling the formation of these structures. The modern microbialites of Laguna Negra in northeastern Argentina [1] offer an opportunity to examine the biological and geochemical differences among microbialites displaying distinct morphological diversity in a single setting. Three broad types of microbialites are found at this site: oncoids, stromatolites, and laminar crusts. Each of these types of microbialites are associated with visually distinct microbial mats. We have examined the structural and isotopic composition of lipid biomarkers from each of these microbialite types, and their associated mats. Sterol profiles detected from microbial mats and microbialites showed abundant C27 to C29 sterols and indicate that primary producers are dominated by algae. Decreased abundances of more labile unsaturated fatty acids relative to more recalcitrant saturated fatty acids were observed in microbialites compared to extant mats suggesting preferential loss of these compounds during diagenesis. Among the three different microbialite morphologies, no statistically discernable differences in biomarker profiles were detected. This implies that morphological changes are due to either geochemical/physical changes across the zone of microbialite formation or changes in community structure that are not observable in the present biomarker set. [1] Gomez et al. (2014) Palaios 29, 233-249

Identification and Characterization of Influenza Virus Entry Inhibitors through Dual Myxovirus High-Throughput Screening.

PubMed

Weisshaar, Marco; Cox, Robert; Morehouse, Zachary; Kumar Kyasa, Shiva; Yan, Dan; Oberacker, Phil; Mao, Shuli; Golden, Jennifer E; Lowen, Anice C; Natchus, Michael G; Plemper, Richard K

2016-08-15

Influenza A virus (IAV) infections cause major morbidity and mortality, generating an urgent need for novel antiviral therapeutics. We recently established a dual myxovirus high-throughput screening protocol that combines a fully replication-competent IAV-WSN strain and a respiratory syncytial virus reporter strain for the simultaneous identification of IAV-specific, paramyxovirus-specific, and broad-spectrum inhibitors. In the present study, this protocol was applied to a screening campaign to assess a diverse chemical library with over 142,000 entries. Focusing on IAV-specific hits, we obtained a hit rate of 0.03% after cytotoxicity testing and counterscreening. Three chemically distinct hit classes with nanomolar potency and favorable cytotoxicity profiles were selected. Time-of-addition, minigenome, and viral entry studies demonstrated that these classes block hemagglutinin (HA)-mediated membrane fusion. Antiviral activity extends to an isolate from the 2009 pandemic and, in one case, another group 1 subtype. Target identification through biolayer interferometry confirmed binding of all hit compounds to HA. Resistance profiling revealed two distinct escape mechanisms: primary resistance, associated with reduced compound binding, and secondary resistance, associated with unaltered binding. Secondary resistance was mediated, unusually, through two different pairs of cooperative mutations, each combining a mutation eliminating the membrane-proximal stalk N-glycan with a membrane-distal change in HA1 or HA2. Chemical synthesis of an analog library combined with in silico docking extracted a docking pose for the hit classes. Chemical interrogation spotlights IAV HA as a major druggable target for small-molecule inhibition. Our study identifies novel chemical scaffolds with high developmental potential, outlines diverse routes of IAV escape from entry inhibition, and establishes a path toward structure-aided lead development. This study is one of the first to apply a fully replication-competent third-generation IAV reporter strain to a large-scale high-throughput screen (HTS) drug discovery campaign, allowing multicycle infection and screening in physiologically relevant human respiratory cells. A large number of potential druggable targets was thus chemically interrogated, but mechanistic characterization, positive target identification, and resistance profiling demonstrated that three chemically promising and structurally distinct hit classes selected for further analysis all block HA-mediated membrane fusion. Viral escape from inhibition could be achieved through primary and secondary resistance mechanisms. In silico docking predicted compound binding to a microdomain located at the membrane-distal site of the prefusion HA stalk that was also previously suggested as a target site for chemically unrelated HA inhibitors. This study identifies an unexpected chemodominance of the HA stalk microdomain for small-molecule inhibitors in IAV inhibitor screening campaigns and highlights a novel mechanism of cooperative resistance to IAV entry blockers. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Identification and Characterization of Influenza Virus Entry Inhibitors through Dual Myxovirus High-Throughput Screening

PubMed Central

Weisshaar, Marco; Cox, Robert; Morehouse, Zachary; Kumar Kyasa, Shiva; Yan, Dan; Oberacker, Phil; Mao, Shuli; Lowen, Anice C.; Natchus, Michael G.

2016-01-01

ABSTRACT Influenza A virus (IAV) infections cause major morbidity and mortality, generating an urgent need for novel antiviral therapeutics. We recently established a dual myxovirus high-throughput screening protocol that combines a fully replication-competent IAV-WSN strain and a respiratory syncytial virus reporter strain for the simultaneous identification of IAV-specific, paramyxovirus-specific, and broad-spectrum inhibitors. In the present study, this protocol was applied to a screening campaign to assess a diverse chemical library with over 142,000 entries. Focusing on IAV-specific hits, we obtained a hit rate of 0.03% after cytotoxicity testing and counterscreening. Three chemically distinct hit classes with nanomolar potency and favorable cytotoxicity profiles were selected. Time-of-addition, minigenome, and viral entry studies demonstrated that these classes block hemagglutinin (HA)-mediated membrane fusion. Antiviral activity extends to an isolate from the 2009 pandemic and, in one case, another group 1 subtype. Target identification through biolayer interferometry confirmed binding of all hit compounds to HA. Resistance profiling revealed two distinct escape mechanisms: primary resistance, associated with reduced compound binding, and secondary resistance, associated with unaltered binding. Secondary resistance was mediated, unusually, through two different pairs of cooperative mutations, each combining a mutation eliminating the membrane-proximal stalk N-glycan with a membrane-distal change in HA1 or HA2. Chemical synthesis of an analog library combined with in silico docking extracted a docking pose for the hit classes. Chemical interrogation spotlights IAV HA as a major druggable target for small-molecule inhibition. Our study identifies novel chemical scaffolds with high developmental potential, outlines diverse routes of IAV escape from entry inhibition, and establishes a path toward structure-aided lead development. IMPORTANCE This study is one of the first to apply a fully replication-competent third-generation IAV reporter strain to a large-scale high-throughput screen (HTS) drug discovery campaign, allowing multicycle infection and screening in physiologically relevant human respiratory cells. A large number of potential druggable targets was thus chemically interrogated, but mechanistic characterization, positive target identification, and resistance profiling demonstrated that three chemically promising and structurally distinct hit classes selected for further analysis all block HA-mediated membrane fusion. Viral escape from inhibition could be achieved through primary and secondary resistance mechanisms. In silico docking predicted compound binding to a microdomain located at the membrane-distal site of the prefusion HA stalk that was also previously suggested as a target site for chemically unrelated HA inhibitors. This study identifies an unexpected chemodominance of the HA stalk microdomain for small-molecule inhibitors in IAV inhibitor screening campaigns and highlights a novel mechanism of cooperative resistance to IAV entry blockers. PMID:27252534

Low-Field Bi-Skyrmion Formation in a Noncentrosymmetric Chimney Ladder Ferromagnet

NASA Astrophysics Data System (ADS)

Takagi, R.; Yu, X. Z.; White, J. S.; Shibata, K.; Kaneko, Y.; Tatara, G.; Rønnow, H. M.; Tokura, Y.; Seki, S.

2018-01-01

The real-space spin texture and the relevant magnetic parameters were investigated for an easy-axis noncentrosymmetric ferromagnet Cr11 Ge19 with Nowotny chimney ladder structure. Using Lorentz transmission electron microscopy, we report the formation of bi-Skyrmions, i.e., pairs of spin vortices with opposite magnetic helicities. The quantitative evaluation of the magnetocrystalline anisotropy and Dzyaloshinskii-Moriya interaction (DMI) proves that the magnetic dipolar interaction plays a more important role than the DMI on the observed bi-Skyrmion formation. Notably, the critical magnetic field value required for the formation of bi-Skyrmions turned out to be extremely small in this system, which is ascribed to strong easy-axis anisotropy associated with the characteristic helix crystal structure. The family of Nowotny chimney ladder compounds may offer a unique material platform where two distinctive Skyrmion formation mechanisms favoring different topological spin textures can become simultaneously active.

Microstructural and mechanical properties on friction welding of dissimilar metals used in motor vehicles

NASA Astrophysics Data System (ADS)

Jesudoss Hynes, N. Rajesh; Shenbaga Velu, P.

2018-02-01

In the last two decades, major car manufacturing companies are exploring the possibilities of joining magnesium with aluminium, via friction welding technique for many crucial automotive applications. Our primary objective, is to carry out an experimental investigation in order to study the behaviour of dissimilar joints. The microscopic structure at the welded joint interface was analysed using an optical microscopy and scanning electron microscope. It was found that, by increasing the value of friction time, the value of the tensile strength increases and the result of tensile strength is found to be 120 MPa at a friction time of 10 s. Micro hardness was found to be higher at the interface of the weldment due to the development of a brittle intermetallic compound. Micro structural studies using SEM reveals, distinct zones such as an unaffected parent metal zone, the heat affected zone, a thermo-mechanically affected zone and a fully deformed plasticised zone.

PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures.

PubMed

Gallina, Anna Maria; Bisignano, Paola; Bergamino, Maurizio; Bordo, Domenico

2013-02-01

A large fraction of the entries contained in the Protein Data Bank describe proteins in complex with low molecular weight molecules such as physiological compounds or synthetic drugs. In many cases, the same molecule is found in distinct protein-ligand complexes. There is an increasing interest in Medicinal Chemistry in comparing protein binding sites to get insight on interactions that modulate the binding specificity, as this structural information can be correlated with other experimental data of biochemical or physiological nature and may help in rational drug design. The web service protein-ligand interaction presented here provides a tool to analyse and compare the binding pockets of homologous proteins in complex with a selected ligand. The information is deduced from protein-ligand complexes present in the Protein Data Bank and stored in the underlying database. Freely accessible at http://bioinformatics.istge.it/pli/.

Application of the Ugi reaction with multiple amino acid-derived components: synthesis and conformational evaluation of piperazine-based minimalist peptidomimetics.

PubMed

Stucchi, Mattia; Cairati, Silvia; Cetin-Atalay, Rengul; Christodoulou, Michael S; Grazioso, Giovanni; Pescitelli, Gennaro; Silvani, Alessandra; Yildirim, Deniz Cansen; Lesma, Giordano

2015-05-07

The concurrent employment of α-amino acid-derived chiral components such as aldehydes and α-isocyanoacetates, in a sequential Ugi reaction/cyclization two-step strategy, opens the door to the synthesis of three structurally distinct piperazine-based scaffolds, characterized by the presence of L-Ala and/or L-Phe-derived side chains and bearing appropriate functionalities to be easily applied in peptide chemistry. By means of computational studies, these scaffolds have been demonstrated to act as minimalist peptidomimetics, able to mimic a well defined range of peptide secondary structures and therefore potentially useful for the synthesis of small-molecule PPI modulators. Preliminary biological evaluation of two different resistant hepatocellular carcinoma cellular lines, for which differentiation versus resistance ability seem to be strongly correlated with well defined types of PPIs, has revealed a promising antiproliferative activity for selected compounds.

Probing the chemical interaction space governed by 4-aminosubstituted benzenesulfonamides and carbonic anhydrase isoforms.

PubMed

Rasti, Behnam; Heravi, Yeganeh Entezari

2018-06-01

Isoform diversity, critical physiological roles and involvement in major diseases/disorders such as glaucoma, epilepsy, Alzheimer's disease, obesity, and cancers have made carbonic anhydrase (CA), one of the most interesting case studies in the field of computer aided drug design. Since applying non-selective inhibitors can result in major side effects, there have been considerable efforts so far to achieve selective inhibitors for different isoforms of CA. Using proteochemometrics approach, the chemical interaction space governed by a group of 4-amino-substituted benzenesulfonamides and human CAs has been explored in the present study. Several validation methods have been utilized to assess the validity, robustness and predictivity power of the proposed proteochemometric model. Our model has offered major structural information that can be applied to design new selective inhibitors for distinct isoforms of CA. To prove the applicability of the proposed model, new compounds have been designed based on the offered discriminative structural features.

Distinct Spacing Between Anionic Groups: An Essential Chemical Determinant for Achieving Thiophene-Based Ligands to Distinguish β-Amyloid or Tau Polymorphic Aggregates.

PubMed

Klingstedt, Therése; Shirani, Hamid; Mahler, Jasmin; Wegenast-Braun, Bettina M; Nyström, Sofie; Goedert, Michel; Jucker, Mathias; Nilsson, K Peter R

2015-06-15

The accumulation of protein aggregates is associated with many devastating neurodegenerative diseases and the existence of distinct aggregated morphotypes has been suggested to explain the heterogeneous phenotype reported for these diseases. Thus, the development of molecular probes able to distinguish such morphotypes is essential. We report an anionic tetrameric oligothiophene compound that can be utilized for spectral assignment of different morphotypes of β-amyloid or tau aggregates present in transgenic mice at distinct ages. The ability of the ligand to spectrally distinguish between the aggregated morphotypes was reduced when the spacing between the anionic substituents along the conjugated thiophene backbone was altered, which verified that specific molecular interactions between the ligand and the protein aggregate are necessary to detect aggregate polymorphism. Our findings provide the structural and functional basis for the development of new fluorescent ligands that can distinguish between different morphotypes of protein aggregates. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution Non-Commercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Identification and Metabolite Profiling of Chemical Activators of Lipid Accumulation in Green Algae.

PubMed

Wase, Nishikant; Tu, Boqiang; Allen, James W; Black, Paul N; DiRusso, Concetta C

2017-08-01

Microalgae are proposed as feedstock organisms useful for producing biofuels and coproducts. However, several limitations must be overcome before algae-based production is economically feasible. Among these is the ability to induce lipid accumulation and storage without affecting biomass yield. To overcome this barrier, a chemical genetics approach was employed in which 43,783 compounds were screened against Chlamydomonas reinhardtii , and 243 compounds were identified that increase triacylglyceride (TAG) accumulation without terminating growth. Identified compounds were classified by structural similarity, and 15 were selected for secondary analyses addressing impacts on growth fitness, photosynthetic pigments, and total cellular protein and starch concentrations. TAG accumulation was verified using gas chromatography-mass spectrometry quantification of total fatty acids, and targeted TAG and galactolipid measurements were performed using liquid chromatography-multiple reaction monitoring/mass spectrometry. These results demonstrated that TAG accumulation does not necessarily proceed at the expense of galactolipid. Untargeted metabolite profiling provided important insights into pathway shifts due to five different compound treatments and verified the anabolic state of the cells with regard to the oxidative pentose phosphate pathway, Calvin cycle, tricarboxylic acid cycle, and amino acid biosynthetic pathways. Metabolite patterns were distinct from nitrogen starvation and other abiotic stresses commonly used to induce oil accumulation in algae. The efficacy of these compounds also was demonstrated in three other algal species. These lipid-inducing compounds offer a valuable set of tools for delving into the biochemical mechanisms of lipid accumulation in algae and a direct means to improve algal oil content independent of the severe growth limitations associated with nutrient deprivation. © 2017 American Society of Plant Biologists. All Rights Reserved.

Structure-property studies on the antioxidant activity of flavonoids present in diet.

PubMed

Teixeira, Susana; Siquet, Christophe; Alves, Carla; Boal, Isabel; Marques, M Paula; Borges, Fernanda; Lima, José L F C; Reis, Salette

2005-10-15

The screening of natural flavonoids for their bioactivity as antioxidants is usually carried out by determinination of their profile as chain-breaking antioxidants, by the evaluation of their direct free radical-scavenging activity as hydrogen- or electron-donating compounds. Since this may not be the only mechanism underlying the antioxidant activity it is important to check the ability of these compounds to act as chelators of transition metal ions. Accordingly, in the present study the acidity constants of catechin and taxifolin, as well as the formation constants of the corresponding copper (II) complexes, were investigated by potentiometry and/or spectrophotometry. Moreover, a detailed quantitative examination of the coordination species formed is presented. In addition, the partition coefficients of both catechin and taxifolin in a biomimetic system (micelles) were determined, since these properties may also contribute to the antioxidant behavior of this type of compound. The log P values determined depend on the electrostatic interactions of the compounds with the differently charged micelles (the highest values were obtained for zwitterionic and cationic micelles). The prooxidant behavior of the compounds was assessed through the oxidation of 2'-deoxyguanosine, induced by a Fenton reaction, catalyzed by copper. The data obtained reveal that the flavonoids under study did not present prooxidant activity, in this particular system. The results obtained are evidence of a clear difference among the pKa, the complexation properties, and the lipophilicity of the flavonoids studied, which can partially explain their distinct antioxidant activity. The most stable geometries of the free compounds were determined by theoretical (ab initio) methods, in order to properly account for the electron correlation effects which occur in these systems, thus allowing a better interpretation of the experimental data.

A review on the synthesis, crystal growth, structure and physical properties of rare earth based quaternary intermetallic compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mumbaraddi, Dundappa; Sarkar, Sumanta; Peter, Sebastian C., E-mail: sebastiancp@jncasr.ac.in

2016-04-15

This review highlights the synthesis and crystal growth of quaternary intermetallic compounds based on rare earth metals. In the first part of this review, we highlight briefly about intermetallics and their versatile properties in comparison to the constituent elements. In the next part, we have discussed about various synthesis techniques with more focus on the metal flux technique towards the well shaped crystal growth of novel compounds. In the subsequent parts, several disordered quaternary compounds have been reviewed and then outlined most known ordered quaternary compounds with their complex structure. A special attention has been given to the ordered compoundsmore » with structural description and relation to the parent binary and ternary compounds. The importance of electronic and structural feature is highlighted as the key roles in designing these materials for emerging applications. - Graphical abstract: Rare earth based quaternary intermetallic compounds crystallize in complex novel crystal structures. The diversity in the crystal structure may induce unique properties and can be considered them as future materials. - Highlights: • Crystal growth and crystal structure of quaternary rare earth based intermetallics. • Structural complexity of quaternary compounds in comparison to the parent compounds. • Novel quaternary compounds display unique crystal structure.« less

Lattice thermal conductivity of monolayer AsP from first-principles molecular dynamics.

PubMed

Sun, Yajing; Shuai, Zhigang; Wang, Dong

2018-05-23

Few-layered arsenic-phosphorus alloys, AsxP(1-x), with a puckered structure have been recently synthesized and demonstrated with fully tunable band gaps and optical properties. It is predicted that the carrier mobility of monolayer AsP compounds is even higher than that of black phosphorene (b-P). The anisotropic and orthogonal electrical and thermal transport properties of the puckered group VA elements make them intriguing materials for thermoelectric applications. Herein, we investigated the thermal transport properties of AsP based on first-principles molecular dynamics and the Boltzmann transport equation. We reveal that monolayer AsP with three different chemical structures possesses thermal conductivities lower than b-P, but with increased anisotropy. Further, these structures behave profoundly different on heat conduction. This can be attributed to the distinct low-frequency optical modes associated with their bonding nature. Our results highlight the impact of atomic arrangement on the thermal conductivity of AsP, and the structure-property relationship established may guide the fabrication of thermoelectric materials via the engineered alloying method.

Genome-Wide Requirements for Resistance to Functionally Distinct DNA-Damaging Agents

PubMed Central

Proctor, Michael; Flaherty, Patrick; Jordan, Michael I; Arkin, Adam P; Davis, Ronald W; Nislow, Corey; Giaever, Guri

2005-01-01

The mechanistic and therapeutic differences in the cellular response to DNA-damaging compounds are not completely understood, despite intense study. To expand our knowledge of DNA damage, we assayed the effects of 12 closely related DNA-damaging agents on the complete pool of ~4,700 barcoded homozygous deletion strains of Saccharomyces cerevisiae. In our protocol, deletion strains are pooled together and grown competitively in the presence of compound. Relative strain sensitivity is determined by hybridization of PCR-amplified barcodes to an oligonucleotide array carrying the barcode complements. These screens identified genes in well-characterized DNA-damage-response pathways as well as genes whose role in the DNA-damage response had not been previously established. High-throughput individual growth analysis was used to independently confirm microarray results. Each compound produced a unique genome-wide profile. Analysis of these data allowed us to determine the relative importance of DNA-repair modules for resistance to each of the 12 profiled compounds. Clustering the data for 12 distinct compounds uncovered both known and novel functional interactions that comprise the DNA-damage response and allowed us to define the genetic determinants required for repair of interstrand cross-links. Further genetic analysis allowed determination of epistasis for one of these functional groups. PMID:16121259

Investigating Differences in Gas-Phase Conformations of 25-Hydroxyvitamin D3 Sodiated Epimers using Ion Mobility-Mass Spectrometry and Theoretical Modeling

NASA Astrophysics Data System (ADS)

Chouinard, Christopher D.; Cruzeiro, Vinícius Wilian D.; Beekman, Christopher R.; Roitberg, Adrian E.; Yost, Richard A.

2017-08-01

Drift tube ion mobility coupled with mass spectrometry was used to investigate the gas-phase structure of 25-hydroxyvitamin D3 (25OHD3) and D2 (25OHD2) epimers, and to evaluate its potential in rapid separation of these compounds. Experimental results revealed two distinct drift species for the 25OHD3 sodiated monomer, whereas only one of these conformations was observed for its epimer (epi25OHD3). The unique species allowed 25OHD3 to be readily distinguished, and the same pattern was observed for 25OHD2 epimers. Theoretical modeling of 25OHD3 epimers identified energetically stable gas-phase structures, indicating that both compounds may adopt a compact "closed" conformation, but that 25OHD3 may also adopt a slightly less energetically favorable "open" conformation that is not accessible to its epimer. Calculated theoretical collision cross-sections for these structures agreed with experimental results to <2%. Experimentation indicated that additional energy in the ESI source (i.e., increased temperature, spray voltage) affected the ratio of 25OHD3 conformations, with the less energetically favorable "open" conformation increasing in relative intensity. Finally, LC-IM-MS results yielded linear quantitation of 25OHD3, in the presence of the epimer interference, at biologically relevant concentrations. This study demonstrates that ion mobility can be used in tandem with theoretical modeling to determine structural differences that contribute to drift separation. These separation capabilities provide potential for rapid (<60 ms) identification of 25OHD3 and 25OHD2 in mixtures with their epimers.

Synthesis, characterization, electrochemical investigation and antioxidant activities of a new hybrid cyclohexaphosphate: Cu1.5Li(C2H10N2)P6O18·7H2O

NASA Astrophysics Data System (ADS)

Sleymi, Samira; Lahbib, Karima; Rahmouni, Nihed; Rzaigui, Mohamed; Besbes-Hentati, Salma; Abid, Sonia

2017-09-01

A new organic-inorganic hybrid transition metal phosphate, Cu1.5Li(C2H10N2)P6O18·7H2O, has been prepared and characterized by X-ray diffraction, spectroscopy (infrared, Raman, diffuse reflectance and UV-Vis) and thermal analysis (TG). In addition, its electrochemical behaviors, as well as its antioxidant and antibacterial activities, have been investigated. Its structure is built up by the alternate linkages between copper and phosphate polyhedra, forming puckered layers with intersecting 12-membered rings, in which the ethylenediammonium cations reside. This compound is the first framework structure constructed from cyclohexaphosphates and three distinct copper cations. Cyclic voltammetry study in an acetonitrile solution reveals the facile anodic oxidation of its organic part on a platinum disk and a progressive growing of a thin film, though the repetitive cycling of potential. The title compound was tested for its in vitro antioxidant activities by 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2‧-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), Ferrous chelating ability (FIC) and Ferric Reducing Power (FRP) methods. The antioxidant activity of Cu1.5Li(C2H10N2)P6O18·7H2O was analyzed simultaneously with its antibacterial capacity against Escherichia coli, Salmonella typhimurium, Staphylococus aureus, Enterococcus feacium, Streptococcus agalactiae and Candida albicans. The tested compound showed significant antioxidant activities with low antibacterial properties.

Unusual open chain quinolinyl peroxol and its alcohol counterpart obtained through a modified Skraup-Doebner-Von Miller quinoline synthesis: theoretical studies and complete (1) H- and (13) C-NMR assignments.

PubMed

Fotie, Jean; Kemami Wangun, Hilaire V; Dreux, Katelyn; Sommerfeld, Thomas; Pittman, Jacob

2012-01-01

Because of their extreme instability, it is generally difficult to synthesize and fully characterize open chain peroxides, also known as peroxols. In our attempt to investigate the mechanism of the Skraup-Doebner-Von Miller quinoline synthesis, we were able to obtain an unusual open chain peroxy-quinoline, namely, 4-(8-ethoxy-2,3-dihydro-1H-cyclopenta[c]quinolin-4-yl)butane-1-peroxol (1), and its alcohol counterpart, namely 4-(8-ethoxy-2,3-dihydro-1H-cyclopenta[c]quinolin-4-yl)butan-1-ol (2) obtained as a side product during the same reaction. Although structurally similar, these two compounds appeared to display some very distinct physical and spectroscopic characteristics. This work reports detailed NMR studies and full (1) H and (13)  C NMR assignments for these two compounds. These assignments are based upon the analysis of the NMR spectra of these compounds including (1) H, (13)  C, COSY, gHSQC and gHMBC. The effect of the peroxide functional group on the chemical shift of neighboring carbons and protons was also investigated by comparing the NMR data of these two compounds. Furthermore, the effects of potential hydrogen bondings in 1, 2, and possible 1-1 dimer, 2-2 dimer and in prototypical model systems, as well as the stability of these compounds, were investigated computationally. The computed dissociation energies and NMR data support the interpretation of the experimental data. Copyright © 2012 John Wiley & Sons, Ltd.

Multiple competing interactions and reentrant ferrimagnetism in Tb 0.8Nd 0.2Mn 6Ge 6

NASA Astrophysics Data System (ADS)

Schobinger-Papamantellos, P.; André, G.; Rodríguez-Carvajal, J.; Duong, N. P.; Buschow, K. H. J.

2001-06-01

The magnetic ordering of the hexagonal compound Tb 0.8Nd 0.2Mn 6Ge 6 has been studied by neutron diffraction and magnetic measurements in the temperature range 1.5-800 K. This compound was found to undergo consecutive magnetic transitions with temperature. The magnetic phase diagram comprises four distinct regions and requires the wave vectors: q1=(0, 0, qz) and q2=0 for its description. The low temperature range (LT): 1.5 K< T< T1=85 K, is characterised by a triple ferrimagnetic conical (spiral) structure with qz=0.128 r.l.u and a net moment along the c direction ( q2=0). The intermediate temperature range displays two transitions: At T1=85 K the conical structure transforms to a simple triple (flat) spiral persisting in range (ITa) 85 K< T< T2≈340 K, with a small thermal variation of the wave vector. Above T2 in range (ITb) T2< T< TS≈390 K the destabilised spiral transforms to a FAN-like structure with a fast decrease of the wave vector length towards zero while a ferrimagnetic planar structure ( q2=0) develops at the cost of the spiral. The planar ferrimagnetic magnetic structure ( q2=0) dominates the high temperature range (HT) 390 K< T< Tc=450 K. The onset of re-entrant ferrimagnetism reflects the interplay of multiple competing inter- and intra- sublattice interactions of the three types of magnetic ions with different crystal field anisotropies. The Nd and Tb sublattices are coupled antiferromagnetically while the Tb-Mn and Nd-Mn interactions are negative and positive, respectively.

A possible link between Balkan endemic nephropathy and the leaching of toxic organic compounds from Pliocene lignite by groundwater: Preliminary investigation

USGS Publications Warehouse

Orem, W.H.; Feder, G.L.; Finkelman, R.B.

1999-01-01

Balkan endemic nephropathy (BEN) is a fatal kidney disease that is known to occur only in clusters of villages in alluvial valleys of tributaries of the Danube River in Bulgaria, Romania, Yugoslavia, Bosnia, and Croatia. The confinement of this disease to a specific geographic area has led to speculation that an environmental factor may be involved in the etiology of BEN. Numerous environmental factors have been suggested as causative agents for producing BEN, including toxic metals in drinking water, metal deficiency in soils of BEN areas, and environmental mycotoxins to name a few. These hypotheses have either been disproved or have failed to conclusively demonstrate a connection to the etiology of BEN, or the clustering of BEN villages. In previous work, we observed a distinct geographic relationship between the distribution of Pliocene lignites in the Balkans and BEN villages. We hypothesized that the long-term consumption of well water containing toxic organic compounds derived from the leaching of nearby Pliocene lignites by groundwater was a primary factor in the etiology of BEN. In our current work, chemical analysis using 13C nuclear magnetic resonance (13CNMR) spectroscopy indicated a high degree of organic functionality in Pliocene lignite from the Balkans, and suggested that groundwater can readily leach organic matter from these coal beds. Semi-quantitative gas chromatography/mass spectroscopy analysis of solvent extracts of groundwater from shallow wells in BEN villages indicated the presence of potentially toxic aromatic compounds, such as napthalene, fluorene, phenanthrene, and pyrene at concentrations in the ppb range. Laboratory leaching of Balkan Pliocene lignites with distilled water yielded soluble organic matter (> 500 MW) containing large amounts of aromatic structures similar to the simple/discrete aromatic compounds detected in well water from BEN villages. These preliminary results are permissive of our hypothesis and suggest that further work on the possible relationship between the etiology of BEN and toxic aromatic substances leached from Pliocene lignites in well water is warranted.A distinct geographic relationship between the distribution of Pliocene lignites in the Balkans and villages where Balkan endemic nephropathy (BEN) occurs has been observed, indicating a possible link between BEN and the long-term consumption of well water containing toxic organic compounds derived from the leaching of nearby Pliocene lignites. Preliminary investigations by NMR spectroscopy, gas chromatography/mass spectroscopy and leaching experiments show a high degree of organic functionality in the Pliocene lignites, high-leachability by groundwater of organic matter from these beds, and the presence of toxic aromatic compounds.

Solvatochromicity of 3-hydroxy-4-(1-(2,4-dihydroxyphenyl)-2-hydroxy-2,2-diphenylethylidene)cyclohexa-2,5-dienone for screening of solvents

NASA Astrophysics Data System (ADS)

Babu, D. Suresh; Singh, W. Marjit; Kalita, Dipjyoti; Baruah, Jubaraj B.

2010-01-01

The quinonic compound 3-hydroxy-4-(1-(2,4-dihydroxyphenyl)-2-hydroxy-2,2-diphenylethylidene)cyclohexa-2,5-dienone ( I) is synthesised by the reaction of benzil with 1,3-dihydroxybenzene in basic medium. Solution of this compound shows visibly distinct colour differences in different solvents. From the different absorption maxima of the compound in visible spectra it can be used as an excellent analytical reagent to screen different solvents.

Infrared nanospectroscopy reveals the chemical nature of pit membranes in water-conducting cells of the plant xylem.

PubMed

Pereira, Luciano; Flores-Borges, Denisele; Bittencourt, Paulo; Mayer, Juliana; Kiyota, Eduardo; Araújo, Pedro; Jansen, Steven; Freitas, Raul; Oliveira, Rafael; Mazzafera, Paulo

2018-06-05

In the xylem of angiosperm plants, microscopic pits through the secondary cell walls connect the water-conducting vessels. Cellulosic meshes originated from primary walls and middle lamella between adjacent vessels, called pit membrane, separates one conduit from another. The intricate structure of the nano-sized pores in pit membranes enables the passage of water under negative pressure without hydraulic failure due to obstruction by gas bubbles (i.e., embolism) under normal conditions or mild drought stress. Since the chemical composition of pit membranes affects embolism formation and bubble behavior, we directly measured pit membrane composition in Populus nigra wood. Here, we characterized the chemical composition of cell wall structures by synchrotron infrared nanospectroscopy and atomic force microscopy-infrared nanospectroscopy with high spatial resolution. Characteristic peaks of cellulose, phenolic compounds, and proteins were found in the intervessel pit membrane of P. nigra wood. In addition, vessel to parenchyma pit membranes and developing cell walls of the vascular cambium showed clear signals of cellulose, proteins, and pectin. We did not find a distinct peak of lignin and other compounds in these structures. Our investigation of the complex chemical composition of intervessel pit membranes furthers our understanding of the flow of water and bubbles between neighboring conduits. The advances presented here pave the way for further label-free studies related to the nano-chemistry of plant cell components. {copyright, serif} 2018 American Society of Plant Biologists. All rights reserved.

Conservative whole-organ scaling contrasts with highly labile suborgan scaling differences among compound eyes of closely related Formica ants.

PubMed

Perl, Craig D; Rossoni, Sergio; Niven, Jeremy E

2017-03-01

Static allometries determine how organ size scales in relation to body mass. The extent to which these allometric relationships are free to evolve, and how they differ among closely related species, has been debated extensively and remains unclear; changes in intercept appear common, but changes in slope are far rarer. Here, we compare the scaling relationships that govern the structure of compound eyes of four closely related ant species from the genus Formica . Comparison among these species revealed changes in intercept but not slope in the allometric scaling relationships governing eye area, facet number, and mean facet diameter. Moreover, the scaling between facet diameter and number was conserved across all four species. In contrast, facet diameters from distinct regions of the compound eye differed in both intercept and slope within a single species and when comparing homologous regions among species. Thus, even when species are conservative in the scaling of whole organs, they can differ substantially in regional scaling within organs. This, at least partly, explains how species can produce organs that adhere to genus wide scaling relationships while still being able to invest differentially in particular regions of organs to produce specific features that match their ecology.

Using X-ray absorption to probe sulfur oxidation states in complex molecules

NASA Astrophysics Data System (ADS)

Vairavamurthy, A.

1998-10-01

X-ray absorption near-edge structure (XANES) spectroscopy offers an important non-destructive tool for determining oxidation states and for characterizing chemical speciation. The technique was used to experimentally verify the oxidation states of sulfur in different types of complex molecules because there are irregularities and uncertainties in assigning the values traditionally. The usual practice of determining oxidation states involves using a set of conventional rules. The oxidation state is an important control in the chemical speciation of sulfur, ranging from -2 to +6 in its different compounds. Experimental oxidation-state values for various types of sulfur compounds, using their XANES peak-energy positions, were assigned from a scale in which elemental sulfur and sulfate are designated as 0 and +6, respectively. Because these XANES-based values differed considerably from conventionally determined oxidation states for most sulfur compounds, a new term 'oxidation index' was coined to describe them. The experimental values were closer to those conventional values obtained by assigning shared electrons to the more electronegative atoms than to those based on other customary rules for assigning them. Because the oxidation index is distinct and characteristic for each different type of sulfur functionality, it becomes an important parameter for characterizing sulfur species, and for experimentally verifying uncertain oxidation states.

Anticancer Properties of Distinct Antimalarial Drug Classes

PubMed Central

Hooft van Huijsduijnen, Rob; Guy, R. Kiplin; Chibale, Kelly; Haynes, Richard K.; Peitz, Ingmar; Kelter, Gerhard; Phillips, Margaret A.; Vennerstrom, Jonathan L.; Yuthavong, Yongyuth; Wells, Timothy N. C.

2013-01-01

We have tested five distinct classes of established and experimental antimalarial drugs for their anticancer potential, using a panel of 91 human cancer lines. Three classes of drugs: artemisinins, synthetic peroxides and DHFR (dihydrofolate reductase) inhibitors effected potent inhibition of proliferation with IC50s in the nM- low µM range, whereas a DHODH (dihydroorotate dehydrogenase) and a putative kinase inhibitor displayed no activity. Furthermore, significant synergies were identified with erlotinib, imatinib, cisplatin, dasatinib and vincristine. Cluster analysis of the antimalarials based on their differential inhibition of the various cancer lines clearly segregated the synthetic peroxides OZ277 and OZ439 from the artemisinin cluster that included artesunate, dihydroartemisinin and artemisone, and from the DHFR inhibitors pyrimethamine and P218 (a parasite DHFR inhibitor), emphasizing their shared mode of action. In order to further understand the basis of the selectivity of these compounds against different cancers, microarray-based gene expression data for 85 of the used cell lines were generated. For each compound, distinct sets of genes were identified whose expression significantly correlated with compound sensitivity. Several of the antimalarials tested in this study have well-established and excellent safety profiles with a plasma exposure, when conservatively used in malaria, that is well above the IC50s that we identified in this study. Given their unique mode of action and potential for unique synergies with established anticancer drugs, our results provide a strong basis to further explore the potential application of these compounds in cancer in pre-clinical or and clinical settings. PMID:24391728

Pyrazoleamide compounds are potent antimalarials that target Na+ homeostasis in intraerythrocytic Plasmodium falciparum

PubMed Central

Vaidya, Akhil B.; Morrisey, Joanne M.; Zhang, Zhongsheng; Das, Sudipta; Daly, Thomas M.; Otto, Thomas D.; Spillman, Natalie J.; Wyvratt, Matthew; Siegl, Peter; Marfurt, Jutta; Wirjanata, Grennady; Sebayang, Boni F.; Price, Ric N.; Chatterjee, Arnab; Nagle, Advait; Stasiak, Marcin; Charman, Susan A.; Angulo-Barturen, Iñigo; Ferrer, Santiago; Belén Jiménez-Díaz, María; Martínez, María Santos; Gamo, Francisco Javier; Avery, Vicky M.; Ruecker, Andrea; Delves, Michael; Kirk, Kiaran; Berriman, Matthew; Kortagere, Sandhya; Burrows, Jeremy; Fan, Erkang; Bergman, Lawrence W.

2014-01-01

The quest for new antimalarial drugs, especially those with novel modes of action, is essential in the face of emerging drug-resistant parasites. Here we describe a new chemical class of molecules, pyrazoleamides, with potent activity against human malaria parasites and showing remarkably rapid parasite clearance in an in vivo model. Investigations involving pyrazoleamide-resistant parasites, whole-genome sequencing and gene transfers reveal that mutations in two proteins, a calcium-dependent protein kinase (PfCDPK5) and a P-type cation-ATPase (PfATP4), are necessary to impart full resistance to these compounds. A pyrazoleamide compound causes a rapid disruption of Na+ regulation in blood-stage Plasmodium falciparum parasites. Similar effect on Na+ homeostasis was recently reported for spiroindolones, which are antimalarials of a chemical class quite distinct from pyrazoleamides. Our results reveal that disruption of Na+ homeostasis in malaria parasites is a promising mode of antimalarial action mediated by at least two distinct chemical classes. PMID:25422853

Investigating the Effect of Emetic Compounds on Chemotaxis in Dictyostelium Identifies a Non-Sentient Model for Bitter and Hot Tastant Research

PubMed Central

Robery, Steven; Mukanowa, Janina; Percie du Sert, Nathalie; Andrews, Paul L. R.; Williams, Robin S. B.

2011-01-01

Novel chemical entities (NCEs) may be investigated for emetic liability in a range of unpleasant experiments involving retching, vomiting or conditioned taste aversion/food avoidance in sentient animals. We have used a range of compounds with known emetic /aversive properties to examine the possibility of using the social amoeba, Dictyostelium discoideum, for research into identifying and understanding emetic liability, and hence reduce adverse animal experimentation in this area. Twenty eight emetic or taste aversive compounds were employed to investigate the acute (10 min) effect of compounds on Dictyostelium cell behaviour (shape, speed and direction of movement) in a shallow chemotaxic gradient (Dunn chamber). Compound concentrations were chosen based on those previously reported to be emetic or aversive in in vivo studies and results were recorded and quantified by automated image analysis. Dictyostelium cell motility was rapidly and strongly inhibited by four structurally distinct tastants (three bitter tasting compounds - denatonium benzoate, quinine hydrochloride, phenylthiourea, and the pungent constituent of chilli peppers - capsaicin). In addition, stomach irritants (copper chloride and copper sulphate), and a phosphodiesterase IV inhibitor also rapidly blocked movement. A concentration-dependant relationship was established for five of these compounds, showing potency of inhibition as capsaicin (IC50 = 11.9±4.0 µM) > quinine hydrochloride (IC50 = 44.3±6.8 µM) > denatonium benzoate (IC50 = 129±4 µM) > phenylthiourea (IC50 = 366±5 µM) > copper sulphate (IC50 = 1433±3 µM). In contrast, 21 compounds within the cytotoxic and receptor agonist/antagonist classes did not affect cell behaviour. Further analysis of bitter and pungent compounds showed that the effect on cell behaviour was reversible and not cytotoxic, suggesting an uncharacterised molecular mechanism of action for these compounds. These results therefore demonstrate that Dictyostelium has potential as a non-sentient model in the analysis of the molecular effects of tastants, although it has limited utility in identification of emetic agents in general. PMID:21931717

Interplay between subsurface structural heterogeneity and multi-species reactive transport in human health risk predictions

NASA Astrophysics Data System (ADS)

Henri, C.; Fernandez-Garcia, D.; de Barros, F.

2013-12-01

The increasing presence of toxic chemicals released in the subsurface has led to a rapid growth of social concerns and to the need to develop and employ models that can predict the impact of groundwater contamination in human health under uncertainty. Monitored natural attenuation is a common remediation action in many contamination cases and represents an attractive decontamination method. However, natural attenuation can lead to the production of subspecies of distinct toxicity that may pose challenges in pollution management strategies. The actual threat that these contaminants pose to human health and ecosystems greatly depends on the interplay between the complexity of the geological system and the toxicity of the pollutants and their byproducts. In this work, we examine the interplay between multispecies reactive transport and the heterogeneous structure of the contaminated aquifer on human health risk predictions. The structure and organization of hydraulic properties of the aquifer can lead to preferential flow channels and fast contamination pathways. Early travel times, associated to channeling effects, are intuitively perceived as an indicator for high risk. However, in the case of multi-species systems, early travel times may also lead a limited production of daughter species that may contain higher toxicity as in the case of chlorinated compounds. In this work, we model a Perchloroethylene (PCE) contamination problem followed by the sequential first-order production/biodegradation of its daughter species Trichloroethylene (TCE), Dichloroethylene (DCE) and Vinyl Chlorine (VC). For this specific case, VC is known to be a highly toxic contaminant. By performing numerical experiments, we evaluate transport for two distinct three-dimensional aquifer structures. First, a multi-Gaussian hydraulic conductivity field and secondly, a geostatistically equivalent connected field. These two heterogeneity structures will provide two distinct ranges of mean travel times and other higher order statistics. Uncertainty on the hydraulic conductivity field is considered through a Monte Carlo scheme, and the total risk (TR) for human health related to the mixtures of the four carcinogenic plumes is evaluated. Results show two distinct spatio-temporal behavior of the TR estimation. At a fixed environmentally sensitive location, aquifers with a high degree of connectivity display a lower TR. On the other hand, at the same environmentally sensitive location, the poorly connected aquifer yields higher TR. Our results reflect the interplay between the characteristic reactive time for each component and the characteristic travel time of the plume since the production of VC depends on these factors.

Automated compound classification using a chemical ontology.

PubMed

Bobach, Claudia; Böhme, Timo; Laube, Ulf; Püschel, Anett; Weber, Lutz

2012-12-29

Classification of chemical compounds into compound classes by using structure derived descriptors is a well-established method to aid the evaluation and abstraction of compound properties in chemical compound databases. MeSH and recently ChEBI are examples of chemical ontologies that provide a hierarchical classification of compounds into general compound classes of biological interest based on their structural as well as property or use features. In these ontologies, compounds have been assigned manually to their respective classes. However, with the ever increasing possibilities to extract new compounds from text documents using name-to-structure tools and considering the large number of compounds deposited in databases, automated and comprehensive chemical classification methods are needed to avoid the error prone and time consuming manual classification of compounds. In the present work we implement principles and methods to construct a chemical ontology of classes that shall support the automated, high-quality compound classification in chemical databases or text documents. While SMARTS expressions have already been used to define chemical structure class concepts, in the present work we have extended the expressive power of such class definitions by expanding their structure-based reasoning logic. Thus, to achieve the required precision and granularity of chemical class definitions, sets of SMARTS class definitions are connected by OR and NOT logical operators. In addition, AND logic has been implemented to allow the concomitant use of flexible atom lists and stereochemistry definitions. The resulting chemical ontology is a multi-hierarchical taxonomy of concept nodes connected by directed, transitive relationships. A proposal for a rule based definition of chemical classes has been made that allows to define chemical compound classes more precisely than before. The proposed structure-based reasoning logic allows to translate chemistry expert knowledge into a computer interpretable form, preventing erroneous compound assignments and allowing automatic compound classification. The automated assignment of compounds in databases, compound structure files or text documents to their related ontology classes is possible through the integration with a chemical structure search engine. As an application example, the annotation of chemical structure files with a prototypic ontology is demonstrated.

Automated compound classification using a chemical ontology

PubMed Central

2012-01-01

Background Classification of chemical compounds into compound classes by using structure derived descriptors is a well-established method to aid the evaluation and abstraction of compound properties in chemical compound databases. MeSH and recently ChEBI are examples of chemical ontologies that provide a hierarchical classification of compounds into general compound classes of biological interest based on their structural as well as property or use features. In these ontologies, compounds have been assigned manually to their respective classes. However, with the ever increasing possibilities to extract new compounds from text documents using name-to-structure tools and considering the large number of compounds deposited in databases, automated and comprehensive chemical classification methods are needed to avoid the error prone and time consuming manual classification of compounds. Results In the present work we implement principles and methods to construct a chemical ontology of classes that shall support the automated, high-quality compound classification in chemical databases or text documents. While SMARTS expressions have already been used to define chemical structure class concepts, in the present work we have extended the expressive power of such class definitions by expanding their structure-based reasoning logic. Thus, to achieve the required precision and granularity of chemical class definitions, sets of SMARTS class definitions are connected by OR and NOT logical operators. In addition, AND logic has been implemented to allow the concomitant use of flexible atom lists and stereochemistry definitions. The resulting chemical ontology is a multi-hierarchical taxonomy of concept nodes connected by directed, transitive relationships. Conclusions A proposal for a rule based definition of chemical classes has been made that allows to define chemical compound classes more precisely than before. The proposed structure-based reasoning logic allows to translate chemistry expert knowledge into a computer interpretable form, preventing erroneous compound assignments and allowing automatic compound classification. The automated assignment of compounds in databases, compound structure files or text documents to their related ontology classes is possible through the integration with a chemical structure search engine. As an application example, the annotation of chemical structure files with a prototypic ontology is demonstrated. PMID:23273256

Effect of lysine at C-terminus of the Dmt-Tic opioid pharmacophore.

PubMed

Balboni, Gianfranco; Onnis, Valentina; Congiu, Cenzo; Zotti, Margherita; Sasaki, Yusuke; Ambo, Akihiro; Bryant, Sharon D; Jinsmaa, Yunden; Lazarus, Lawrence H; Trapella, Claudio; Salvadori, Severo

2006-09-07

Substitution of Gly with side-chain-protected or unprotected Lys in lead compounds containing the opioid pharmacophore Dmt-Tic [H-Dmt-Tic-Gly-NH-CH(2)-Ph, mu agonist/delta antagonist; H-Dmt-Tic-Gly-NH-Ph, mu agonist/delta agonist; and H-Dmt-Tic-NH-CH(2)-Bid, delta agonist (Bid = 1H-benzimidazole-2-yl)] yielded a new series of compounds endowed with distinct pharmacological activities. Compounds (1-10) included high delta- (Ki(delta) = 0.068-0.64 nM) and mu-opioid affinities (Ki(mu) = 0.13-5.50 nM), with a bioactivity that ranged from mu-opioid agonism {10, H-Dmt-Tic-NH-CH[(CH2)4-NH2]-Bid (IC50 GPI = 39.7 nM)} to a selective mu-opioid antagonist [3, H-Dmt-Tic-Lys-NH-CH2-Ph (pA2(mu) = 7.96)] and a selective delta-opioid antagonist [5, H-Dmt-Tic-Lys(Ac)-NH-Ph (pA2(delta) = 12.0)]. The presence of a Lys linker provides new lead compounds in the formation of opioid peptidomimetics containing the Dmt-Tic pharmacophore with distinct agonist and/or antagonist properties.

Reactivity of molecular dioxygen towards a series of isostructural dichloroiron(III) complexes with tripodal tetraamine ligands: general access to mu-oxodiiron(III) complexes and effect of alpha-fluorination on the reaction kinetics.

PubMed

Thallaj, Nasser K; Rotthaus, Olaf; Benhamou, Leila; Humbert, Nicolas; Elhabiri, Mourad; Lachkar, Mohammed; Welter, Richard; Albrecht-Gary, Anne-Marie; Mandon, Dominique

2008-01-01

We have synthesized the mono, di-, and tri-alpha-fluoro ligands in the tris(2-pyridylmethyl)amine (TPA) series, namely, FTPA, F(2)TPA and F(3)TPA, respectively. Fluorination at the alpha-position of these nitrogen-containing tripods shifts the oxidation potential of the ligand by 45-70 mV per added fluorine atom. The crystal structures of the dichloroiron(II) complexes with FTPA and F(2)TPA reveal that the iron center lies in a distorted octahedral geometry comparable to that already found in TPAFeCl(2). All spectroscopic data indicate that the geometry is retained in solution. These three isostructural complexes all react with molecular dioxygen to yield stable mu-oxodiiron(III) complexes. Crystal structure analyses are reported for each of these three mu-oxo compounds. With TPA, a symmetrical structure is obtained for a dicationic compound with the tripod coordinated in the kappa(4)N coordination mode. With FTPA, the compound is a neutral mu-oxodiiron(III) complex with a kappa(3)N coordination mode of the ligand. Oxygenation of the F(2)TPA complex gave a neutral unsymmetrical compound, the structure of which is reminiscent of that already found with the trifluorinated ligand. On reduction, all mu-oxodiiron(III) complexes revert to the starting iron(II) species. The oxygenation reaction parallels the well-known formation of mu-oxo derivatives from dioxygen in the chemistry of porphyrins reported almost three decades ago. The striking feature of the series of iron(II) precursors is the effect of the ligand on the kinetics of oxygenation of the complexes. Whereas the parent complex undergoes 90 % conversion over 40 h, the monofluorinated ligand provides a complex that has fully reacted after 30 h, whereas the reaction time for the complex with the difluorinated ligand is only 10 h. Analysis of the spectroscopic data reveals that formation of the mu-oxo complexes proceeds in two distinct reversible kinetic steps with k(1) approximately 10 k(2). For TPAFeCl(2) and FTPAFeCl(2) only small variations in the k(1) and k(2) values are observed. By contrast, F(2)TPAFeCl(2) exhibits k(1) and k(2) values that are ten times higher. These differences in kinetics are interpreted in the light of structural and electronic effects, especially the Lewis acidity at the metal center. Our results suggest coordination of dioxygen as an initial step in the process leading to formation of mu-oxodiiron(III) compounds, by contrast with an unlikely outer-sphere reduction of dioxygen, which generally occurs at negative potentials.

Tritium labeling of organic compounds deposited on porous structures

DOEpatents

Ehrenkaufer, Richard L. E.; Wolf, Alfred P.; Hembree, Wylie C.

1979-01-01

An improved process for labeling organic compounds with tritium is carried out by depositing the selected compound on the extensive surface of a porous structure such as a membrane filter and exposing the membrane containing the compound to tritium gas activated by the microwave discharge technique. The labeled compound is then recovered from the porous structure.

The incorporation of butyrophenones and related compounds into a pharmacophore for dopamine D2 antagonists.

PubMed

Froimowitz, M; Cody, V

1997-08-01

This study is an attempt to incorporate the butyrophenones, an important class of nontricyclic antipsychotic drugs, into a previously proposed pharmacophore model of tricyclic dopamine D2 receptor antagonist ligands. Conformational energy calculations were performed using the MM3-92 program on spiperone, as a representative butyrophenone, and milenperone and R48455, as related compounds with more limited conformational freedom. Twenty seven conformers were evaluated for spiperone with MM3-92 calculations and nine of these were within 1.1 kcal/mole of the global minima indicating the flexibility of the compound. A conformational analysis of twenty crystal structures of butyrophenones was also performed and six distinct conformers were represented. All of the energy minimized conformers of spiperone were superimposed in a least squares sense onto loxapine as a relatively rigid, typical D2 antagonist and a pair of mirror image conformers, which are observed in one crystal structure of spiperone, were found to be the best fit. However, it was not possible to discriminate between these two conformers since they fit the pharmacophore model equally well. The para-fluoro and carbonyl group of the butyrophenones were found to correspond best to the oxygen and chlorine atoms of loxapine, respectively. The conformations of milenperone and R48455 were also consistent with the two putative biologically active forms of spiperone and the pharmacophore model. Conformational energy calculations were also performed on molindone, an antipsychotic drug in clinical use, which can be related to the butyrophenones since both have a carbonyl group adjacent to an aromatic ring. A putative biologically active form was proposed for molindone and this was related to the structure of piquindone, a rigid analog of molindone. All of the compounds were found to be entirely consistent with the pharmacophore model. However, as previously found, there is great variability in the distance between the ammonium nitrogen and the center of the relevant aromatic ring with the most extreme case in the present study being R48455 where the distance is 7.2 A. The results of the present study should also be relevant to the structures of novel, atypical antipsychotic drugs such as risperidone which appear to be analogs of the butyrophenones.

Investigation of supramolecular synthons and structural characterisation of aminopyridine-carboxylic acid derivatives

PubMed Central

2014-01-01

Background Co-crystal is a structurally homogeneous crystalline material that contains two or more neutral building blocks that are present in definite stoichiometric amounts. The main advantage of co-crystals is their ability to generate a variety of solid forms of a drug that have distinct physicochemical properties from the solid co-crystal components. In the present investigation, five co-crystals containing 2-amino-6-chloropyridine (AMPY) moiety were synthesized and characterized. Results The crystal structure of 2-amino-6-chloropyridine (AMPY) (I), and the robustness of pyridine-acid supramolecular synthon were discussed in four stoichiometry co-crystals of AMPY…BA (II), AMPY…2ABA (III), AMPY…3CLBA (IV) and AMPY…4NBA (V). The abbreviated designations used are benzoic acid (BA), 2-aminobenzoic acid (2ABA), 3-chlorobenzoic acid (3CLBA) and 4-nitrobenzoic acid (4NBA). All the crystalline materials have been characterized by 1HNMR, 13CNMR, IR, photoluminescence, TEM analysis and X-ray diffraction. The supramolecular assembly of each co-crystal is analyzed and discussed. Conclusions Extensive N---H · · · N/N---H · · · O/O---H · · · N hydrogen bonds are found in (I-V), featuring different supramolecular synthons. In the crystal structure, for compound (I), the 2-amino-6-chloropyridine molecules are linked together into centrosymmetric dimers by hydrogen bonds to form homosynthon, whereas for compounds (II-V), the carboxylic group of the respective acids (benzoic acid, 2-aminobenzoic acid, 3-chlorobenzoic acid and 4-nitrobenzoic acid) interacts with pyridine molecule in a linear fashion through a pair of N---H · · · O and O---H · · · N hydrogen bonds, generating cyclic hydrogen-bonded motifs with the graph-set notation R 2 2 8 , to form heterosynthon. In compound (II), another intermolecular N---H · · · O hydrogen bonds further link these heterosynthons into zig-zag chains. Whereas in compounds (IV) and (V), these heterosynthons are centrosymmetrically paired via N---H · · · O hydrogen bonds and each forms a complementary DADA [D = donor and A = acceptor] array of quadruple hydrogen bonds, with graph-set notation R238, R228 and R238. PMID:24887234

Investigation of supramolecular synthons and structural characterisation of aminopyridine-carboxylic acid derivatives.

PubMed

Hemamalini, Madhukar; Loh, Wan-Sin; Quah, Ching Kheng; Fun, Hoong-Kun

2014-01-01

Co-crystal is a structurally homogeneous crystalline material that contains two or more neutral building blocks that are present in definite stoichiometric amounts. The main advantage of co-crystals is their ability to generate a variety of solid forms of a drug that have distinct physicochemical properties from the solid co-crystal components. In the present investigation, five co-crystals containing 2-amino-6-chloropyridine (AMPY) moiety were synthesized and characterized. The crystal structure of 2-amino-6-chloropyridine (AMPY) (I), and the robustness of pyridine-acid supramolecular synthon were discussed in four stoichiometry co-crystals of AMPY…BA (II), AMPY…2ABA (III), AMPY…3CLBA (IV) and AMPY…4NBA (V). The abbreviated designations used are benzoic acid (BA), 2-aminobenzoic acid (2ABA), 3-chlorobenzoic acid (3CLBA) and 4-nitrobenzoic acid (4NBA). All the crystalline materials have been characterized by (1)HNMR, (13)CNMR, IR, photoluminescence, TEM analysis and X-ray diffraction. The supramolecular assembly of each co-crystal is analyzed and discussed. Extensive N---H · · · N/N---H · · · O/O---H · · · N hydrogen bonds are found in (I-V), featuring different supramolecular synthons. In the crystal structure, for compound (I), the 2-amino-6-chloropyridine molecules are linked together into centrosymmetric dimers by hydrogen bonds to form homosynthon, whereas for compounds (II-V), the carboxylic group of the respective acids (benzoic acid, 2-aminobenzoic acid, 3-chlorobenzoic acid and 4-nitrobenzoic acid) interacts with pyridine molecule in a linear fashion through a pair of N---H · · · O and O---H · · · N hydrogen bonds, generating cyclic hydrogen-bonded motifs with the graph-set notation [Formula: see text] , to form heterosynthon. In compound (II), another intermolecular N---H · · · O hydrogen bonds further link these heterosynthons into zig-zag chains. Whereas in compounds (IV) and (V), these heterosynthons are centrosymmetrically paired via N---H · · · O hydrogen bonds and each forms a complementary DADA [D = donor and A = acceptor] array of quadruple hydrogen bonds, with graph-set notation [Formula: see text], [Formula: see text] and [Formula: see text].

Distinctive effect on nerve growth factor-induced PC12 cell neurite outgrowth by two unique neolignan enantiomers from Illicium merrillianum

PubMed Central

Tian, Xinhui; Yue, Rongcai; Zeng, Huawu; Li, Honglin; Shan, Lei; He, Weiwei; Shen, Yunheng; Zhang, Weidong

2015-01-01

Merrillianoid (1), a racemic neolignan possessing the characteristic benzo-2,7-dioxabicyclo[3.2.1]octane moiety, was isolated from the branches and leaves of Illicium merrillianum. Chiral separation of 1 gave two enantiomers (+)−1 and (−)−1. The structure of 1 was established by comprehensive spectroscopic analysis and single crystal X-ray diffraction. The absolute configurations of enantiomers were determined by quantum mechanical calculation. Compound (+)−1 exhibited a better neurotrophic activity than racemate 1 by promoting nerve growth factor (NGF) induced PC12 cell neurite outgrowth, while (−)−1 showed a distinctive inhibitory effect. Furthermore, a mechanism study indicated that the two enantiomers influenced NGF-induced neurite outgrowth of PC12 cells possibly by interacting with the trkA receptor, and extracellular signal regulated kinases 1/2 (ERK1/2) and mitogen-activated protein kinase (MEK) in Ras/ERK signal cascade. But the phosphorylation level of serine/threonine kinase Akt1 and Akt2 in PI3K/Akt signal pathway showed no significant difference between (+)−1 and (−)−1. PMID:26585042

Comparative metagenomics reveals different hydrocarbon degradative abilities from enriched oil-drilling waste.

PubMed

Napp, Amanda P; Pereira, José Evandro S; Oliveira, Jorge S; Silva-Portela, Rita C B; Agnez-Lima, Lucymara F; Peralba, Maria C R; Bento, Fátima M; Passaglia, Luciane M P; Thompson, Claudia E; Vainstein, Marilene H

2018-06-11

The oil drilling process generates large volumes of waste with inadequate treatments. Here, oil drilling waste (ODW) microbial communities demonstrate different hydrocarbon degradative abilities when exposed to distinct nutrient enrichments as revealed by comparative metagenomics. The ODW was enriched in Luria Broth (LBE) and Potato Dextrose (PDE) media to examine the structure and functional variations of microbial consortia. Two metagenomes were sequenced on Ion Torrent platform and analyzed using MG-RAST. The STAMP software was used to analyze statistically significant differences amongst different attributes of metagenomes. The microbial diversity presented in the different enrichments was distinct and heterogeneous. The metabolic pathways and enzymes were mainly related to the aerobic hydrocarbons degradation. Moreover, our results showed efficient biodegradation after 15 days of treatment for aliphatic hydrocarbons (C8-C33) and polycyclic aromatic hydrocarbons (PAHs), with a total of about 50.5% and 46.4% for LBE and 44.6% and 37.9% for PDE, respectively. The results obtained suggest the idea that the enzymatic apparatus have the potential to degrade petroleum compounds. Copyright © 2018 Elsevier Ltd. All rights reserved.

Navigating into the binding pockets of the HER family protein kinases: discovery of novel EGFR inhibitor as antitumor agent.

PubMed

Liu, Wei; Ning, Jin-Feng; Meng, Qing-Wei; Hu, Jing; Zhao, Yan-Bin; Liu, Chao; Cai, Li

2015-01-01

The epidermal growth factor receptor (EGFR) family has been validated as a successful antitumor drug target for decades. Known EGFR inhibitors were exposed to distinct drug resistance against the various EGFR mutants within non-small-cell lung cancer (NSCLC), particularly the T790M mutation. Although so far a number of studies have been reported on the development of third-generation EGFR inhibitors for overcoming the resistance issue, the design procedure largely depends on the intuition of medicinal chemists. Here we retrospectively make a detailed analysis of the 42 EGFR family protein crystal complexes deposited in the Protein Data Bank (PDB). Based on the analysis of inhibitor binding modes in the kinase catalytic cleft, we identified a potent EGFR inhibitor (compound A-10) against drug-resistant EGFR through fragment-based drug design. This compound showed at least 30-fold more potency against EGFR T790M than the two control molecules erlotinib and gefitinib in vitro. Moreover, it could exhibit potent HER2 inhibitory activities as well as tumor growth inhibitory activity. Molecular docking studies revealed a structural basis for the increased potency and mutant selectivity of this compound. Compound A-10 may be selected as a promising candidate in further preclinical studies. In addition, our findings could provide a powerful strategy to identify novel selective kinase inhibitors on the basis of detailed kinase-ligand interaction space in the PDB.

Indications of Transformation Products from Hydraulic Fracturing Additives in Shale Gas Wastewater

NASA Astrophysics Data System (ADS)

Elsner, Martin; Hoelzer, Kathrin; Sumner, Andrew J.; Karatum, Osman; Nelson, Robert K.; Drollette, Brian D.; O'Connor, Megan P.; D'Ambro, Emma; Getzinger, Gordon J.; Ferguson, P. Lee; Reddy, Christopher M.; Plata, Desiree L.

2016-04-01

Unconventional natural gas development (UNGD) generates large volumes of wastewater, whose detailed composition must be known for adequate risk assessment and treatment. In particular, there is a need to elucidate the structures of organic chemical additives, extracted geogenic compounds, and transformation products. This study investigated six Fayetteville Shale UNGD wastewater samples for their organic composition using purge-and-trap gas chromatography-mass spectrometry (P&T-GC-MS) in combination with liquid-liquid extraction with comprehensive two-dimensional gas chromatography-time of flight-mass spectrometry (GCxGC-TOF-MS). Following application of strict compound identification confidence criteria, we classified compounds according to their putative origin. Samples displayed distinct chemical distributions composed of typical geogenic substances (hydrocarbons), disclosed UNGD additives (e.g., hydrocarbons, phthalates, such as diisobutyl phthalate, and radical initiators, such as azobisisobutyronitrile), and undisclosed compounds (e.g., halogenated hydrocarbons, such as 2-bromohexane or 4-bromoheptane). Undisclosed chloromethyl alkanoates (chloromethyl propanoate, pentanoate, and octanoate) were identified as putative delayed acids (those that release acidic moieties only after hydrolytic cleavage, whose rate could potentially be controlled), suggesting they were deliberately introduced to react in the subsurface. Identification of halogenated methanes and acetones, in contrast, suggested they were formed as unintended by-products. Our study highlights the possibility that UNGD operations generate transformation products, knowledge of which is crucial for risk assessment and treatment strategies, and underscores the value of disclosing potential precursors that are injected into the subsurface.

Navigating into the binding pockets of the HER family protein kinases: discovery of novel EGFR inhibitor as antitumor agent

PubMed Central

Liu, Wei; Ning, Jin-Feng; Meng, Qing-Wei; Hu, Jing; Zhao, Yan-Bin; Liu, Chao; Cai, Li

2015-01-01

The epidermal growth factor receptor (EGFR) family has been validated as a successful antitumor drug target for decades. Known EGFR inhibitors were exposed to distinct drug resistance against the various EGFR mutants within non-small-cell lung cancer (NSCLC), particularly the T790M mutation. Although so far a number of studies have been reported on the development of third-generation EGFR inhibitors for overcoming the resistance issue, the design procedure largely depends on the intuition of medicinal chemists. Here we retrospectively make a detailed analysis of the 42 EGFR family protein crystal complexes deposited in the Protein Data Bank (PDB). Based on the analysis of inhibitor binding modes in the kinase catalytic cleft, we identified a potent EGFR inhibitor (compound A-10) against drug-resistant EGFR through fragment-based drug design. This compound showed at least 30-fold more potency against EGFR T790M than the two control molecules erlotinib and gefitinib in vitro. Moreover, it could exhibit potent HER2 inhibitory activities as well as tumor growth inhibitory activity. Molecular docking studies revealed a structural basis for the increased potency and mutant selectivity of this compound. Compound A-10 may be selected as a promising candidate in further preclinical studies. In addition, our findings could provide a powerful strategy to identify novel selective kinase inhibitors on the basis of detailed kinase–ligand interaction space in the PDB. PMID:26229444

Structural diversity of anti-pancreatic cancer capsimycins identified in mangrove-derived Streptomyces xiamenensis 318 and post-modification via a novel cytochrome P450 monooxygenase

PubMed Central

Yu, He-Lin; Jiang, Shu-Heng; Bu, Xu-Liang; Wang, Jia-Hua; Weng, Jing-Yi; Yang, Xiao-Mei; He, Kun-Yan; Zhang, Zhi-Gang; Ao, Ping; Xu, Jun; Xu, Min-Juan

2017-01-01

Polycyclic tetramate macrolactams (PTMs) were identified as distinct secondary metabolites of the mangrove-derived Streptomyces xiamenensis 318. Together with three known compounds—ikarugamycin (1), capsimycin (2) and capsimycin B (3)—two new compounds, capsimycin C (4) with trans-diols and capsimycin D (5) with trans-configurations at C-13/C-14, have been identified. The absolute configurations of the tert/tert-diols moiety was determined in 4 by NMR spectroscopic analysis, CD spectral comparisons and semi-synthetic method. The post-modification mechanism of the carbocyclic ring at C-14/C-13 of compound 1 in the biosynthesis of an important intermediate 3 was investigated. A putative cytochrome P450 superfamily gene, SXIM_40690 (ikaD), which was proximally localized to the ikarugamycin biosynthetic pathway, was characterized. In vivo gene inactivation and complementation experiment confirmed that IkaD catalysed the epoxide-ring formation reaction and further hydroxylation of ethyl side chain to form capsimycin G (3′). Binding affinities and kinetic parameters for the interactions between ikarugamycin (1) and capsimycin B (3) with IkaD were measured with Surface Plasmon Resonance. The intermediate compound 3′ was isolated and identified as 30-hydroxyl-capsimycin B. The caspimycins 2 and 3, were transferred to methoxyl derivatives, 6 and 7, under acidic and heating conditions. Compounds 1–3 exhibited anti-proliferative activities against pancreatic carcinoma with IC50 values of 1.30–3.37 μM. PMID:28098172

Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Begley, Darren W.; Hartley, Robert C.; Davies, Douglas R.

As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification ofmore » several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chrencik, Jill E.; Orans, Jillian; Moore, Linda B.

The human nuclear xenobiotic receptor, pregnane X receptor (PXR), detects a variety of structurally distinct endogenous and xenobiotic compounds and controls expression of genes central to drug and cholesterol metabolism. The macrolide antibiotic rifampicin, a front-line treatment for tuberculosis, is an established PXR agonist and, at 823 Da, is one of the largest known ligands for the receptor. We present the 2.8 {angstrom} crystal structure of the ligand-binding domain of human PXR in complex with rifampicin. We also use structural and mutagenesis data to examine the origins of the directed promiscuity exhibited by the PXRs across species. Three structurally flexiblemore » loops adjacent to the ligand-binding pocket of PXR are disordered in this crystal structure, including the 200-210 region that is part of a sequence insert novel to the promiscuous PXRs relative to other members of the nuclear receptor superfamily. The 4-methyl-1-piperazinyl ring of rifampicin, which would lie adjacent to the disordered protein regions, is also disordered and not observed in the structure. Taken together, our results indicate that one wall of the PXR ligand-binding cavity can remain flexible even when the receptor is in complex with an activating ligand. These observations highlight the key role that structural flexibility plays in PXR's promiscuous response to xenobiotics.« less

Overlapping and Divergent Actions of Structurally Distinct Histone Deacetylase Inhibitors in Cardiac Fibroblasts.

PubMed

Schuetze, Katherine B; Stratton, Matthew S; Blakeslee, Weston W; Wempe, Michael F; Wagner, Florence F; Holson, Edward B; Kuo, Yin-Ming; Andrews, Andrew J; Gilbert, Tonya M; Hooker, Jacob M; McKinsey, Timothy A

2017-04-01

Inhibitors of zinc-dependent histone deacetylases (HDACs) profoundly affect cellular function by altering gene expression via changes in nucleosomal histone tail acetylation. Historically, investigators have employed pan-HDAC inhibitors, such as the hydroxamate trichostatin A (TSA), which simultaneously targets members of each of the three zinc-dependent HDAC classes (classes I, II, and IV). More recently, class- and isoform-selective HDAC inhibitors have been developed, providing invaluable chemical biology probes for dissecting the roles of distinct HDACs in the control of various physiologic and pathophysiological processes. For example, the benzamide class I HDAC-selective inhibitor, MGCD0103 [ N -(2-aminophenyl)-4-[[(4-pyridin-3-ylpyrimidin-2-yl)amino]methyl] benzamide], was shown to block cardiac fibrosis, a process involving excess extracellular matrix deposition, which often results in heart dysfunction. Here, we compare the mechanisms of action of structurally distinct HDAC inhibitors in isolated primary cardiac fibroblasts, which are the major extracellular matrix-producing cells of the heart. TSA, MGCD0103, and the cyclic peptide class I HDAC inhibitor, apicidin, exhibited a common ability to enhance histone acetylation, and all potently blocked cardiac fibroblast cell cycle progression. In contrast, MGCD0103, but not TSA or apicidin, paradoxically increased expression of a subset of fibrosis-associated genes. Using the cellular thermal shift assay, we provide evidence that the divergent effects of HDAC inhibitors on cardiac fibroblast gene expression relate to differential engagement of HDAC1- and HDAC2-containing complexes. These findings illustrate the importance of employing multiple compounds when pharmacologically assessing HDAC function in a cellular context and during HDAC inhibitor drug development. Copyright © 2017 by The American Society for Pharmacology and Experimental Therapeutics.

Dihydroconiferyl alcohol - A cell division factor from Acer species.

PubMed

Lee, T S; Purse, J G; Pryce, R J; Horgan, R; Wareing, P F

1981-10-01

A compound that stimulated growth of soybean callus was isolated from spring sap of sycamore (Acer pseudoplatanus L.). Insufficient compound was isolated to permit it to be characterised. A compound with identical properties was isolated from commercial maple syrup, the concentrated spring sap of Acer saccharum L. The compound was identified as 3-(3-methoxy-4-hydroxyphenyl)-propan-1-ol (dihydroconiferyl alcohol, DCA). DCA was also active in the tobacco callus and radish leaf senescence assays, but was inactive in four other tests for cytokinin activity. DCA acted synergistically with kinetin to promote soybean callus growth. It is concluded that DCA has properties distinct from those of purine cytokinins.

Electron-Poor Polar Intermetallics: Complex Structures, Novel Clusters, and Intriguing Bonding with Pronounced Electron Delocalization.

PubMed

Lin, Qisheng; Miller, Gordon J

2018-01-16

Intermetallic compounds represent an extensive pool of candidates for energy related applications stemming from magnetic, electric, optic, caloric, and catalytic properties. The discovery of novel intermetallic compounds can enhance understanding of the chemical principles that govern structural stability and chemical bonding as well as finding new applications. Valence electron-poor polar intermetallics with valence electron concentrations (VECs) between 2.0 and 3.0 e - /atom show a plethora of unprecedented and fascinating structural motifs and bonding features. Therefore, establishing simple structure-bonding-property relationships is especially challenging for this compound class because commonly accepted valence electron counting rules are inappropriate. During our efforts to find quasicrystals and crystalline approximants by valence electron tuning near 2.0 e - /atom, we observed that compositions close to those of quasicrystals are exceptional sources for unprecedented valence electron-poor polar intermetallics, e.g., Ca 4 Au 10 In 3 containing (Au 10 In 3 ) wavy layers, Li 14.7 Mg 36.8 Cu 21.5 Ga 66 adopting a type IV clathrate framework, and Sc 4 Mg x Cu 15-x Ga 7.5 that is incommensurately modulated. In particular, exploratory syntheses of AAu 3 T (A = Ca, Sr, Ba and T = Ge, Sn) phases led to interesting bonding features for Au, such as columns, layers, and lonsdaleite-type tetrahedral frameworks. Overall, the breadth of Au-rich polar intermetallics originates, in part, from significant relativistics effect on the valence electrons of Au, effects which result in greater 6s/5d orbital mixing, a small effective metallic radius, and an enhanced Mulliken electronegativity, all leading to ultimate enhanced binding with nearly all metals including itself. Two other successful strategies to mine electron-poor polar intermetallics include lithiation and "cation-rich" phases. Along these lines, we have studied lithiated Zn-rich compounds in which structural complexity can be realized by small amounts of Li replacing Zn atoms in the parent binary compounds CaZn 2 , CaZn 3 , and CaZn 5 ; their phase formation and bonding schemes can be rationalized by Fermi surface-Brillouin zone interactions between nearly free-electron states. "Cation-rich", electron-poor polar intermetallics have emerged using rare earth metals as the electropositive ("cationic") component together metal/metalloid clusters that mimic the backbones of aromatic hydrocarbon molecules, which give evidence of extensive electronic delocalization and multicenter bonding. Thus, we can identify three distinct, valence electron-poor, polar intermetallic systems that have yielded unprecedented phases adopting novel structures containing complex clusters and intriguing bonding characteristics. In this Account, we summarize our recent specific progress in the developments of novel Au-rich BaAl 4 -type related structures, shown in the "gold-rich grid", lithiation-modulated Ca-Li-Zn phases stabilized by different bonding characteristics, and rare earth-rich polar intermetallics containing unprecedented hydrocarbon-like planar Co-Ge metal clusters and pronounced delocalized multicenter bonding. We will focus mainly on novel structural motifs, bonding analyses, and the role of valence electrons for phase stability.

Human aldo-keto reductases 1B1 and 1B10: a comparative study on their enzyme activity toward electrophilic carbonyl compounds.

PubMed

Shen, Yi; Zhong, Linlin; Johnson, Stephen; Cao, Deliang

2011-05-30

Aldo-keto reductase family 1 member B1 (AKR1B1, 1B1 in brief) and aldo-keto reductase family 1 member B10 (AKR1B10, 1B10 in brief) are two proteins with high similarities in their amino acid sequences, stereo structures, and substrate specificity. However, these two proteins exhibit distinct tissue distributions; 1B10 is primarily expressed in the gastrointestinal tract and adrenal gland, whereas 1B1 is ubiquitously present in all tissues/organs, suggesting their difference in biological functions. This study evaluated in parallel the enzyme activity of 1B1 and 1B10 toward alpha, beta-unsaturated carbonyl compounds with cellular and dietary origins, including acrolein, crotonaldehyde, 4-hydroxynonenal, trans-2-hexenal, and trans-2,4-hexadienal. Our results showed that 1B10 had much better enzyme activity and turnover rates toward these chemicals than 1B1. By detecting the enzymatic products using high-performance liquid chromatography, we measured their activity to carbonyl compounds at low concentrations. Our data showed that 1B10 efficiently reduced the tested carbonyl compounds at physiological levels, but 1B1 was less effective. Ectopically expressed 1B10 in 293T cells effectively eliminated 4-hydroxynonenal at 5 μM by reducing to 1,4-dihydroxynonene, whereas endogenously expressed 1B1 did not. The 1B1 and 1B10 both showed enzyme activity to glutathione-conjugated carbonyl compounds, but 1B1 appeared more active in general. Together our data suggests that 1B10 is more effectual in eliminating free electrophilic carbonyl compounds, but 1B1 seems more important in the further detoxification of glutathione-conjugated carbonyl compounds. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

The crystal structures of two chalcones: (2E)-1-(5-chloro-thio-phen-2-yl)-3-(2-methyl-phen-yl)prop-2-en-1-one and (2E)-1-(anthracen-9-yl)-3-[4-(propan-2-yl)phen-yl]prop-2-en-1-one.

PubMed

Girisha, Marisiddaiah; Yathirajan, Hemmige S; Jasinski, Jerry P; Glidewell, Christopher

2016-08-01

In the crystal of compound (I), C14H11ClOS, mol-ecules are linked by C-H⋯O hydrogen bonds to form simple C(5) chains. Compound (II), C26H22O, crystallizes with Z' = 2 in space group P-1; one of the mol-ecules is fully ordered but the other is disordered over two sets of atomic sites having occupancies 0.644 (3) and 0.356 (3). The two disordered components differ from one another in the orientation of the isopropyl substituents, and both differ from the ordered mol-ecules in the arrangement of the central propenone spacer unit, so that the crystal of (II) contains three distinct conformers. The ordered and disordered conformers each form a C(8) chain built from a single type of C-H⋯O hydrogen bond but those formed by the disordered conformers differ from that formed by the ordered form.

Direct Effects of Physcion, Chrysophanol, Emodin, and Pachybasin on Germination and Appressorium Formation of the Barley ( Hordeum vulgare L.) Powdery Mildew Fungus Blumeria graminis f. sp. hordei (DC.) Speer.

PubMed

Hildebrandt, Ulrich; Marsell, Alexander; Riederer, Markus

2018-04-04

Several anthraquinone derivatives are active components of fungicidal formulations particularly effective against powdery mildew fungi. The antimildew effect of compounds such as physcion and chrysophanol is largely attributed to host plant defense induction. However, so far a direct fungistatic/fungicidal effect of anthraquinone derivatives on powdery mildew fungi has not been unequivocally demonstrated. By applying a Formvar-based in vitro system we demonstrate a direct, dose-dependent effect of physcion, chrysophanol, emodin, and pachybasin on conidial germination and appressorium formation of Blumeria graminis f. sp. hordei (DC.) Speer, the causative agent of barley ( Hordeum vulgare L.) powdery mildew. Physcion was the most effective among the tested compounds. At higher doses, physcion mainly inhibited conidial germination. At lower rates, however, a distinct interference with appressorium formation became discernible. Physcion and others may act by modulating both the infection capacity of the powdery mildew pathogen and host plant defense. Our results suggest a specific arrangement of substituents at the anthraquinone backbone structure being crucial for the direct antimildew effect.

Acute toxicity assessment of perfluorinated carboxylic acids towards the Baltic microalgae.

PubMed

Latała, Adam; Nędzi, Marcin; Stepnowski, Piotr

2009-09-01

The presence of high-energy carbon-fluorine bonds in perfluoro compounds lends them great stability and causes them to be environmentally persistent. Relatively little is known about the acute toxicity of perfluorinated carboxylic acids (PFCAs) to ecotoxicological markers such as aquatic plants and animals. This study tested the toxicity of these compounds to the green alga Chlorella vulgaris, the diatom Skeletonema marinoi and the blue-green alga Geitlerinema amphibium, which are species representative of the algal flora of the Baltic Sea. The EC(50) values obtained range from 0.28 mM to 12.84 mM. A distinct relationship between hydrophobicity and toxicity is demonstrated. For every extra perfluoromethylene group in the alkyl chain, the toxicity increases twofold. LogEC(50) values are very well correlated linearly with both the number of carbon atoms in the perfluoroalkyl chain and the partition coefficients. The results also indicate that there are clear differences between the responses of particular taxonomic groups of algae: blue-green algae and diatoms are far more sensitive to PFCAs than green algae, probably because of differences in cell wall structure.

Calcium phenylphosphonate as a host for 4-aminobenzoic acid-Synthesis, characterization, and cation adsorption from ethanol solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lazarin, Angelica M., E-mail: amlazarin2@uem.br; Ganzerli, Thiago A.; Sernaglia, Rosana L.

2009-11-15

Crystalline lamellar calcium phenylphosphonate retained 4-aminobenzoic acid inside its cavity without leaching. The intense infrared bands in the 1160-695 cm{sup -1} interval confirmed the presence of the phosphonate groups attached to the inorganic layer, with sharp and intense peaks in X-ray diffraction patterns, which gave basal distances of 1532 and 1751 pm for the original and the intercalated compounds, respectively. The thermogravimetric curves of both layered compounds showed the release of water molecules and the organic moiety in distinct stages, to yield a final Ca(PO{sub 3}){sub 2} residue. Solid-state {sup 31}P nuclear magnetic resonance spectra presented only one peak formore » the phenylphosphonate groups attached to the main inorganic polymeric structure near 12.4 ppm. The adsorption isotherms from ethanol gave the maximum adsorption capacities of 1.68 and 0.50 mmol g{sup -1} for copper and cobalt, respectively, whose average stability constants followed Co > Cu; the number of ligands was determined as four for both cations.« less

Global Analysis Reveals Families of Chemical Motifs Enriched for hERG Inhibitors

PubMed Central

Du, Fang; Babcock, Joseph J.; Yu, Haibo; Zou, Beiyan; Li, Min

2015-01-01

Promiscuous inhibition of the human ether-à-go-go-related gene (hERG) potassium channel by drugs poses a major risk for life threatening arrhythmia and costly drug withdrawals. Current knowledge of this phenomenon is derived from a limited number of known drugs and tool compounds. However, in a diverse, naïve chemical library, it remains unclear which and to what degree chemical motifs or scaffolds might be enriched for hERG inhibition. Here we report electrophysiology measurements of hERG inhibition and computational analyses of >300,000 diverse small molecules. We identify chemical ‘communities’ with high hERG liability, containing both canonical scaffolds and structurally distinctive molecules. These data enable the development of more effective classifiers to computationally assess hERG risk. The resultant predictive models now accurately classify naïve compound libraries for tendency of hERG inhibition. Together these results provide a more complete reference map of characteristic chemical motifs for hERG liability and advance a systematic approach to rank chemical collections for cardiotoxicity risk. PMID:25700001

Distribution and incorporation mode of the herbicide MCPA in soil derived organo-clay complexes.

PubMed

Riefer, Patrick; Klausmeyer, Timm; Schmidt, Burkhard; Schäffer, Andreas; Schwarzbauer, Jan

2017-08-03

The incorporation of xenobiotics into soil, especially via covalent bonds or sequestration has a major influence on the environmental behavior including toxicity, mobility, and bioavailability. The incorporation mode of 4-chloro-2-methylphenoxyacetic acid (MCPA) into organo-clay complexes has been investigated under a low (8.5 mg MCPA/kg soil) and high (1000 mg MCPA/kg soil) applied concentration, during an incubation period of up to 120 days. Emphasis was laid on the elucidation of distinct covalent linkages between non-extractable MCPA residues and humic sub-fractions (humic acids, fulvic acids, and humin). The cleavage of compounds by a sequential chemical degradation procedure (OH - , BBr 3 , RuO 4 , TMAH thermochemolysis) revealed for both concentration levels ester/amide bonds as the predominate incorporation modes followed by ether linkages. A possible influence of the soil microbial activity on the mode of incorporation could be observed in case of the high level samples. Structure elucidation identified MCPA as the only nonextractable substance, whereas the metabolite 4-chloro-2-methylphenol was additionally found as bioavailable and bioaccessible compound.

A combined temperature-dependent electron and single-crystal X-ray diffraction study of the fresnoite compound Rb 2V 4+V 25+O 8

NASA Astrophysics Data System (ADS)

Withers, Ray L.; Höche, Thomas; Liu, Yun; Esmaeilzadeh, Saeid; Keding, Ralf; Sales, Brian

2004-10-01

High-purity Rb2V3O8 has been grown and temperature-dependent electron and single-crystal X-ray diffraction used to carefully investigate its fresnoite-type reciprocal lattice. In contrast to other recently investigated representatives of the fresnoite family of compounds, Rb2V3O8 is not incommensurately modulated with an incommensurate basal plane primary modulation wave vector given by q∼0.3 <110>*. A careful low-temperature electron diffraction study has, however, revealed the existence of weak incommensurate satellite reflections characterized by the primitive primary modulation wave vector q1∼0.16c*. The reciprocal space positioning of these incommensurate satellite reflections, the overall (3+1)-d superspace group symmetry, as well as the shapes of the refined displacement ellipsoids determined from single-crystal XRD refinement, are all consistent with their arising from a distinct type of condensed rigid unit modes (RUMs) of distortion of the Rb2V3O8 parent structure.

T-p phase diagrams and the barocaloric effect in materials with successive phase transitions

NASA Astrophysics Data System (ADS)

Gorev, M. V.; Bogdanov, E. V.; Flerov, I. N.

2017-09-01

An analysis of the extensive and intensive barocaloric effect (BCE) at successive structural phase transitions in some complex fluorides and oxyfluorides was performed. The high sensitivity of these compounds to a change in the chemical pressure allows one to vary the succession and parameters of the transformations (temperature, entropy, baric coefficient) over a wide range and obtain optimal values of the BCE. A comparison of different types of schematic T-p phase diagrams with the complicated T( p) dependences observed experimentally shows that in some ranges of temperature and pressure the BCE in compounds undergoing successive transformations can be increased due to a summation of caloric effects associated with distinct phase transitions. The maximum values of the extensive and intensive BCE in complex fluorides and oxyfluorides can be realized at rather low pressure (0.1-0.3 GPa). In a narrow temperature range around the triple points conversion from conventional BCE to inverse BCE is observed, which is followed by a gigantic change of both \\vertΔ S_BCE\\vert and \\vertΔ T_AD\\vert .

Progress in the medicinal chemistry of silicon: C/Si exchange and beyond.

PubMed

Fujii, Shinya; Hashimoto, Yuichi

2017-04-01

Application of silyl functionalities is one of the most promising strategies among various 'elements chemistry' approaches for the development of novel and distinctive drug candidates. Replacement of one or more carbon atoms of various biologically active compounds with silicon (so-called sila-substitution) has been intensively studied for decades, and is often effective for alteration of activity profile and improvement of metabolic profile. In addition to simple C/Si exchange, several novel approaches for utilizing silicon in medicinal chemistry have been suggested in recent years, focusing on the intrinsic differences between silicon and carbon. Sila-substitution offers great potential for enlarging the chemical space of medicinal chemistry, and provides many options for structural development of drug candidates.

[Possibilities of modern imaging technologies in early diagnosis of Alzheimer disease].

PubMed

Unschuld, Paul G

2015-04-01

Recent advances in neuroimaging technology and image analysis algorithms have significantly contributed to a better understanding of spatial and temporal aspects of brain change associated with Alzheimer Disease. The current review will demonstrate how functional (fMRI) and structural magnetic resonance imaging (MRI) techniques may be used to identify distinct patterns of brain change associated with disease progression and also increased risk for Alzheimer Disease. Moreover, Positron Emission Tomography (PET) based measures of glucosemetabolism (Fluorodeoxyglucose, FDG) and Amyloid-beta plaque density (11-C-Pittsburgh Compound B, PiB and 18-F) will be reviewed regarding their diagnostic value for assessing the individual degree of Alzheimer -pathology and thus complement the information provided by MRI and other clinical measures.

Synthesis and biology of cyclic imine toxins, an emerging class of potent, globally distributed marine toxins.

PubMed

Stivala, Craig E; Benoit, Evelyne; Aráoz, Rómulo; Servent, Denis; Novikov, Alexei; Molgó, Jordi; Zakarian, Armen

2015-03-01

From a small group of exotic compounds isolated only two decades ago, Cyclic Imine (CI) toxins have become a major class of marine toxins with global distribution. Their distinct chemical structure, biological mechanism of action, and intricate chemistry ensures that CI toxins will continue to be the subject of fascinating fundamental studies in the broad fields of chemistry, chemical biology, and toxicology. The worldwide occurrence of potent CI toxins in marine environments, their accumulation in shellfish, and chemical stability are important considerations in assessing risk factors for human health. This review article aims to provide an account of chemistry, biology, and toxicology of CI toxins from their discovery to the present day.

Identification of proton-pump inhibitor drugs that inhibit Trichomonas vaginalis uridine nucleoside ribohydrolase.

PubMed

Shea, Tara A; Burburan, Paola J; Matubia, Vivian N; Ramcharan, Sandy S; Rosario, Irving; Parkin, David W; Stockman, Brian J

2014-02-15

Trichomonas vaginalis continues to be a major health problem with drug-resistant strains increasing in prevalence. Novel antitrichomonal agents that are mechanistically distinct from current therapies are needed. The NIH Clinical Compound Collection was screened to find inhibitors of the uridine ribohydrolase enzyme required by the parasite to scavenge uracil for its growth. The proton-pump inhibitors omeprazole, pantoprazole, and rabeprazole were identified as inhibitors of this enzyme, with IC50 values ranging from 0.3 to 14.5 μM. This suggests a molecular mechanism for the in vitro antitrichomonal activity of these proton-pump inhibitors, and may provide important insights toward structure-based drug design. Copyright © 2014 Elsevier Ltd. All rights reserved.

Designing Single-Ion Magnets and Phosphorescent Materials with 1-Methylimidazole-5-carboxylate and Transition-Metal Ions.

PubMed

García-Valdivia, Antonio A; Seco, Jose M; Cepeda, Javier; Rodríguez-Diéguez, Antonio

2017-11-20

Detailed structural, magnetic, and photoluminescence (PL) characterization of four new compounds based on 1-methylimidazole-5-carboxylate (mimc) ligand and transition metal ions, namely [Ni(mimc) 2 (H 2 O) 4 ] (1), [Co(μ-mimc) 2 ] n (2), {[Cu 2 (μ-mimc) 4 (H 2 O)]·2H 2 O} n (3), and [Cd(μ-mimc) 2 (H 2 O)] n (4) is reported. The structural diversity found in the family of compounds derives from the coordination versatility of the ligand, which coordinates as a terminal ligand to give a supramolecular network of monomeric entities in 1 or acts as a bridging linker to build isoreticular 2D coordination polymers (CPs) in 2-4. Magnetic direct-current (dc) susceptibility data have been measured for compounds 1-3 to analyze the exchange interactions among paramagnetic centers, which have been indeed supported by calculations based on broken symmetry (BS) and density functional theory (DFT) methodology. The temperature dependence of susceptibility and magnetization data of 2 are indicative of easy-plane anisotropy (D = +12.9 cm -1 , E = +0.5 cm -1 ) that involves a bistable M s = ±1/2 ground state. Alternating-current (ac) susceptibility curves exhibit field-induced single-ion magnet (SIM) behavior that occurs below 14 K, which is characterized by two spin relaxation processes of distinct nature: fast relaxation of single ions proceeding through multiple mechanisms (U eff = 26 K) and a slow relaxation attributed to interactions along the polymeric crystal building. Exhaustive PL analysis of compound 4 in the solid state confirms low-temperature phosphorescent green emission consisting of radiative lifetimes in the range of 0.25-0.43 s, which explains the afterglow observed during about 1 s after the removal of the UV source. Time-dependent DFT and computational calculations to estimate phosphorescent vertical transitions have been also employed to provide an accurate description of the PL performance of this long-lasting phosphor.

Caged Garcinia Xanthones, a Novel Chemical Scaffold with Potent Antimalarial Activity.

PubMed

Ke, Hangjun; Morrisey, Joanne M; Qu, Shiwei; Chantarasriwong, Oraphin; Mather, Michael W; Theodorakis, Emmanuel A; Vaidya, Akhil B

2017-01-01

Caged Garcinia xanthones (CGXs) constitute a family of natural products that are produced by tropical/subtropical trees of the genus Garcinia CGXs have a unique chemical architecture, defined by the presence of a caged scaffold at the C ring of a xanthone moiety, and exhibit a broad range of biological activities. Here we show that synthetic CGXs exhibit antimalarial activity against Plasmodium falciparum, the causative parasite of human malaria, at the intraerythrocytic stages. Their activity can be substantially improved by attaching a triphenylphosphonium group at the A ring of the caged xanthone. Specifically, CR135 and CR142 were found to be highly effective antimalarial inhibitors, with 50% effective concentrations as low as ∼10 nM. CGXs affect malaria parasites at multiple intraerythrocytic stages, with mature stages (trophozoites and schizonts) being more vulnerable than immature rings. Within hours of CGX treatment, malaria parasites display distinct morphological changes, significant reduction of parasitemia (the percentage of infected red blood cells), and aberrant mitochondrial fragmentation. CGXs do not, however, target the mitochondrial electron transport chain, the target of the drug atovaquone and several preclinical candidates. CGXs are cytotoxic to human HEK293 cells at the low micromolar level, which results in a therapeutic window of around 150-fold for the lead compounds. In summary, we show that CGXs are potent antimalarial compounds with structures distinct from those of previously reported antimalarial inhibitors. Our results highlight the potential to further develop Garcinia natural product derivatives as novel antimalarial agents. Copyright © 2016 American Society for Microbiology.

The discriminative effects of the kappa-opioid hallucinogen salvinorin A in nonhuman primates: dissociation from classic hallucinogen effects.

PubMed

Butelman, Eduardo R; Rus, Szymon; Prisinzano, Thomas E; Kreek, Mary Jeanne

2010-06-01

The widely available hallucinogen salvinorin A is a unique example of a plant-derived compound selective for kappa-opioid receptors and may produce effects distinct from those of other compounds with classic hallucinogenic or dissociative properties which are also abused in humans. The objective of this study is to characterize the salvinorin A discriminative cue in nonhuman primates with high kappa-receptor genetic homology to humans. Adult rhesus monkeys (n = 3) were trained to discriminate salvinorin A (0.015 mg/kg, s.c.) from vehicle, in a food-reinforced operant discrimination assay. Parallel studies, using unconditioned behavioral endpoints (facial relaxation and ptosis) also evaluated the kappa-opioid receptor mediation of salvinorin A in vivo function. Monkeys trained to discriminate salvinorin A generalized structurally diverse, centrally penetrating kappa-agonists (bremazocine, U69,593, and U50,488). By contrast, mu- and delta-opioid agonists (fentanyl and SNC80, respectively) were not generalized, nor were the serotonergic 5HT2 hallucinogen psilocybin or the dissociative N-methyl-D-aspartic acid antagonist, ketamine. The discriminative effects of salvinorin A were blocked by the opioid antagonist quadazocine (0.32 mg/kg), but not by the 5HT2 antagonist ketanserin (0.1 mg/kg). Consistent with these findings, salvinorin and kappa-agonists (e.g., U69,593) produce effects in the unconditioned endpoints (e.g., ptosis), whereas psilocybin was inactive. These findings support the conclusion that the interoceptive/discriminative cue produced by salvinorin A is mediated by agonism at kappa-receptors and is mechanistically distinct from that produced by a classic serotonergic hallucinogen.

Identification of New and Distinctive Exposures from Little Cigars

PubMed Central

Klupinski, Theodore P.; Strozier, Erich D.; Friedenberg, David A.; Brinkman, Marielle C.; Gordon, Sydney M.; Clark, Pamela I.

2016-01-01

Little cigar mainstream smoke is less well-characterized than cigarette mainstream smoke in terms of chemical composition. This study compared four popular little cigar products against four popular cigarette products to determine compounds that are either unique to or more abundant in little cigars. These compounds are categorized as new or distinctive exposures, respectively. Total particulate matter samples collected from machine-generated mainstream smoke were extracted with methylene chloride, and the extracts were analyzed using two-dimensional gas chromatography–time-of-flight mass spectrometry. The data were evaluated using novel data-processing algorithms that account for characteristics specific to the selected analytical technique and variability associated with replicate sample analyses. Among more than 25 000 components detected across the complete data set, ambrox was confirmed as a new exposure, and 3-methylbutanenitrile and 4-methylimidazole were confirmed as distinctive exposures. Concentrations of these compounds for the little cigar mainstream smoke were estimated at approximately 0.4, 0.7, and 12 μg/rod, respectively. In achieving these results, this study has demonstrated the capability of a powerful analytical approach to identify previously uncharacterized tobacco-related exposures from little cigars. The same approach could also be applied to other samples to characterize constituents associated with tobacco product classes or specific tobacco products of interest. Such analyses are critical in identifying tobacco-related exposures that may affect public health. PMID:26605856

Key cytokines of adaptive immunity are differentially induced in rainbow trout kidney by a group of structurally related geranyl aromatic derivatives.

PubMed

Valenzuela, Beatriz; Obreque, Javiera; Soto-Aguilera, Sarita; Maisey, Kevin; Imarai, Mónica; Modak, Brenda

2016-02-01

Filifolinone is a semi-synthetic terpenoid derivative obtained from Heliotropium filifolium that increases the expression level of pro-inflammatory and anti-inflammatory cytokines in kidney cells of salmon. Because cytokines are produced in response to a foreign organism and by distinct other signals modulating immune responses, we further studied the potential immunomodulatory effects of a group of structural related terpenoid derivatives from H. filifolium on salmonids to determine the relationship between the chemical structure of the derivatives and their ability to modify cytokine expression and the lymphoid content. The resin and four 3H-spiro 1-benzofuran-2,1'-cyclohexane derivatives were tested in vivo in rainbow trout (Oncorhynchus mykiss) by quantifying the transcript levels of antiviral and T helper-type cytokines and T and B cells in the kidney. Three of the four terpenoids differ only in the C-7'substituent of the cyclohexane and the presence of the ketone group at this position in Filifolinone appeared responsible of an important up-regulation of IFN-α1, IFN-γ, IL-4/13A and IL-17D in the kidney of the treated trout. In addition, the absence of a methoxy group in carbon 7 of the benzene ring, found in all compounds but not in Folifolinoic acid, produced a significant reduction of IFN-γ, IL-12 and IL-4/13A transcripts. B cells were not affected by the compound treatment but Filifolinoic acid and the resin induced a significant reduction of T cells. Altogether, results showed that immunomodulating responses observed in the trout by effect of 3H-spiro 1-benzofuran-2,1'-cyclohexane derivatives is related to the presence of the ketone group in the carbon 7' and the methoxy group in carbon 7 of the benzene ring, being Filifolinone the most active immunostimulatory compound identified. Copyright © 2015 Elsevier Ltd. All rights reserved.

Giant crystal-electric-field effect and complex magnetic behavior in single-crystalline CeRh3Si2

NASA Astrophysics Data System (ADS)

Pikul, A. P.; Kaczorowski, D.; Gajek, Z.; Stȩpień-Damm, J.; Ślebarski, A.; Werwiński, M.; Szajek, A.

2010-05-01

Single-crystalline CeRh3Si2 was investigated by means of x-ray diffraction, magnetic susceptibility, magnetization, electrical resistivity, and specific-heat measurements carried out in wide temperature and magnetic field ranges. Moreover, the electronic structure of the compound was studied at room temperature by cerium core-level x-ray photoemission spectroscopy (XPS). The physical properties were analyzed in terms of crystalline electric field and compared with results of ab initio band-structure calculations performed within the density-functional theory approach. The compound was found to crystallize in the orthorhombic unit cell of the ErRh3Si2 type (space group Imma No.74, Pearson symbol: oI24 ) with the lattice parameters a=7.1330(14)Å , b=9.7340(19)Å , and c=5.6040(11)Å . Analysis of the magnetic and XPS data revealed the presence of well-localized magnetic moments of trivalent cerium ions. All the physical properties were found to be highly anisotropic over the whole temperature range studied and influenced by exceptionally strong crystalline electric field with the overall splitting of the 4f1 ground multiplet exceeding 5700 K. Antiferromagnetic order of the cerium magnetic moments at TN=4.70(1)K and their subsequent spin rearrangement at Tt=4.48(1)K manifest themselves as distinct anomalies in the temperature characteristic of all the physical properties investigated and exhibit complex evolution in an external magnetic field. A tentative magnetic B-T phase diagram, constructed for B parallel to the b axis being the easy magnetization direction, shows very complex magnetic behavior of CeRh3Si2 , similar to that recently reported for an isostructural compound CeIr3Si2 . The electronic band-structure calculations corroborated the antiferromagnetic ordering of the cerium magnetic moments and well-reproduced the experimental XPS valence-band spectrum.

Praseodymium methanesulfonate catalyzed one-pot synthesis of 3,4-dihydropyrimidin-2-(1H)-ones.

PubMed

Wang, Min; Song, Zhiguo; Gong, Hong; Jiang, Heng

2008-01-01

A series of 3,4-dihydropyrimidin-2-(1H)-ones compounds was synthesized efficiently by a one-pot cyclocondensation of an aldehyde, 1,3-dicarbonyl compound, and urea in absolute ethanol under refluxing temperature using praseodymium methanesulfonate as catalyst. After the reaction, the catalyst can be easily recovered and reused several times without distinct decrease in reaction yields.

Synthesis and characterization of 5-bis(benzyl thio)-1, 3, 4-thiadiazole complexes with fac-ReBr3(CO) 32-

USDA-ARS?s Scientific Manuscript database

Reactions of 2,5-bis(benzylthio)-1,3,4-thiadiazole (Compound 1) with a common organometallic rhenium starting material [NEt4]2[fac-[Re(I)Br3(CO)3] yielded two distinct types of complexes. Both complexes coordinate only through the nitrogen of the thiadiazole ring. Reaction of Compound 1 with the rhe...

Ce{sub 2}PdIn{sub 8}, Ce{sub 3}PdIn{sub 11} and Ce{sub 5}Pd{sub 2}In{sub 19}—members of homological series based on AuCu{sub 3}- and PtHg{sub 2}-type structural units

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tursina, A.; Nesterenko, S.; Seropegin, Y.

Crystal structures of three members of a unique homological series with the general formula Ce{sub m}Pd{sub n}In{sub 3m+2n} based on the AuCu{sub 3} and PtHg{sub 2} structure types were studied by single-crystal X-ray diffraction. The compounds crystallize with space group P4/mmm (Z=1) and the lattice parameters: a=4.6900(9) Å, c=12.185(6) Å for Ce{sub 2}PdIn{sub 8}, a=4.6846(8) Å, c=16.846(8) Å for Ce{sub 3}PdIn{sub 11}, and a=4.70120(10) Å, c=29.1359(4) Å for Ce{sub 5}Pd{sub 2}In{sub 19}. The crystal structures of Ce{sub 3}PdIn{sub 11} and Ce{sub 5}Pd{sub 2}In{sub 19} represent new types. The three structures constitute of [CeIn{sub 3}] cuboctahedra layers and [PdIn{sub 2}] rectangularmore » polyhedra layers, alternating along the tetragonal c-axis in accordance with the m:n proportion. The magnetic and electrical transport properties of the novel compounds Ce{sub 3}PdIn{sub 11} and Ce{sub 5}Pd{sub 2}In{sub 19} were investigated down to 1.72 K. Both indides are Curie–Weiss paramagnets due to the presence of fairly well localized 4f electrons of trivalent cerium ions. The electrical resistivity of both materials is dominated over an extended temperature range by strong spin–flip Kondo interactions with the characteristic temperature scale of 20–30 K. - Graphical abstract: TOC Figure Crystal structures of Ce{sub 3}PdIn{sub 11}, Ce{sub 2}PdIn{sub 8}, and Ce{sub 5}Pd{sub 2}In{sub 19}. Highlights: ► Large section of Ce–Pd–In phase diagram was examined. ► Three distinct ternary phases were identified, two of them for the first time. ► Crystal structures of two novel compounds constitute new structure types. ► The determined crystal structures show close mutual relationship. ► Ce{sub 3}PdIn{sub 11} and Ce{sub 5}Pd{sub 2}In{sub 19} are paramagnetic Kondo lattices.« less

Higher coordinate gold(I) complexes with the weak Lewis base tri(4-fluorophenyl) phosphine. Synthesis, structural, luminescence, and DFT studies

NASA Astrophysics Data System (ADS)

Agbeworvi, George; Assefa, Zerihun; Sykora, Richard E.; Taylor, Jared; Crawford, Carlos

2016-03-01

The structures and spectroscopic properties of two high coordinate gold(I) phosphine complexes with the TFFPP=tri(4-fluorophenyl)phosphine ligand are reported. Synthesis in a 1:3 metal to ligand ratio provided the compound [AuCl(TFFPP)3] (2) that crystallize in the P 1 bar space group, where the asymmetric unit consists of three independent molecules. In all three sites, two sets of bond angles display distinctly different ranges. The three P-Au-P angles have average values of 117.92°, 117.57°, and 114.78° for sites A, B, and C, with the corresponding P-Au-Cl angles of 98.31°, 99.05°, and 103.38°, respectively. The chloride ion coordinates as the fourth ligand, at the corresponding Au-Cl distance of 2.7337, 2.6825, and 2.6951 Å for the three sites. This distance is longer by 0.40-0.45 Å than the Au-Cl distance found in the mono TFFPP complex 1 (2.285 Å) indicating a weakening of the Au-Cl interaction as the coordination number increases. In compound 3, [Au(TFFPP)3]Cl·½CH2Cl2·H2O, the structure consists of three phosphine ligands bound to the gold(I) atom, but the Cl- exists as uncoordinated counter anion. The structural differences observed in the two complexes are attributable to crystal-packing effects caused by the introduction of H-bonding as well as enhanced intra and inter-molecular π-interaction in 3. The photoluminescence of the complexes compared with that of the ligand show ligand centered emission perturbed by the metal coordination. Theoretical DFT studies conducted on these complexes supports assignments of the electronic transitions observed in these systems.

Chemical Composition of Soil Horizons and Aggregate Size Fractions Under the Hawaiian Fern Dicranopteris and Angiosperm Cheirodendrom

NASA Astrophysics Data System (ADS)

Stewart, C. E.; Amatangelo, K.; Neff, J.

2007-12-01

Soil organic matter (SOM) inherits much of its chemical nature from the dominant vegetation, including phenolic (lignin-derived), aromatic, and aliphatic (cutin and wax-derived) compounds. However, relatively stable recalcitrant compounds may also be formed as a result of condensation and complexation reactions through decomposition and protected with association with mineral particles. The Hawaiian fern species Dicranopteris decomposes more slowly than the angiosperm, Cheirodendrom due to high concentrations of recalcitrant C compounds. These aliphatic fern leaf waxes are well-preserved and may comprise a large portion of the recalcitrant organic matter in these soils. Our objective was to determine the chemical composition of the SOM under the O- (litter-dominated) and the A- (mineral) horizons formed under fern and angiosperm vegetation. To determine the effect of mineral-association, we fractioned the soil into four size classes; 850-590 μm, 590-180 μm, 180-53 μm and <53 μm and characterized the SOM via pyrolysis-gas chromatography-mass spectrometry (py-GC/MS). As the soils developed from the O- to the A-horizon, there was a decrease of lignin-derived phenolic compounds and an increase in more recalcitrant, aromatic and aliphatic C. Soils under ferns had greater relative concentrations of phenolic compounds, while the angiosperms had greater concentrations of fatty-acid methyl esters and furans (some polysaccharide-derived). Differences between size fractions were most evident in the O-horizon of both species. Recalcitrant fern-derived cutin and leaf waxes (alkene and alkanes structures) occurred in the 180-53 μm fraction, which has been shown to be the most stable of the aggregate-size fractions. Soils developed under fern versus angiosperm vegetation have distinct chemical signatures, which likely determine the recalcitrance of the SOM.

How Sensitive Are Transdermal Transport Predictions by Microscopic Stratum Corneum Models to Geometric and Transport Parameter Input?

PubMed

Wen, Jessica; Koo, Soh Myoung; Lape, Nancy

2018-02-01

While predictive models of transdermal transport have the potential to reduce human and animal testing, microscopic stratum corneum (SC) model output is highly dependent on idealized SC geometry, transport pathway (transcellular vs. intercellular), and penetrant transport parameters (e.g., compound diffusivity in lipids). Most microscopic models are limited to a simple rectangular brick-and-mortar SC geometry and do not account for variability across delivery sites, hydration levels, and populations. In addition, these models rely on transport parameters obtained from pure theory, parameter fitting to match in vivo experiments, and time-intensive diffusion experiments for each compound. In this work, we develop a microscopic finite element model that allows us to probe model sensitivity to variations in geometry, transport pathway, and hydration level. Given the dearth of experimentally-validated transport data and the wide range in theoretically-predicted transport parameters, we examine the model's response to a variety of transport parameters reported in the literature. Results show that model predictions are strongly dependent on all aforementioned variations, resulting in order-of-magnitude differences in lag times and permeabilities for distinct structure, hydration, and parameter combinations. This work demonstrates that universally predictive models cannot fully succeed without employing experimentally verified transport parameters and individualized SC structures. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

New marine natural products from sponges (Porifera) of the order Dictyoceratida (2001 to 2012); a promising source for drug discovery, exploration and future prospects.

PubMed

Mehbub, Mohammad F; Perkins, Michael V; Zhang, Wei; Franco, Christopher M M

2016-01-01

The discovery of new drugs can no longer rely primarily on terrestrial resources, as they have been heavily exploited for over a century. During the last few decades marine sources, particularly sponges, have proven to be a most promising source of new natural products for drug discovery. This review considers the order Dictyoceratida in the Phylum Porifera from which the largest number of new marine natural products have been reported over the period 2001-2012. This paper examines all the sponges from the order Dictyoceratida that were reported as new compounds during the time period in a comprehensive manner. The distinctive physical characteristics and the geographical distribution of the different families are presented. The wide structural diversity of the compounds produced and the variety of biological activities they exhibited is highlighted. As a representative of sponges, insights into this order and avenues for future effective natural product discovery are presented. The research institutions associated with the various studies are also highlighted with the aim of facilitating collaborative relationships, as well as to acknowledge the major international contributors to the discovery of novel sponge metabolites. The order Dictyoceratida is a valuable source of novel chemical structures which will continue to contribute to a new era of drug discovery. Copyright © 2015 Elsevier Inc. All rights reserved.

Dentin Biomodification: Strategies, Renewable Resources and Clinical Applications

PubMed Central

Bedran-Russo, Ana K.; Pauli, Guido F.; Chen, Shao-Nong; McAlpine, James; Castellan, Carina S.; Phansalkar, Rasika S; Aguiar, Thaiane R.; Vidal, Cristina M.P.; Napotilano, José; Nam, Joo-Won; Leme, Ariene A.

2014-01-01

Objectives The biomodification of dentin is a biomimetic approach, mediated by bioactive agents, to enhance and reinforce the dentin by locally altering the biochemistry and biomechanical properties. This review provides an overview of key dentin matrix components, targeting effects of biomodification strategies, the chemistry of renewable natural sources, and current research on their potential clinical applications. Methods The PubMed database and collected literature were used as a resource for peer-reviewed articles to highlight the topics of dentin hierarchical structure, biomodification agents, and laboratorial investigations of their clinical applications. In addition, new data is presented on laboratorial methods for the standardization of proanthocyanidin-rich preparations as a renewable source of plant-derived biomodification agents. Results Biomodification agents can be categorized as physical methods and chemical agents. Synthetic and naturally occurring chemical strategies present distinctive mechanism of interaction with the tissue. Initially thought to be driven only by inter- or intra-molecular collagen induced non-enzymatic collagen cross-linking, multiple interactions with other dentin components are fundamental for the long-term biomechanics and biostability of the tissue. Oligomeric proanthocyanidins show promising bioactivity, and their chemical complexity requires systematic evaluation of the active compounds to produce a fully standardized intervention material from renewable resource, prior to their detailed clinical evaluation. Significance Understanding the hierarchical structure of dentin and the targeting effect of the bioactive compounds will establish their use in both dentin-biomaterials interface and caries management. PMID:24309436

Bromination of Marine Dissolved Organic Matter following Full Scale Electrochemical Ballast Water Disinfection.

PubMed

Gonsior, Michael; Mitchelmore, Carys; Heyes, Andrew; Harir, Mourad; Richardson, Susan D; Petty, William Tyler; Wright, David A; Schmitt-Kopplin, Philippe

2015-08-04

An extensively diverse array of brominated disinfection byproducts (DBPs) were generated following electrochemical disinfection of natural coastal/estuarine water, which is one of the main treatment methods currently under consideration for ballast water treatment. Ultra-high-resolution mass spectrometry revealed 462 distinct brominated DBPs at a relative abundance in the mass spectra of more than 1%. A brominated DBP with a relative abundance of almost 22% was identified as 2,2,4-tribromo-5-hydroxy-4-cyclopentene-1,3-dione, which is an analogue to several previously described 2,2,4-trihalo-5-hydroxy-4-cyclopentene-1,3-diones in drinking water. Several other brominated molecular formulas matched those of other known brominated DBPs, such as dibromomethane, which could be generated by decarboxylation of dibromoacetic acid during ionization, dibromophenol, dibromopropanoic acid, dibromobutanoic acid, bromohydroxybenzoic acid, bromophenylacetic acid, bromooxopentenoic acid, and dibromopentenedioic acid. Via comparison to previously described chlorine-containing analogues, bromophenylacetic acid, dibromooxopentenoic acid, and dibromopentenedioic acid were also identified. A novel compound at a 4% relative abundance was identified as tribromoethenesulfonate. This compound has not been previously described as a DBP, and its core structure of tribromoethene has been demonstrated to show toxicological implications. Here we show that electrochemical disinfection, suggested as a candidate for successful ballast water treatment, caused considerable production of some previously characterized DBPs in addition to novel brominated DBPs, although several hundred compounds remain structurally uncharacterized. Our results clearly demonstrate that electrochemical and potentially direct chlorination of ballast water in estuarine and marine systems should be approached with caution and the concentrations, fate, and toxicity of DBP need to be further characterized.

A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain.

PubMed

Patel, Disha; Antwi, Janet; Koneru, Pratibha C; Serrao, Erik; Forli, Stefano; Kessl, Jacques J; Feng, Lei; Deng, Nanjie; Levy, Ronald M; Fuchs, James R; Olson, Arthur J; Engelman, Alan N; Bauman, Joseph D; Kvaratskhelia, Mamuka; Arnold, Eddy

2016-11-04

HIV-1 integrase (IN) is essential for virus replication and represents an important multifunctional therapeutic target. Recently discovered quinoline-based allosteric IN inhibitors (ALLINIs) potently impair HIV-1 replication and are currently in clinical trials. ALLINIs exhibit a multimodal mechanism of action by inducing aberrant IN multimerization during virion morphogenesis and by competing with IN for binding to its cognate cellular cofactor LEDGF/p75 during early steps of HIV-1 infection. However, quinoline-based ALLINIs impose a low genetic barrier for the evolution of resistant phenotypes, which highlights a need for discovery of second-generation inhibitors. Using crystallographic screening of a library of 971 fragments against the HIV-1 IN catalytic core domain (CCD) followed by a fragment expansion approach, we have identified thiophenecarboxylic acid derivatives that bind at the CCD-CCD dimer interface at the principal lens epithelium-derived growth factor (LEDGF)/p75 binding pocket. The most active derivative (5) inhibited LEDGF/p75-dependent HIV-1 IN activity in vitro with an IC 50 of 72 μm and impaired HIV-1 infection of T cells at an EC 50 of 36 μm The identified lead compound, with a relatively small molecular weight (221 Da), provides an optimal building block for developing a new class of inhibitors. Furthermore, although structurally distinct thiophenecarboxylic acid derivatives target a similar pocket at the IN dimer interface as the quinoline-based ALLINIs, the lead compound, 5, inhibited IN mutants that confer resistance to quinoline-based compounds. Collectively, our findings provide a plausible path for structure-based development of second-generation ALLINIs. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Not all boronic acids with a five-membered cycle induce tremor, neuronal damage and decreased dopamine.

PubMed

Pérez-Rodríguez, Maribel; García-Mendoza, Esperanza; Farfán-García, Eunice D; Das, Bhaskar C; Ciprés-Flores, Fabiola J; Trujillo-Ferrara, José G; Tamay-Cach, Feliciano; Soriano-Ursúa, Marvin A

2017-09-01

Several striatal toxins can be used to induce motor disruption. One example is MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine), whose toxicity is accepted as a murine model of parkinsonism. Recently, 3-Thienylboronic acid (3TB) was found to produce motor disruption and biased neuronal damage to basal ganglia in mice. The aim of this study was to examine the toxic effects of four boronic acids with a close structural relationship to 3TB (all having a five-membered cycle), as well as boric acid and 3TB. These boron-containing compounds were compared to MPTP regarding brain access, morphological disruption of the CNS, and behavioral manifestations of such disruption. Data was collected through acute toxicity evaluations, motor behavior tests, necropsies, determination of neuronal survival by immunohistochemistry, Raman spectroscopic analysis of brain tissue, and HPLC measurement of dopamine in substantia nigra and striatum tissue. Each compound showed a distinct profile for motor disruption. For example, motor activity was not disrupted by boric acid, but was decreased by two boronic acids (caused by a sedative effect). 3TB, 2-Thienyl and 2-furanyl boronic acid gave rise to shaking behavior. The various manifestations generated by these compounds can be linked, in part, to different levels of dopamine (measured by HPLC) and degrees of neuronal damage in the basal ganglia and cerebellum. Clearly, motor disruption is not induced by all boronic acids with a five-membered cycle as substituent. Possible explanations are given for the diverse chemico-morphological changes and degrees of disruption of the motor system, considering the role of boron and the structure-toxicity relationship. Copyright © 2017 Elsevier B.V. All rights reserved.

The Lγ Phase of Pulmonary Surfactant.

PubMed

Kumar, Kamlesh; Chavarha, Mariya; Loney, Ryan W; Weiss, Thomas M; Rananavare, Shankar B; Hall, Stephen B

2018-06-05

To determine how different components affect the structure of pulmonary surfactant, we measured X-ray scattering by samples derived from calf surfactant. The surfactant phospholipids demonstrated the essential characteristics of the L γ phase: a unit cell with a lattice constant appropriate for two bilayers, and crystalline chains detected by wide-angle X-ray scattering (WAXS). The electron density profile, obtained from scattering by oriented films at different relative humidities (70-97%), showed that the two bilayers, arranged as mirror images, each contain two distinct leaflets with different thicknesses and profiles. The detailed structures suggest one ordered leaflet that would contain crystalline chains and one disordered monolayer likely to contain the anionic compounds, which constitute ∼10% of the surfactant phospholipids. The spacing and temperature dependence detected by WAXS fit with an ordered leaflet composed of dipalmitoyl phosphatidylcholine. Physiological levels of cholesterol had no effect on this structure. Removing the anionic phospholipids prevented formation of the L γ phase. The cationic surfactant proteins inhibited L γ structures, but at levels unlikely related to charge. Because the L γ phase, if arranged properly, could produce a self-assembled ordered interfacial monolayer, the structure could have important functional consequences. Physiological levels of the proteins, however, inhibit formation of the L γ structures at high relative humidities, making their physiological significance uncertain.

Fragmentation study of iridoid glycosides including epimers by liquid chromatography-diode array detection/electrospray ionization mass spectrometry and its application in metabolic fingerprint analysis of Gardenia jasminoides Ellis.

PubMed

Zhou, Tingting; Liu, Hua; Wen, Jun; Fan, Guorong; Chai, Yifeng; Wu, Yutian

2010-09-15

A high-performance liquid chromatography-diode array detection/electrospray ionization mass spectrometry (HPLC-DAD/ESI-MS) method was applied to the characterization of ten iridoid glycosides in Gardenia jasminoides Ellis, a traditional Chinese medicine. During the process of structural elucidation, two groups of isomers including two epimers were structurally characterized and differentiated according to their distinctive fragmentation patterns which were closely related to their isomeric differentiations. Subsequently, the major compounds were purified by multi-dimensional chromatography and semi-preparative HPLC and the structure identification was confirmed with NMR techniques. The major fragmentation pathways of iridoid glycosides in Gardenia jasminoides Ellis obtained through the MS data were schemed systematically, which provided the best sensitivity and specificity for characterization of the iridoid glycosides especially the isomers so far. Based on the fragmentation patterns of iridoid glycosides concluded, seven major iridoid glycosides were characterized in rat plasma after intravenous administration of Gardenia jasminoides Ellis. Copyright 2010 John Wiley & Sons, Ltd.

Strong cooperative coupling of pressure-induced magnetic order and nematicity in FeSe

DOE PAGES

Kothapalli, K.; Bohmer, A. E.; Jayasekara, W. T.; ...

2016-09-01

A hallmark of the iron-based superconductors is the strong coupling between magnetic, structural and electronic degrees of freedom. However, a universal picture of the normal state properties of these compounds has been confounded by recent investigations of FeSe where the nematic (structural) and magnetic transitions appear to be decoupled. Here, using synchrotron-based high-energy x-ray diffraction and time-domain Mossbauer spectroscopy, we show that nematicity and magnetism in FeSe under applied pressure are indeed strongly coupled. Distinct structural and magnetic transitions are observed for pressures between 1.0 and 1.7 GPa and merge into a single first-order transition for pressures ≳1.7 GPa, reminiscentmore » of what has been found for the evolution of these transitions in the prototypical system Ba(Fe 1–xCo x) 2As 2. Lastly, our results are consistent with a spin-driven mechanism for nematic order in FeSe and provide an important step towards a universal description of the normal state properties of the iron-based superconductors.« less

Insights into the structure of mixed CO 2/CH 4 in gas hydrates

DOE PAGES

Everett, S. Michelle; Rawn, Claudia J.; Chakoumakos, Bryan C.; ...

2015-05-12

The exchange of carbon dioxide for methane in natural gas hydrates is an attractive approach to harvesting CH 4 for energy production while simultaneously sequestering CO 2. In addition to the energy and environmental implications, the solid solution of clathrate hydrate (CH 4) 1-x(CO 2) x·5.75H 2O provides a model system to study how the distinct bonding and shapes of CH 4 and CO 2 influence the structure and properties of the compound. In this paper, high-resolution neutron diffraction was used to examine mixed CO 2/CH 4 gas hydrates. CO 2-rich hydrates had smaller lattice parameters, which were attributed tomore » the higher affinity of the CO 2 molecule interacting with H 2O molecules that form the surrounding cages, and resulted in a reduction in the unit-cell volume. Experimental nuclear scattering densities illustrate how the cage occupants and energy landscape change with composition. Finally, these results provide important insights on the impact and mechanisms for the structure of mixed CH 4/CO 2 gas hydrate.« less

Synthesis and characterization of hexaarylbenzenes with five or six different substituents enabled by programmed synthesis

NASA Astrophysics Data System (ADS)

Suzuki, Shin; Segawa, Yasutomo; Itami, Kenichiro; Yamaguchi, Junichiro

2015-03-01

Since its discovery in 1825, benzene has served as one of the most used and indispensable building blocks of chemical compounds, ranging from pharmaceuticals and agrochemicals to plastics and those used in organic electronic devices. Benzene has six hydrogen atoms that can each be replaced by different substituents, which means that the structural diversity of benzene derivatives is intrinsically extraordinary. The number of possible substituted benzenes from n different substituents is (2n + 2n2 + 4n3 + 3n4 + n6)/12. However, owing to a lack of general synthetic methods for making multisubstituted benzenes, this potentially huge structural diversity has not been fully exploited. Here, we describe a programmed synthesis of hexaarylbenzenes using C-H activation, cross-coupling and [4+2] cycloaddition reactions. The present method allows for the isolation and structure-property characterization of hexaarylbenzenes with distinctive aryl substituents at all positions for the first time. Moreover, the established protocol can be applied to the synthesis of tetraarylnaphthalenes and pentaarylpyridines.

Structural modulation of silver complexes and their distinctive catalytic properties.

PubMed

Zhao, Yue; Chen, Kai; Fan, Jian; Okamura, Taka-aki; Lu, Yi; Luo, Li; Sun, Wei-Yin

2014-02-07

A family of silver(I) complexes, [Ag2(L)2(OOCCF3)2] (1), [Ag(L)0.5(OOCCF3)] (2), [Ag(L)2](OOCCF3)(H2O)2 (3), was obtained by reactions of 4,4'-di(2-oxazolinyl)biphenyl (L) and AgOOCCF3 in different reaction media. Compound 1 has a 1D chain structure with alternative connections between the Ag(I) and L ligand. When the crystal nucleation inductor, pyrazine, was added into the reaction system, complex 2 was isolated with no pyrazine observed in its structure. In 2, the 1D inorganic chains formed by Ag(I) cations and OOCCF3(-) anions were connected by the L ligand to produce a 2D network. When a different inductor, imidazole, was added into the reaction system, 3 with (4,4) topology was synthesized, and again no imidazole was found in 3. When 1-3 were used as catalysts for cycloaddition reactions between imino esters and methyl acrylate, 3 affords the highest yield, in which the particular size of the channels in 3 led to its selective catalytic performance.

The cytotoxicity of organobismuth compounds with certain molecular structures can be diminished by replacing the bismuth atom with an antimony atom in the molecules.

PubMed

Kohri, Kumiko; Yoshida, Eiko; Yasuike, Shuji; Fujie, Tomoya; Yamamoto, Chika; Kaji, Toshiyuki

2015-06-01

Organic-inorganic hybrid molecules, which are composed of an organic structure and metal(s), are indispensable for synthetic chemical reactions; however, their toxicity has been incompletely understood. In the present study, we discovered two cytotoxic organobismuth compounds whose cytotoxicity diminished upon replacement of the intramolecular bismuth atom with an antimony atom. The intracellular accumulation of the organobismuth compounds was much higher than that of the organoantimony compounds with the corresponding organic structures. We also showed that both the organic structure and bismuth atom are required for certain organobismuth compounds to exert their cytotoxic effect, suggesting that the cytotoxicity of such a compound is a result of an interaction between the organic structure and the bismuth atom. The present data suggest that organobismuth compounds with certain molecular structures exhibit cytotoxicity via an interaction between the molecular structure and the bismuth atom, and this cytotoxicity can be diminished by replacing the bismuth atom with an antimony atom, resulting in lower intracellular accumulation.

Structural and functional insights into the HIV-1 maturation inhibitor binding pocket.

PubMed

Waki, Kayoko; Durell, Stewart R; Soheilian, Ferri; Nagashima, Kunio; Butler, Scott L; Freed, Eric O

2012-01-01

Processing of the Gag precursor protein by the viral protease during particle release triggers virion maturation, an essential step in the virus replication cycle. The first-in-class HIV-1 maturation inhibitor dimethylsuccinyl betulinic acid [PA-457 or bevirimat (BVM)] blocks HIV-1 maturation by inhibiting the cleavage of the capsid-spacer peptide 1 (CA-SP1) intermediate to mature CA. A structurally distinct molecule, PF-46396, was recently reported to have a similar mode of action to that of BVM. Because of the structural dissimilarity between BVM and PF-46396, we hypothesized that the two compounds might interact differentially with the putative maturation inhibitor-binding pocket in Gag. To test this hypothesis, PF-46396 resistance was selected for in vitro. Resistance mutations were identified in three regions of Gag: around the CA-SP1 cleavage site where BVM resistance maps, at CA amino acid 201, and in the CA major homology region (MHR). The MHR mutants are profoundly PF-46396-dependent in Gag assembly and release and virus replication. The severe defect exhibited by the inhibitor-dependent MHR mutants in the absence of the compound is also corrected by a second-site compensatory change far downstream in SP1, suggesting structural and functional cross-talk between the HIV-1 CA MHR and SP1. When PF-46396 and BVM were both present in infected cells they exhibited mutually antagonistic behavior. Together, these results identify Gag residues that line the maturation inhibitor-binding pocket and suggest that BVM and PF-46396 interact differentially with this putative pocket. These findings provide novel insights into the structure-function relationship between the CA MHR and SP1, two domains of Gag that are critical to both assembly and maturation. The highly conserved nature of the MHR across all orthoretroviridae suggests that these findings will be broadly relevant to retroviral assembly. Finally, the results presented here provide a framework for increased structural understanding of HIV-1 maturation inhibitor activity.

Epothilones as lead structures for the synthesis-based discovery of new chemotypes for microtubule stabilization.

PubMed

Feyen, Fabian; Cachoux, Frédéric; Gertsch, Jürg; Wartmann, Markus; Altmann, Karl-Heinz

2008-01-01

Epothilones are macrocyclic bacterial natural products with potent microtubule-stabilizing and antiproliferative activity. They have served as successful lead structures for the development of several clinical candidates for anticancer therapy. However, the structural diversity of this group of clinical compounds is rather limited, as their structures show little divergence from the original natural product leads. Our own research has explored the question of whether epothilones can serve as a basis for the development of new structural scaffolds, or chemotypes, for microtubule stabilization that might serve as a basis for the discovery of new generations of anticancer drugs. We have elaborated a series of epothilone-derived macrolactones whose overall structural features significantly deviate from those of the natural epothilone scaffold and thus define new structural families of microtubule-stabilizing agents. Key elements of our hypermodification strategy are the change of the natural epoxide geometry from cis to trans, the incorporation of a conformationally constrained side chain, the removal of the C3-hydroxyl group, and the replacement of C12 with nitrogen. So far, this approach has yielded analogs 30 and 40 that are the most advanced, the most rigorously modified, structures, both of which are potent antiproliferative agents with low nanomolar activity against several human cancer cell lines in vitro. The synthesis was achieved through a macrolactone-based strategy or a high-yielding RCM reaction. The 12-aza-epothilone ("azathilone" 40) may be considered a "non-natural" natural product that still retains most of the overall structural characteristics of a true natural product but is structurally unique, because it lies outside of the general scope of Nature's biosynthetic machinery for polyketide synthesis. Like natural epothilones, both 30 and 40 promote tubulin polymerization in vitro and at the cellular level induce cell cycle arrest in mitosis. These facts indicate that cancer cell growth inhibition by these compounds is based on the same mechanistic underpinnings as those for natural epothilones. Interestingly, the 9,10-dehydro analog of 40 is significantly less active than the saturated parent compound, which is contrary to observations for natural epothilones B or D. This may point to differences in the bioactive conformations of N-acyl-12-aza-epothilones like 40 and natural epothilones. In light of their distinct structural features, combined with an epothilone-like (and taxol-like) in vitro biological profile, 30 and 40 can be considered as representative examples of new chemotypes for microtubule stabilization. As such, they may offer the same potential for pharmacological differentiation from the original epothilone leads as various newly discovered microtubule-stabilizing natural products with macrolactone structures, such as laulimalide, peloruside, or dictyostatin.

Characterization of condensed tannins and carbohydrates in hot water bark extracts of European softwood species.

PubMed

Bianchi, Sauro; Kroslakova, Ivana; Janzon, Ron; Mayer, Ingo; Saake, Bodo; Pichelin, Frédéric

2015-12-01

Condensed tannins extracted from European softwood bark are recognized as alternatives to synthetic phenolics. The extraction is generally performed in hot water, leading to simultaneous extraction of other bark constituents such as carbohydrates, phenolic monomers and salts. Characterization of the extract's composition and identification of the extracted tannins' molecular structure are needed to better identify potential applications. Bark from Silver fir (Abies alba [Mill.]), European larch (Larix decidua [Mill.]), Norway spruce (Picea abies [Karst.]), Douglas fir (Pseudotsuga menziesii [Mirb.]) and Scots pine (Pinus sylvestris [L.]) were extracted in water at 60°C. The amounts of phenolic monomers, condensed tannins, carbohydrates, and inorganic compounds in the extract were determined. The molecular structures of condensed tannins and carbohydrates were also investigated (HPLC-UV combined with thiolysis, MALDI-TOF mass spectrometry, anion exchange chromatography). Distinct extract compositions and tannin structures were found in each of the analysed species. Procyanidins were the most ubiquitous tannins. The presence of phenolic glucosides in the tannin oligomers was suggested. Polysaccharides such as arabinans, arabinogalactans and glucans represented an important fraction of all extracts. Compared to traditionally used species (Mimosa and Quebracho) higher viscosities as well as faster chemical reactivities are expected in the analysed species. The most promising species for a bark tannin extraction was found to be larch, while the least encouraging results were detected in pine. A better knowledge of the interaction between the various extracted compounds is deemed an important matter for investigation in the context of industrial applications of such extracts. Copyright © 2015 Elsevier Ltd. All rights reserved.

Biophysical and X-ray crystallographic analysis of Mps1 kinase inhibitor complexes.

PubMed

Chu, Matthew L H; Lang, Zhaolei; Chavas, Leonard M G; Neres, João; Fedorova, Olga S; Tabernero, Lydia; Cherry, Mike; Williams, David H; Douglas, Kenneth T; Eyers, Patrick A

2010-03-02

The dual-specificity protein kinase monopolar spindle 1 (Mps1) is a central component of the mitotic spindle assembly checkpoint (SAC), a sensing mechanism that prevents anaphase until all chromosomes are bioriented on the metaphase plate. Partial depletion of Mps1 protein levels sensitizes transformed, but not untransformed, human cells to therapeutic doses of the anticancer agent Taxol, making it an attractive novel therapeutic cancer target. We have previously determined the X-ray structure of the catalytic domain of human Mps1 in complex with the anthrapyrazolone kinase inhibitor SP600125. In order to validate distinct inhibitors that target this enzyme and improve our understanding of nucleotide binding site architecture, we now report a biophysical and structural evaluation of the Mps1 catalytic domain in the presence of ATP and the aspecific model kinase inhibitor staurosporine. Collective in silico, enzymatic, and fluorescent screens also identified several new lead quinazoline Mps1 inhibitors, including a low-affinity compound termed Compound 4 (Cpd 4), whose interaction with the Mps1 kinase domain was further characterized by X-ray crystallography. A novel biophysical analysis demonstrated that the intrinsic fluorescence of SP600125 changed markedly upon Mps1 binding, allowing spectrophotometric displacement analysis and determination of dissociation constants for ATP-competitive Mps1 inhibitors. By illuminating the structure of the Mps1 ATP-binding site our results provide novel biophysical insights into Mps1-ligand interactions that will be useful for the development of specific Mps1 inhibitors, including those employing a therapeutically validated quinazoline template.

Effect of physical sediments reworking on hydrocarbon degradation and bacterial community structure in marine coastal sediments.

PubMed

Duran, Robert; Bonin, Patricia; Jezequel, Ronan; Dubosc, Karine; Gassie, Claire; Terrisse, Fanny; Abella, Justine; Cagnon, Christine; Militon, Cecile; Michotey, Valérie; Gilbert, Franck; Cuny, Philippe; Cravo-Laureau, Cristiana

2015-10-01

The present study aimed to examine whether the physical reworking of sediments by harrowing would be suitable for favouring the hydrocarbon degradation in coastal marine sediments. Mudflat sediments were maintained in mesocosms under conditions as closer as possible to those prevailing in natural environments with tidal cycles. Sediments were contaminated with Ural blend crude oil, and in half of them, harrowing treatment was applied in order to mimic physical reworking of surface sediments. Hydrocarbon distribution within the sediment and its removal was followed during 286 days. The harrowing treatment allowed hydrocarbon compounds to penetrate the first 6 cm of the sediments, and biodegradation indexes (such as n-C18/phytane) indicated that biodegradation started 90 days before that observed in untreated control mesocosms. However, the harrowing treatment had a severe impact on benthic organisms reducing drastically the macrofaunal abundance and diversity. In the harrowing-treated mesocosms, the bacterial abundance, determined by 16S rRNA gene Q-PCR, was slightly increased; and terminal restriction fragment length polymorphism (T-RFLP) analyses of 16S rRNA genes showed distinct and specific bacterial community structure. Co-occurrence network and canonical correspondence analyses (CCA) based on T-RFLP data indicated the main correlations between bacterial operational taxonomic units (OTUs) as well as the associations between OTUs and hydrocarbon compound contents further supported by clustered correlation (ClusCor) analysis. The analyses highlighted the OTUs constituting the network structural bases involved in hydrocarbon degradation. Negative correlations indicated the possible shifts in bacterial communities that occurred during the ecological succession.

Synthesis, spectroscopic, and molecular structure characterizations of some azo derivatives of 2-hydroxyacetophenone

NASA Astrophysics Data System (ADS)

Albayrak, Çiğdem; Gümrükçüoğlu, İsmail E.; Odabaşoğlu, Mustafa; İskeleli, Nazan Ocak; Ağar, Erbil

2009-08-01

Some novel azo compounds were prepared by the reaction of 2-hydroxyacetophenone with aniline and its substituted derivatives. The structures of synthesized azo compounds were determined by IR, UV-Vis, 1H NMR and 13C NMR spectroscopic techniques and the structures of some of these compounds were also determined by X-ray diffraction studies. Structural analysis using IR in solid state shows that the azo form is favoured in the azo compounds whereas UV-Vis analysis of the azo compounds in solution has shown that there is a azo and ionic form. The azo compounds in the basic solvents dimethylformamide (DMF) and dimethylsulfoxide (DMSO) are both azo and ionic form while these compounds in ethyl alcohol (EtOH) and chloroform (CHCl 3) are only azo form.

A strategy to improve the identification reliability of the chemical constituents by high-resolution mass spectrometry-based isomer structure prediction combined with a quantitative structure retention relationship analysis: Phthalide compounds in Chuanxiong as a test case.

PubMed

Zhang, Qingqing; Huo, Mengqi; Zhang, Yanling; Qiao, Yanjiang; Gao, Xiaoyan

2018-06-01

High-resolution mass spectrometry (HRMS) provides a powerful tool for the rapid analysis and identification of compounds in herbs. However, the diversity and large differences in the content of the chemical constituents in herbal medicines, especially isomerisms, are a great challenge for mass spectrometry-based structural identification. In the current study, a new strategy for the structural characterization of potential new phthalide compounds was proposed by isomer structure predictions combined with a quantitative structure-retention relationship (QSRR) analysis using phthalide compounds in Chuanxiong as an example. This strategy consists of three steps. First, the structures of phthalide compounds were reasonably predicted on the basis of the structure features and MS/MS fragmentation patterns: (1) the collected raw HRMS data were preliminarily screened by an in-house database; (2) the MS/MS fragmentation patterns of the analogous compounds were summarized; (3) the reported phthalide compounds were identified, and the structures of the isomers were reasonably predicted. Second, the QSRR model was established and verified using representative phthalide compound standards. Finally, the retention times of the predicted isomers were calculated by the QSRR model, and the structures of these peaks were rationally characterized by matching retention times of the detected chromatographic peaks and the predicted isomers. A multiple linear regression QSRR model in which 6 physicochemical variables were screened was built using 23 phthalide standards. The retention times of the phthalide isomers in Chuanxiong were well predicted by the QSRR model combined with reasonable structure predictions (R 2 =0.955). A total of 81 peaks were detected from Chuanxiong and assigned to reasonable structures, and 26 potential new phthalide compounds were structurally characterized. This strategy can improve the identification efficiency and reliability of homologues in complex materials. Copyright © 2018 Elsevier B.V. All rights reserved.

A multinuclear solid-state NMR study of the dimethyltin chalcogenides ((CH 3) 2SnE) 3, E  S,Se,Te

NASA Astrophysics Data System (ADS)

Gay, Ian D.; Jones, C. H. W.; Sharma, R. D.

The solid-state NMR spectra, measured using MAS, are reported for 13C, 119Sn, 77Se, and 125Te in the compounds (Me 2SnE) 3, E  S, Se, or Te. For ((CH 3) 2SnS) 3, tetragonal, three inequivalent carbons and two inequivalent tins are observed consistent with a reinterpretation of the crystal structure data of this compound which shows a twofold axis through opposing tin and sulfur atoms, the molecule being in a twisted-boat conformation. For the monoclinic form six inequivalent carbons and three inequivalent tins were observed. Chemical shifts for 13C and 119Sn and the magnitudes of the 2JSn Sn coupling constants are reported. The tetragonal forms of ((CH 3) 2SnSe) 3 and ((CH 3) 2SnTe) 3 show the presence of two inequivalent tin and chalcogen atoms and three inequivalent carbons, again consistent with a twofold axis. In these compounds it is possible to identify the three different observed single-bond coupling constants with the distinct crystallographically determined tin-chalcogen bonds. The 13C, 119Sn, 77Se, and 125Te chemical shifts are reported, together with the magnitude of 1JSn E (E  Se or Te). In addition to isotropic shifts and couplings, chemical-shift anisotropies are reported for Sn, Se, and Te.

A novel assay for discovery and characterization of pro-apoptotic drugs and for monitoring apoptosis in patient sera.

PubMed

Bivén, K; Erdal, H; Hägg, M; Ueno, T; Zhou, R; Lynch, M; Rowley, B; Wood, J; Zhang, C; Toi, M; Shoshan, M C; Linder, S

2003-06-01

We have developed an apoptosis assay based on measurement of a neoepitope of cytokeratin-18 (CK18-Asp396) exposed after caspase-cleavage and detected by the monoclonal antibody M30. The total amount of caspase-cleaved CK18 which has accumulated in cells and tissue culture media during apoptosis is measured by ELISA. The sensitivity is sufficient for use in the 96-well format to allow high-through-put screening of drug libraries. We here describe strategies allowing classification of pro-apoptotic compounds according to their profiles of induction of apoptosis in the presence of pharmacological inhibitors. The time course of induction of CK18 cleavage can furthermore be used to distinguish structurally similar compounds. We propose that compounds that induce rapid CK18 cleavage have mechanisms of actions distinct from conventional genotoxic and microtubuli-targeting agents, and we present one example of an agent that induces almost immediate mitochondrial depolarization and cytochrome c release. Finally, CK18-Asp396 cleavage products are released from cells in tissue culture, and presumably from tumor cells in vivo. These products can be measured in sera from cancer patients. We present evidence suggesting that it will be possible to use the M30-ELISA assay for measuring chemotherapy-induced apoptosis in patient sera, opening possibilities for monitoring therapy.

Host lignin composition affects haustorium induction in the parasitic plants Phtheirospermum japonicum and Striga hermonthica.

PubMed

Cui, Songkui; Wada, Syogo; Tobimatsu, Yuki; Takeda, Yuri; Saucet, Simon B; Takano, Toshiyuki; Umezawa, Toshiaki; Shirasu, Ken; Yoshida, Satoko

2018-04-01

Parasitic plants in the family Orobanchaceae are destructive weeds of agriculture worldwide. The haustorium, an essential parasitic organ used by these plants to penetrate host tissues, is induced by host-derived phenolic compounds called haustorium-inducing factors (HIFs). The origin of HIFs remains unknown, although the structures of lignin monomers resemble that of HIFs. Lignin is a natural phenylpropanoid polymer, commonly found in secondary cell walls of vascular plants. We therefore investigated the possibility that HIFs are derived from host lignin. Various lignin-related phenolics, quinones and lignin polymers, together with nonhost and host plants that have different lignin compositions, were tested for their haustorium-inducing activity in two Orobanchaceae species, a facultative parasite, Phtheirospermum japonicum, and an obligate parasite, Striga hermonthica. Lignin-related compounds induced haustoria in P. japonicum and S. hermonthica with different specificities. High concentrations of lignin polymers induced haustorium formation. Treatment with laccase, a lignin degradation enzyme, promoted haustorium formation at low concentrations. The distinct lignin compositions of the host and nonhost plants affected haustorium induction, correlating with the response of the different parasitic plants to specific types of lignin-related compounds. Our study provides valuable insights into the important roles of lignin biosynthesis and degradation in the production of HIFs. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Similar bowtie structures and distinct largest strong components are identified in the transcriptional regulatory networks of Arabidopsis thaliana during photomorphogenesis and heat shock.

PubMed

Luo, Shitao; Zhang, Fengming; Ruan, Yingfei; Li, Jie; Zhang, Zheng; Sun, Yan; Deng, Shixiong; Peng, Rui

2018-06-01

Photomorphogenesis and heat shock are critical biological processes of plants. A recent research constructed the transcriptional regulatory networks (TRNs) of Arabidopsis thaliana during these processes using DNase-seq. In this study, by strong decomposition, we revealed that each of these TRNs can be represented as a similar bowtie structure with only one non-trivial and distinct strong component. We further identified distinct patterns of variation of a few light-related genes in these bowtie structures during photomorphogenesis. These results suggest that bowtie structure may be a common property of TRNs of plants, and distinct variation patterns of genes in bowtie structures of TRNs during biological processes may reflect distinct functions. Overall, our study provides an insight into the molecular mechanisms underlying photomorphogenesis and heat shock, and emphasizes the necessity to investigate the strong connectivity structures while studying TRNs. Copyright © 2018 Elsevier B.V. All rights reserved.

Insights into Antimicrobial Peptides from Spiders and Scorpions

PubMed Central

Wang, Xiuqing; Wang, Guangshun

2015-01-01

The venoms of spiders and scorpions contain a variety of chemical compounds. Antimicrobial peptides (AMPs) from these organisms were first discovered in the 1990s. As of May 2015, there were 42 spider’s and 63 scorpion’s AMPs in the Antimicrobial Peptide Database (http://aps.unmc.edu/AP). These peptides have demonstrated broad or narrow-spectrum activities against bacteria, fungi, viruses, and parasites. In addition, they can be toxic to cancer cells, insects and erythrocytes. To provide insight into such an activity spectrum, this article discusses the discovery, classification, structure and activity relationships, bioinformatics analysis, and potential applications of spider and scorpion AMPs. Our analysis reveals that, in the case of linear peptides, spiders use both glycine-rich and helical peptide models for defense, whereas scorpions use two distinct helical peptide models with different amino acid compositions to exert the observed antimicrobial activities and hemolytic toxicity. Our structural bioinformatics study improves the knowledge in the field and can be used to design more selective peptides to combat tumors, parasites, and viruses. PMID:27165405

Electronic origin of high-temperature superconductivity in single-layer FeSe superconductor.

PubMed

Liu, Defa; Zhang, Wenhao; Mou, Daixiang; He, Junfeng; Ou, Yun-Bo; Wang, Qing-Yan; Li, Zhi; Wang, Lili; Zhao, Lin; He, Shaolong; Peng, Yingying; Liu, Xu; Chen, Chaoyu; Yu, Li; Liu, Guodong; Dong, Xiaoli; Zhang, Jun; Chen, Chuangtian; Xu, Zuyan; Hu, Jiangping; Chen, Xi; Ma, Xucun; Xue, Qikun; Zhou, X J

2012-07-03

The recent discovery of high-temperature superconductivity in iron-based compounds has attracted much attention. How to further increase the superconducting transition temperature (T(c)) and how to understand the superconductivity mechanism are two prominent issues facing the current study of iron-based superconductors. The latest report of high-T(c) superconductivity in a single-layer FeSe is therefore both surprising and significant. Here we present investigations of the electronic structure and superconducting gap of the single-layer FeSe superconductor. Its Fermi surface is distinct from other iron-based superconductors, consisting only of electron-like pockets near the zone corner without indication of any Fermi surface around the zone centre. Nearly isotropic superconducting gap is observed in this strictly two-dimensional system. The temperature dependence of the superconducting gap gives a transition temperature T(c)~ 55 K. These results have established a clear case that such a simple electronic structure is compatible with high-T(c) superconductivity in iron-based superconductors.

Interlaced crystals having a perfect Bravais lattice and complex chemical order revealed by real-space crystallography

DOE PAGES

Shen, Xiao; Hernandez-Pagan, Emil; Zhou, Wu; ...

2014-11-14

The search for optimal thermoelectric materials aims for structures in which the crystalline order is disrupted to lower the thermal conductivity without degradation of the electron conductivity. Here we report the synthesis and characterization of ternary nanoparticles (two cations and one anion) that exhibit a new form of crystal-line order: an uninterrupted, perfect, global Bravais lattice, in which the two cations exhibit a wide array of distinct ordering patterns within the cation sublattice, form-ing interlaced domains and phases. Partitioning into domains and phases is not unique; the corresponding boundaries have no structural defects or strain and entail no energy cost.more » We call this form of crystalline order “interlaced crystals” and present the example of hexagonal-CuInS 2. Interlacing is possible in multi-cation tetrahedral-ly-bonded compound with an average of two electrons per bond. Interlacing has min-imal effect on electronic properties, but should strongly reduce phonon transport, making interlaced crystals attractive for thermoelectric applications.« less

Crystal structure of 4,4′-(disulfanediyl)dibutanoic acid–4,4′-bipyridine (1/1)

PubMed Central

Atria, Ana María; Garland, Maria Teresa; Baggio, Ricardo

2014-01-01

4,4′-(Disulfanediyl)dibutanoic acid (dtba) and 4,4′-bipyridine (4,4′-bpy) crystallize in an 1:1 ratio, leading to the title co-crystal with composition C8H14O4S2·C10H8N2. A distinctive feature of the crystal structure is the geometry of the dtba moiety, which appears to be stretched [with a 9.98 (1) Å span between outermost carbons] and acts as an hydrogen-bonding connector, forming linear chains along [-211] with the 4,4′-bpy moiety by way of O—H⋯N hydrogen bonds and C—H⋯O interactions. The influence of the mol­ecular shape on the hydrogen-bonding pattern is analysed by comparing the title compound and two other 4,4′-bpy co-crystals with closely related mol­ecules of similar formulation but different geometry, showing the way in which this correlates with the packing arrangement. PMID:25309167

Ethnic and Gender Considerations in the Use of Facial Injectables: Asian Patients.

PubMed

Liew, Steven

2015-11-01

Asians have distinct facial characteristics due to underlying skeletal and morphological features that differ greatly with those of whites. This together with the higher sun protection factor and the differences in the quality of the skin and soft tissue create a profound effect on their aging process. Understanding of these differences and their effects in the aging process in Asians is crucial in determining effective utilization and placement of injectable products to ensure optimal aesthetic outcomes. For younger Asian women, the main treatment goal is to address the inherent structural deficits through reshaping and the provision of facial support. Facial injectables are used to provide anterior projection, to reduce facial width, and to lengthen facial height. In the older group, the aim is for rejuvenation and also to address the underlying structural issues that has compounded due to age-related volume loss. Asian women requesting cosmetic procedures do not want to be Westernized but rather seeking to enhance and optimize their Asian ethnic features.

A general strategy for synthesis of cyclophane-braced peptide macrocycles via palladium-catalysed intramolecular sp3 C-H arylation

NASA Astrophysics Data System (ADS)

Zhang, Xuekai; Lu, Gang; Sun, Meng; Mahankali, Madhu; Ma, Yanfei; Zhang, Mingming; Hua, Wangde; Hu, Yuting; Wang, Qingbing; Chen, Jinghuo; He, Gang; Qi, Xiangbing; Shen, Weijun; Liu, Peng; Chen, Gong

2018-05-01

New methods capable of effecting cyclization, and forming novel three-dimensional structures while maintaining favourable physicochemical properties are needed to facilitate the development of cyclic peptide-based drugs that can engage challenging biological targets, such as protein-protein interactions. Here, we report a highly efficient and generally applicable strategy for constructing new types of peptide macrocycles using palladium-catalysed intramolecular C(sp3)-H arylation reactions. Easily accessible linear peptide precursors of simple and versatile design can be selectively cyclized at the side chains of either aromatic or modified non-aromatic amino acid units to form various cyclophane-braced peptide cycles. This strategy provides a powerful tool to address the long-standing challenge of size- and composition-dependence in peptide macrocyclization, and generates novel peptide macrocycles with uniquely buttressed backbones and distinct loop-type three-dimensional structures. Preliminary cell proliferation screening of the pilot library revealed a potent lead compound with selective cytotoxicity toward proliferative Myc-dependent cancer cell lines.

The Structure and Composition Statistics of 6A Binary and Ternary Crystalline Materials.

PubMed

Hever, Alon; Oses, Corey; Curtarolo, Stefano; Levy, Ohad; Natan, Amir

2018-01-16

The fundamental principles underlying the arrangement of elements into solid compounds with an enormous variety of crystal structures are still largely unknown. This study presents a general overview of the structure types appearing in an important subset of the solid compounds, i.e., binary and ternary compounds of the 6A column oxides, sulfides and selenides. It contains an analysis of these compounds, including the prevalence of various structure types, their symmetry properties, compositions, stoichiometries and unit cell sizes. It is found that these compound families include preferred stoichiometries and structure types that may reflect both their specific chemistry and research bias in the available empirical data. Identification of nonoverlapping gaps and missing stoichiometries in these structure populations may be used as guidance in the search for new materials.

Templating Influence of Molecular Precursors on Pr(OH)3 Nanostructures.

PubMed

Hemmer, Eva; Cavelius, Christian; Huch, Volker; Mathur, Sanjay

2015-07-06

Four new praseodymium alkoxo and amido compounds ([Pr3(μ3-OtBu)2(μ2-OtBu)3(OtBu)4(HOtBu)2] (1), [Pr{OC(tBu)3}3(THF)] (2), [PrCl{N(SiMe3)2}2(THF)]2 (3), and [PrCl{OC(tBu)3}2(THF)]2 (4)) were synthesized and structurally characterized by single-crystal X-ray diffraction analysis. Application of these compounds in solvothermal synthesis of praseodymium oxide/hydroxide nanostructures showed their templating influence on the morphology and phase composition of the resulting solid-state materials. Differential reactivity of the chosen alkoxide ligands toward water and the different arrangements of metal-oxygen units in the studied precursor compounds strongly influenced the kinetics of hydrolysis and cross-condensation reactions as manifested in the morphological changes and phase composition of the final products. Thermal decomposition studies of 1-4 confirmed their conversion into the corresponding oxide phases. Activation of compounds 1, 2, and 4 by either a base or a stoichiometric amount of water showed the distinct influence of their chemical configuration on the obtained nanopowders: whereas 1 solely produced nanorods of Pr(OH)3, 2 predominantly formed a mixture of rod-shaped and spherical particles. The solvothermal decomposition of 4 resulted in Pr(OH)2Cl or PrOCl due to the presence of Cl ligands in the molecular precursor. The resultant materials were thoroughly characterized to demonstrate the relationship between precursor chemistry and the processing parameters that are clearly manifested in the morphology and phase of the final ceramics.

Virtual screening using the ligand ZINC database for novel lipoxygenase-3 inhibitors.

PubMed

Monika; Kour, Janmeet; Singh, Kulwinder

2013-01-01

The leukotrienes constitute a group of arachidonic acid-derived compounds with biologic activities suggesting important roles in inflammation and immediate hypersensitivity. Epidermis-type lipoxygenase-3 (ALOXE3), a distinct subclass within the multigene family of mammalian lipoxygenases, is a novel isoenzyme involved in the metabolism of leukotrienes and plays a very important role in skin barrier functions. Lipoxygenase selective inhibitors such as azelastine and zileuton are currently used to reduce inflammatory response. Nausea, pharyngolaryngeal pain, headache, nasal burning and somnolence are the most frequently reported adverse effects of these drugs. Therefore, there is still a need to develop more potent lipoxygenase inhibitors. In this paper, we report the screening of various compounds from the ZINC database (contains over 21 million compounds) using the Molegro Virtual Docker software against the ALOXE3 protein. Screening was performed using molecular constraints tool to filter compounds with physico-chemical properties similar to the 1N8Q bound ligand protocatechuic acid. The analysis resulted in 4319 Lipinski compliant hits which are docked and scored to identify structurally novel ligands that make similar interactions to those of known ligands or may have different interactions with other parts of the binding site. Our screening approach identified four molecules ZINC84299674; ZINC76643455; ZINC84299122 & ZINC75626957 with MolDock score of -128.901, -120.22, -116.873 & - 102.116 kcal/mol, respectively. Their energy scores were better than the 1N8Q bound co-crystallized ligand protocatechuic acid (with MolDock score of -77.225 kcal/mol). All the ligands were docked within the binding pocket forming interactions with amino acid residues.

Deodorization of Arthrospira platensis biomass for further scale-up food applications.

PubMed

Cuellar-Bermúdez, Sara P; Barba-Davila, Bertha; Serna-Saldivar, Sergio O; Parra-Saldivar, Roberto; Rodriguez-Rodriguez, José; Morales-Davila, Sandra; Goiris, Koen; Muylaert, Koenraad; Chuck-Hernández, Cristina

2017-12-01

Given the importance of A. platensis as a potential food protein source, we describe an affordable deodorization process that does not significantly affect the nutritional value of algae biomass. Ethanol, acetone or hexane were used to deodorize algae biomass and then to identify the profile of volatile compounds associated with its distinctive odor. Sensorial characteristics were improved in the biomass cake after the proposed solvent extraction. Panelists identified the ethanolic extract with the most pronounced algae-related odor. Gas chromatography-mass spectrometry analysis showed that a mixture of 20 different compounds derived from fatty acids and amino acids contributed to the characteristic smell of A. platensis biomass. The results of the present study show that the ethanol solvent-free A. platensis biomass contained > 600 g kg -1 protein, < 10 g kg -1  crude fat and > 65% in vitro protein digestibility, similar to the original biomass. The Fourier transform infrared spectroscopy secondary protein structure was comparable among samples, indicating that the only change after ethanol extraction was a reduction of the algae smell. The various extraction procedures investigated in the present study were effective in deodorizing the algae biomass. The most effective protocol was the removal of odoriferous compounds with ethanol. This particular procedure yielded an algae biomass with an improved sensorial traits. The results of the present study should help with the identification of odoriferous compounds derived from fatty acids, pigments and proteins associated with A. platensis. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Rapid LC-MS/MS profiling of protein amino acids and metabolically related compounds for large-scale assessment of metabolic phenotypes.

PubMed

Gu, Liping; Jones, A Daniel; Last, Robert L

2012-01-01

Amino acids extracted from a biological matrix can be resolved and measured using a 6-min per sample method through high-performance liquid chromatography with a short C18 column and rapid gradient using the ion-pairing reagent perfluoroheptanoic acid. LC-tandem mass spectrometry with multiple reaction monitoring (MRM) transitions selective for each compound allows simultaneous quantification of the 20 proteinogenic amino acids and 5 metabolically related compounds. Distinct MRM transitions were also established for selective detection of the isomers leucine/isoleucine and threonine/homoserine.

Identifying Novel Molecular Structures for Advanced Melanoma by Ligand-Based Virtual Screening

PubMed Central

Wang, Zhao; Lu, Yan; Seibel, William; Miller, Duane D.; Li, Wei

2009-01-01

We recently discovered a new class of thiazole analogs that are highly potent against melanoma cells. To expand the structure-activity relationship study and to explore potential new molecular scaffolds, we performed extensive ligand-based virtual screening against a compound library containing 342,910 small molecules. Two different approaches of virtual screening were carried out using the structure of our lead molecule: 1) connectivity-based search using Scitegic Pipeline Pilot from Accelerys and 2) molecular shape similarity search using Schrodinger software. Using a testing compound library, both approaches can rank similar compounds very high and rank dissimilar compounds very low, thus validating our screening methods. Structures identified from these searches were analyzed, and selected compounds were tested in vitro to assess their activity against melanoma cancer cell lines. Several molecules showed good anticancer activity. While none of the identified compounds showed better activity than our lead compound, they provided important insight into structural modifications for our lead compound and also provided novel platforms on which we can optimize new classes of anticancer compounds. One of the newly synthesized analogs based on this virtual screening has improved potency and selectivity against melanoma. PMID:19445498

Structure-activity relationship of three synthesized benzimidazole-based oligosaccharides in human platelet activation.

PubMed

Chang, Yi; Hsu, Wen-Hsien; Yang, Wen-Bin; Jayakumar, Thanasekaran; Lee, Tzu-Yin; Sheu, Joen-Rong; Lu, Wan-Jung; Li, Jiun-Yi

2017-11-01

Antiplatelet agents have considerable benefits in the treatment of thromboembolic diseases; however, these agents still have substantial limitations due to their severe side-effects. In this study, the antiplatelet activity of three newly synthesized saccharide based benzimidazole derivatives, M3BIM, Malto-BIM and Melibio-BIM, in collagen and thrombin-stimulated human platelets in vitro was examined. Among the compounds tested, only compound M3BIM exerted concentration (20-60 µM)-dependent inhibitory effects against collagen (1 µg/ml) and thrombin (0.01 U/ml)-induced washed human platelet aggregation. Moreover, at a concentration of 60 µM, M3BIM distinctly abolished collagen-induced adenosine triphosphate (ATP) release and intracellular Ca2+ mobilization. Additionally, this compound attenuated the collagen-induced phosphorylation of p47, a marker of the activation of protein kinase C (PKC) and p38 mitogen-activated protein kinase (MAPK). However, Malto-BIM and Melibio-BIM were not effective in this regard. Moreover, the toxic effects of these compounds were evaluated using zebrafish embryo toxicity (ZET) assay, and the results revealed that all three compounds had no comparative cytotoxicity within the range of 25-200 µM. Overall, the results of this study provide evidence for the inhibitory effects of M3BIM on collagen-induced platelet aggregation in vitro compared to other imidazole derivatives. The presence of 1-imidazolyl moiety at one end with a longer chain length (three sugar moieties) may be mainly responsible for the observed effects of M3BIM. These results suggest that compound M3BIM may be used as a potential candidate for the treatment of aberrant platelet activation-related diseases as it inhibits the activation of p47 and p38 MAPK, and reduces ATP release and Ca2+ mobilization.

DMF, but not other fumarates, inhibits NF-κB activity in vitro in an Nrf2-independent manner.

PubMed

Gillard, Geoffrey O; Collette, Brian; Anderson, John; Chao, Jianhua; Scannevin, Robert H; Huss, David J; Fontenot, Jason D

2015-06-15

Fumarate-containing pharmaceuticals are potent therapeutic agents that influence multiple cellular pathways. Despite proven clinical efficacy, there is a significant lack of data that directly defines the molecular mechanisms of action of related, yet distinct fumarate compounds. We systematically compared the impact of dimethyl fumarate (DMF), monomethyl fumarate (MMF) and a mixture of monoethyl fumarate salts (Ca(++), Mg(++), Zn(++); MEF) on defined cellular responses. We demonstrate that DMF inhibited NF-κB-driven cytokine production and nuclear translocation of p65 and p52 in an Nrf2-independent manner. Equivalent doses of MMF and MEF did not affect NF-κB signaling. These results highlight a key difference in the biological impact of related, yet distinct fumarate compounds. Copyright © 2015. Published by Elsevier B.V.

Structure-based discovery of fiber-binding compounds that reduce the cytotoxicity of amyloid beta

DOE PAGES

Jiang, Lin; Liu, Cong; Leibly, David; ...

2013-07-16

Amyloid protein aggregates are associated with dozens of devastating diseases including Alzheimer’s, Parkinson’s, ALS, and diabetes type 2. While structure-based discovery of compounds has been effective in combating numerous infectious and metabolic diseases, ignorance of amyloid structure has hindered similar approaches to amyloid disease. Here we show that knowledge of the atomic structure of one of the adhesive, steric-zipper segments of the amyloid-beta (Aβ) protein of Alzheimer’s disease, when coupled with computational methods, identifies eight diverse but mainly flat compounds and three compound derivatives that reduce Aβ cytotoxicity against mammalian cells by up to 90%. Although these compounds bind tomore » Aβ fibers, they do not reduce fiber formation of Aβ. Structure-activity relationship studies of the fiber-binding compounds and their derivatives suggest that compound binding increases fiber stability and decreases fiber toxicity, perhaps by shifting the equilibrium of Aβ from oligomers to fibers.« less

Poly(butylene terephthalate) based novel achiral stationary phase investigated under supercritical fluid chromatography conditions.

PubMed

Nagai, Kanji; Shibata, Tohru; Shinkura, Satoshi; Ohnishi, Atsushi

2018-05-11

Poly(butylene terephthalate) based novel stationary phase (SP), composed of planar aromatic phenyl group together with ester group monomer units, was designed for supercritical fluid chromatography (SFC) use. As expected from its structure, this phase shows planarity recognition of isomeric aromatics and closely similar compounds. Interestingly, for most analytes, the retention behavior of this SP is significantly distinct from that of the 2-ethylpyridine based SPs which is among the most well-known SFC dedicated phases. Although the poly(butylene terephthalate) is coated on silica gel, the performance of the column did not change by using extended range modifiers such as THF, dichloromethane or ethyl acetate and column robustness was confirmed by cycle durability testing. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Ecofriendly antiglare film derived from biomass using ultraviolet curing nanoimprint lithography for high-definition display

NASA Astrophysics Data System (ADS)

Takei, Satoshi; Murakami, Gaku; Mori, Yuto; Ichikawa, Takumi; Sekiguchi, Atsushi; Obata, Tsutomu; Yokoyama, Yoshiyuki; Mizuno, Wataru; Sumioka, Junji; Horita, Yuji

2013-07-01

Nanopatterning of an ecofriendly antiglare film derived from biomass using an ultraviolet curing nanoimprint lithography is reported. Developed sugar-related organic compounds with liquid glucose and trehalose derivatives derived from biomass produced high-quality imprint images of pillar patterns with a 230-nm diameter. Ecofriendly antiglare film with liquid glucose and trehalose derivatives derived from biomass was indicated to achieve the real refraction index of 1.45 to 1.53 at 350 to 800 nm, low imaginary refractive index of <0.005 and low volumetric shrinkage of 4.8% during ultraviolet irradiation. A distinctive bulky glucose structure in glucose and trehalose derivatives was considered to be effective for minimizing the volumetric shrinkage of resist film during ultraviolet irradiation, in addition to suitable optical properties for high-definition display.

Multiple molecular mechanisms for multidrug resistance transporters.

PubMed

Higgins, Christopher F

2007-04-12

The acquisition of multidrug resistance is a serious impediment to improved healthcare. Multidrug resistance is most frequently due to active transporters that pump a broad spectrum of chemically distinct, cytotoxic molecules out of cells, including antibiotics, antimalarials, herbicides and cancer chemotherapeutics in humans. The paradigm multidrug transporter, mammalian P-glycoprotein, was identified 30 years ago. Nonetheless, success in overcoming or circumventing multidrug resistance in a clinical setting has been modest. Recent structural and biochemical data for several multidrug transporters now provide mechanistic insights into how they work. Organisms have evolved several elegant solutions to ridding the cell of such cytotoxic compounds. Answers are emerging to questions such as how multispecificity for different drugs is achieved, why multidrug resistance arises so readily, and what chance there is of devising a clinical solution.

Crystal structure of iron(III) perchlorate nona­hydrate

PubMed Central

Hennings, Erik; Schmidt, Horst; Voigt, Wolfgang

2014-01-01

Since the discovery of perchlorate salts on Mars and the known occurrence of ferric salts in the regolith, there is a distinct possibility that the title compound could form on the surface of Mars. [Fe(H2O)6](ClO4)3·3H2O was crystallized from aqueous solutions at low temperatures according to the solid–liquid phase diagram. It consists of Fe(H2O)6 octa­hedra (point group symmetry -3.) and perchlorate anions (point group symmetry .2) as well as non-coordinating water mol­ecules, as part of a second hydrogen-bonded coordination sphere around the cation. The perchlorate appears to be slightly disordered, with major–minor component occupancies of 0.773 (9):0.227 (9). PMID:25552970

Preparative isolation of oligomeric procyanidins from Hawthorn (Crataegus spp.).

PubMed

Zumdick, S; Petereit, F; Luftmann, H; Hensel, A

2009-04-01

The oligomeric procyanidins (OPC) from Hawthorn leaves and flowers (Crataegi folium cum flore) are considered to be in part responsible for the cardiotonic clinical activity of the herbal material. Effective methods for rapid isolation of these heterogenous oligomeric clusters with defined molecular weight as reference compounds are not published until now. Therefore the water soluble fraction of an acetone/water (7 + 3) extract of Hawthorn leaves and flowers was fractionated by a combination of MPLC on RP-18 material and preparative HPLC using a diol stationary phase. This procedure resulted in the effective isolation of procyanidins with a distinct degree of polymerization (DP) from dimers DP2 up to tridecamers DP13. Exact mass measurements with negative ESI-TOF/MS were employed to confirm the respective structures of the isolated procyanidins.

Oxidation of municipal wastewater by free radicals mechanism. A UV/Vis spectroscopy study.

PubMed

Giannakopoulos, E; Isari, E; Bourikas, K; Karapanagioti, H K; Psarras, G; Oron, G; Kalavrouziotis, I K

2017-06-15

This study investigates the oxidation of municipal wastewater (WW) by complexation with natural polyphenols having radical scavenging activity, such as (3,4,5 tri-hydroxy-benzoic acid) gallic acid (GA) in alkaline pH (>7), under ambient O 2 and temperature. Physicochemical and structural characteristics of GA-WW complex-forming are evaluated by UV/Vis spectroscopy. The comparative analysis among UV/Vis spectra of GA monomer, GA-GA polymer, WW compounds, and GA-WW complex reveals significant differences within 350-450 and 500-900 nm. According to attenuated total reflectance (ATR) spectroscopy and thermogravimetric analysis (TGA), these spectra differences correspond to distinct complexes formed. This study suggests a novel role of natural polyphenols on the degradation and humification of wastes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Synthesis and structural investigation of new Co1-xNixTeO4 (x = 0, 0.2, 0.5, 0.8 and 1) compounds

NASA Astrophysics Data System (ADS)

Patel, Akhilesh K.; Singh, Harishchandra; Suresh, K. G.

2018-05-01

The new polycrystalline compounds Co1-xNixTeO4 (x = 0, 0.2, 0.5, 0.8 and 1) were prepared by sol-gel method and their structural properties have been studied. Structural investigation through Rietveld method shows monoclinic structure with space group P21/c for all compounds. All compounds polyhedral structure found to be in octahedral form with cations (M) at the center and six oxygen atoms at corner of octahedral structure. The lattice parameters variation with Ni substitution are found to be decreasing with Ni substitution.

LigandBox: A database for 3D structures of chemical compounds

PubMed Central

Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

2013-01-01

A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

LigandBox: A database for 3D structures of chemical compounds.

PubMed

Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

2013-01-01

A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.

Structural insights into binding of small molecule inhibitors to Enhancer of Zeste Homolog 2

NASA Astrophysics Data System (ADS)

Kalinić, Marko; Zloh, Mire; Erić, Slavica

2014-11-01

Enhancer of Zeste Homolog 2 (EZH2) is a SET domain protein lysine methyltransferase (PKMT) which has recently emerged as a chemically tractable and therapeutically promising epigenetic target, evidenced by the discovery and characterization of potent and highly selective EZH2 inhibitors. However, no experimental structures of the inhibitors co-crystallized to EZH2 have been resolved, and the structural basis for their activity and selectivity remains unknown. Considering the need to minimize cross-reactivity between prospective PKMT inhibitors, much can be learned from understanding the molecular basis for selective inhibition of EZH2. Thus, to elucidate the binding of small-molecule inhibitors to EZH2, we have developed a model of its fully-formed cofactor binding site and used it to carry out molecular dynamics simulations of protein-ligand complexes, followed by molecular mechanics/generalized born surface area calculations. The obtained results are in good agreement with biochemical inhibition data and reflect the structure-activity relationships of known ligands. Our findings suggest that the variable and flexible post-SET domain plays an important role in inhibitor binding, allowing possibly distinct binding modes of inhibitors with only small variations in their structure. Insights from this study present a good basis for design of novel and optimization of existing compounds targeting the cofactor binding site of EZH2.

Hydrothermal synthesis, crystal structure, and magnetic properties of a new inorganic vanadium(III) phosphate with a chain structure.

PubMed

Ferdov, Stanislav; Reis, Mario S; Lin, Zhi; Ferreira, Rute A Sá

2008-11-03

A new vanadium(III) phosphate, Na3V(OH)(HPO4)(PO4), has been synthesized by using mild hydrothermal conditions under autogeneous pressure. This material represents a very rare example of sodium vanadium(III) phosphate with a chain structure. The crystal structure has been determined by refinement of powder X-ray diffraction data, starting from the atomic coordinates of an isotypic compound, Na3Al(OH)(HPO4)(PO4), which was obtained under high temperature and high pressure. The phase crystallizes in monoclinic space group C2/m (No. 12) with lattice parameters a = 15.423(9) A, b = 7.280(0) A, c = 7.070(9) A, beta = 96.79(7) degrees, V = 788.3(9) A(3), and Z = 4. The structure consists of one-dimensional chains composed of corner-sharing VO5(OH) octahedra running along the b direction. They are decorated by isolated PO4 and HPO4 tetrahedra sharing two of their corners with the ones of the vanadium octahedra. The interconnection between the chains is assured by three crystallographically distinct Na(+) cations. Magnetic investigation confirms the 3+ oxidation state of the vanadium ions and reveals an antiferromagnetic arrangement between those ions through the chain.

Extending the applicability of the Goldschmidt tolerance factor to arbitrary ionic compounds

PubMed Central

Sato, Toyoto; Takagi, Shigeyuki; Deledda, Stefano; Hauback, Bjørn C.; Orimo, Shin-ichi

2016-01-01

Crystal structure determination is essential for characterizing materials and their properties, and can be facilitated by various tools and indicators. For instance, the Goldschmidt tolerance factor (T) for perovskite compounds is acknowledged for evaluating crystal structures in terms of the ionic packing. However, its applicability is limited to perovskite compounds. Here, we report on extending the applicability of T to ionic compounds with arbitrary ionic arrangements and compositions. By focussing on the occupancy of constituent spherical ions in the crystal structure, we define the ionic filling fraction (IFF), which is obtained from the volumes of crystal structure and constituent ions. Ionic compounds, including perovskites, are arranged linearly by the IFF, providing consistent results with T. The linearity guides towards finding suitable unit cell and composition, thus tackling the main obstacle for determining new crystal structures. We demonstrate the utility of the IFF by solving the structure of three hydrides with new crystal structures. PMID:27032978

Extending the applicability of the Goldschmidt tolerance factor to arbitrary ionic compounds.

PubMed

Sato, Toyoto; Takagi, Shigeyuki; Deledda, Stefano; Hauback, Bjørn C; Orimo, Shin-ichi

2016-04-01

Crystal structure determination is essential for characterizing materials and their properties, and can be facilitated by various tools and indicators. For instance, the Goldschmidt tolerance factor (T) for perovskite compounds is acknowledged for evaluating crystal structures in terms of the ionic packing. However, its applicability is limited to perovskite compounds. Here, we report on extending the applicability of T to ionic compounds with arbitrary ionic arrangements and compositions. By focussing on the occupancy of constituent spherical ions in the crystal structure, we define the ionic filling fraction (IFF), which is obtained from the volumes of crystal structure and constituent ions. Ionic compounds, including perovskites, are arranged linearly by the IFF, providing consistent results with T. The linearity guides towards finding suitable unit cell and composition, thus tackling the main obstacle for determining new crystal structures. We demonstrate the utility of the IFF by solving the structure of three hydrides with new crystal structures.

Preparation and Characterization of Organic-Inorganic Hybrid Macrocyclic Compounds: Cyclic Ladder-like Polyphenylsilsesquioxanes.

PubMed

Zhang, Wenchao; Wang, Xiaoxia; Wu, Yiwei; Qi, Zhi; Yang, Rongjie

2018-04-02

Organic-inorganic hybrid macrocyclic compounds, cyclic polyphenylsilsesquioxanes (cyc-PSQs), have been synthesized through hydrolysis and condensation reactions of phenyltrichlorosilane. Structural characterization has revealed that cyc-PSQs consist of a closed-ring double-chain siloxane inorganic backbone bearing organic phenyl groups. The cyc-PSQ molecules have been simulated and structurally optimized using the Forcite tool as implemented in Materials Studio. Structurally optimized cyc-PSQs are highly symmetrical and regular with high stereoregularity, consistent with the dimensions of their experimentally derived structures. Thermogravimetric analysis showed that these macrocyclic compounds have excellent thermal stability. In addition to these perfectly structured compounds, macrocyclic compounds with the same ring ladder structure but bearing an additional Si-OH group, cyc-PSQs-OH, have also been synthesized. A possible mechanism for the formation of the closed-ring molecular structures of cyc-PSQs and cyc-PSQs-OH is proposed.

Indole compounds may be promising medicines for ulcerative colitis.

PubMed

Sugimoto, Shinya; Naganuma, Makoto; Kanai, Takanori

2016-09-01

Indole compounds are extracted from indigo plants and have been used as blue or purple dyes for hundreds of years. In traditional Chinese medicine, herbal agents in combination with Qing-Dai (also known as indigo naturalis) have been used to treat patients with ulcerative colitis (UC) and to remedy inflammatory conditions. Recent studies have noted that indole compounds can be biosynthesized from tryptophan metabolites produced by various enzymes derived from intestinal microbiota. In addition to their action on indole compounds, the intestinal microbiota produce various tryptophan metabolites that mediate critical functions through distinct pathways and enzymes. Furthermore, some indole compounds, such as indigo and indirubin, act as ligands for the aryl hydrocarbon receptor. This signaling pathway stimulates mucosal type 3 innate lymphoid cells to produce interleukin-22, which induces antimicrobial peptide and tight junction molecule production, suggesting a role for indole compounds during the mucosal healing process. Thus, indole compounds may represent a novel treatment strategy for UC patients. In this review, we describe the origin and function of this indole compound-containing Chinese herb, as well as the drug development of indole compounds.

Comparative analysis of machine learning methods in ligand-based virtual screening of large compound libraries.

PubMed

Ma, Xiao H; Jia, Jia; Zhu, Feng; Xue, Ying; Li, Ze R; Chen, Yu Z

2009-05-01

Machine learning methods have been explored as ligand-based virtual screening tools for facilitating drug lead discovery. These methods predict compounds of specific pharmacodynamic, pharmacokinetic or toxicological properties based on their structure-derived structural and physicochemical properties. Increasing attention has been directed at these methods because of their capability in predicting compounds of diverse structures and complex structure-activity relationships without requiring the knowledge of target 3D structure. This article reviews current progresses in using machine learning methods for virtual screening of pharmacodynamically active compounds from large compound libraries, and analyzes and compares the reported performances of machine learning tools with those of structure-based and other ligand-based (such as pharmacophore and clustering) virtual screening methods. The feasibility to improve the performance of machine learning methods in screening large libraries is discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Altay, A.; Carter, C.B., E-mail: cbcarter@engr.uconn.ed; Rulis, P.

Calcium aluminates, compounds in the CaO-Al{sub 2}O{sub 3} phase system, are used in high-temperature cements and refractory oxides and have wide range of potential technological applications due to their interesting optical, electrical, thermal, and mechanical properties. They are used in both crystalline and glassy form; the glass is an isotropic material while the crystalline materials may be highly anisotropic. This paper will consider two particular crystalline materials, CA{sub 2} and CA{sub 6}, but the results should be applicable to all calcium aluminates. Although CA{sub 2} and CA{sub 6} crystals contain the same chemical species, Ca, Al, and O, the coordinationmore » and local environments of these species are different in the two structures and hence they show very different energy-loss near-edge structures (ELNES) when examined by electron energy-loss spectroscopy (EELS) in the TEM. The data obtained using ELNES can effectively provide a fingerprint for each compound and a map for their electronic structure. Once such fingerprints are obtained, they can be used to identify nano-sized particles/grains or material at interfaces and grain boundaries. In the present study, the local symmetry fingerprints for CA{sub 2} and CA{sub 6} structures are reported combining experimental spectra with electronic-structure calculations that allow the different features in the spectra to be interpreted. Al-L{sub 2,3} and O-K edge core-loss spectra from CA{sub 2} and CA{sub 6} were measured experimentally using electron energy-loss spectroscopy in a monochromated scanning transmission electron microscope. The near-edge structures were calculated for the different phases using the orthogonalized linear combination of atomic-orbitals method, and took account of core-hole interactions. It is shown that CA{sub 2} and CA{sub 6} structures exhibit distinctive experimental ELNES fingerprints so that these two phases can be separately identified even when present in small volumes. - Graphical abstract: Projection of the CA{sub 2} structure viewed in the [010] direction. Green atoms represent the Ca{sup 2+} ions and blue atoms represent the Al{sup 3+} ions. Two unit cells are outlined..« less

Fuel inventory and deposition in castellated structures in JET-ILW

NASA Astrophysics Data System (ADS)

Rubel, M.; Petersson, P.; Zhou, Y.; Coad, J. P.; Lungu, C.; Jepu, I.; Porosnicu, C.; Matveev, D.; Kirschner, A.; Brezinsek, S.; Widdowson, A.; Alves, E.; Contributors, JET

2017-06-01

Since 2011 the JET tokamak has been operated with a metal ITER-like wall (JET-ILW) including castellated beryllium limiters and lamellae-type bulk tungsten tiles in the divertor. This has allowed for a large scale test of castellated plasma-facing components (PFC). Procedures for sectioning the limiters into single blocks of castellation have been developed. This facilitated morphology studies of morphology of surfaces inside the grooves for limiters after experimental campaigns 2011-2012 and 2013-2014. The deposition in the 0.4-0.5 mm wide grooves of the castellation is ‘shallow’. It reaches 1-2 mm into the 12 mm deep gap. Deuterium concentrations are small (mostly below 1  ×  1018 cm-2). The estimated total amount of deuterium in all the castellated limiters does not exceed the inventory of the plasma-facing surfaces (PFS) of the limiters. There are only traces of Ni, Cr and Fe deposited in the castellation gaps. The same applies to the carbon content. Also low deposition of D, Be and C has been measured on the sides of the bulk tungsten lamellae pieces. Modelling clearly reflects: (a) a sharp decrease in the measured deposition profiles and(b) an increase in deposition with the gap width. Both experimental and modelling data give a strong indication and information to ITER that narrow gaps in the castellated PFC are essential. X-ray diffraction on PFS has clearly shown two distinct composition patterns: Be with an admixture of Be-W intermetallic compounds (e.g. Be22W) in the deposition zone, whilst only pure Be has been detected in the erosion zone. The lack of compound formation in the erosion zone indicates that no distinct changes in the thermo-mechanical properties of the Be PFC might be expected.

Molecular fractionation of dissolved organic matter with metal salts.

PubMed

Riedel, Thomas; Biester, Harald; Dittmar, Thorsten

2012-04-17

Coagulation of dissolved organic matter (DOM) by hydrolyzing metals is an important environmental process with particular relevance, e.g., for the cycling of organic matter in metal-rich aquatic systems or the flocculation of organic matter in wastewater treatment plants. Often, a nonremovable fraction of DOM remains in solution even at low DOM/metal ratios. Because coagulation by metals results from interactions with functional groups, we hypothesize that noncoagulating fractions have a distinct molecular composition. To test the hypothesis, we analyzed peat-derived dissolved organic matter remaining in solution after mixing with salts of Ca, Al, and Fe using 15 T Electrospray Ionization Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (ESI-FT-ICR-MS). Addition of metals resulted in a net removal of DOM. Also a reduction of molecular diversity was observed, as the number of peaks from the ESI-FT-ICR-MS spectra decreased. At DOM/metal ratios of ∼9 Ca did not show any preference for distinct molecular fractions, while Fe and Al removed preferentially the most oxidized compounds (O/C ratio >0.4) of the peat leachate. Lowering DOM/metal ratios to ∼1 resulted in further removal of less oxidized as well as more aromatic compounds ("black carbon"). Molecular composition in the residual solution after coagulation was more saturated, less polar, and less oxidized compared to the original peat leachate and exhibited a surprising similarity with DOM of marine origin. By identifying more than 9200 molecular formulas we can show that structural properties (saturation and aromaticity) and oxygen content of individual DOM molecules play an important role in coagulation with metals. We conclude that polyvalent cations not only alter the net mobility but also the very molecular composition of DOM in aquatic environments.

Polymeric Sulfated Amino Acid Surfactants: A New Class of Versatile Chiral Selectors for Micellar Electrokinetic Chromatography (MEKC) and MEKC-MS

PubMed Central

Ali Rizvi, Syed Asad; Zheng, Jie; Apkarian, Robert P.; Dublin, Steven N.; Shamsi, Shahab A.

2008-01-01

In this work, three amino acids derived (L-leucinol, L-isoleucinol and L-valinol) sulfated chiral surfactants are synthesized and polymerized. These chiral sulfated surfactants are thoroughly characterized to determine critical micelle concentration, aggregation number, polarity, optical rotation and partial specific volume. For the first time the morphological behavior of polymeric sulfated surfactants is revealed using cryogenic high-resolution electron microscopy (cryo-HRSEM). The polysodium N-undecenoyl-L-leucine sulfate (poly-L-SUCLS) shows distinct tubular structure, while polysodium N-undecenoyl-L-valine sulfate (poly-L-SUCVS) also shows tubular morphology but without any distinct order of the tubes. On the other hand, polysodium N-undecenoyl-L-isoleucine sulfate (poly-L-SUCILS) displays random distribution of coiled/curved filaments with heavy association of tightly and loosely bound water. All three polymeric sulfated surfactants are compared for enantio-separation of broad range of structurally diverse racemic compounds at very acidic, neutral and basic pH conditions in micellar electrokinetic chromatography (MEKC). A small combinatorial library of 10 structurally related phenylethylamines (PEAs) is investigated for chiral separation under acidic and moderately acidic to neutral pH conditions using an experimental design. In contrast to neutral pH conditions, at acidic pH, significantly enhanced chiral resolution is obtained for class I and class II PEAs due to the compact structure of polymeric sulfated surfactants. It is observed that the presence of hydroxy group on the benzene ring of PEAs resulted in deterioration of enantioseparation. A sensitive MEKC-mass spectrometry (MS) method is developed for one of the PEA (e.g., (±)-pseudoephedrine) in human urine. Very low limit of detection (LOD) is obtained at pH 2.0 (LOD 325 ng/mL), which is ca 16 times better compared to pH 8.0 (LOD 5.2 µg/mL). Other broad range of chiral analytes (β-blockers, phenoxypropionic acid, benzoin derivatives, PTH-amino acids, and benzodiazepinones) studied also provided improved chiral separation at low pH compared to high pH conditions. Among the three polymeric sulfated surfactants, poly-L-SUCILS with two chiral centers on the polymer head group provided overall higher enantioresolution for the investigated acidic, basic and neutral compounds. This work clearly demonstrates for the first time the superiority of chiral separation and sensitive MS detection at low pH over conventional high pH chiral separation and detection employing anionic chiral polymeric surfactants in MEKC and MEKC-MS. PMID:17263313

Fabrication and microstructures of functional gradient SiBCN–Nb composite by hot pressing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Min, E-mail: lcxsunmin@163.com; Fu, Ruoyu; Chen, Jun

2016-04-15

A functional gradient material with five layers composed of SiBCN ceramic and niobium (Nb) was prepared successfully by hot pressing. The phase composition, morphology features and microstructures were investigated in each layer of the gradient material. The Nb-containing compounds involving NbC, Nb{sub 6}C{sub 5}, Nb{sub 4}C{sub 3}, Nb{sub 5}Si{sub 3} and NbN increase with the volume fraction of Nb increasing in the sub-layer. They are randomly scattered (≤ 25 vol.% Nb), then strip-like, and finally distribute continuously (≥ 75 vol.% Nb). The size of BN(C) and SiC grains in Nb-containing layers is larger than in 100% SiBCN layer due tomore » the loss of the capsule-like structures. No distinct interfaces form in the transition regions indicating the gradual changes in phase composition and microstructures. - Highlights: • A functional gradient SiBCN–Nb material was prepared successfully by hot pressing. • Phase composition, morphology features and microstructures were investigated. • Thermodynamic calculation was used to aid in the phase analysis. • No distinct interfaces form typical of the functional gradient material.« less

Separation and Classification of Lipids Using Differential Ion Mobility Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shvartsburg, Alexandre A.; Isaac, Georgis; Leveque, Nathalie

2011-04-12

Correlations between the dimensions of a 2-D separation create trend lines that normally depend on structural or functional characteristics of the compound class and thus facilitate classification of unknowns. This broadly applies to conventional ion mobility spectrometry (IMS)/mass spectrometry (MS), where the major biomolecular classes (e.g., lipids, peptides, nucleotides) occupy different trend line domains. However, strong correlation between the IMS and MS separations for ions of same charge has impeded finer distinctions. Differential IMS (or FAIMS) is generally much less correlated to MS and thus should better separate the trend lines and associated domains. We report the first observation ofmore » chemical class separation by trend lines using FAIMS, here for lipids. For all lipids, FAIMS is indeed more independent of MS than conventional IMS, and subclasses (such as phospho-, glycero-, or sphingolipids) form distinct, often non-overlapping domains. Even finer categories with different functional groups or degrees of unsaturation are often separated. As expected, resolution improves in He-rich gases: at ~70% He, glycerolipid isomers with different positions of fatty acid attachment can be resolved. These results open the door for lipidomics application of FAIMS, particularly shotgun lipidomics and targeted analyses of bioactive lipids.« less

Current progress in isolation and characterization of toxins isolated from Pfiesteria piscicida.

PubMed Central

Moeller, P D; Morton, S L; Mitchell, B A; Sivertsen, S K; Fairey, E R; Mikulski, T M; Glasgow, H; Deamer-Melia, N J; Burkholder, J M; Ramsdell, J S

2001-01-01

The isolation and partial purification of toxic substances derived from Pfiesteria piscicida Steidinger & Burkholder extracts is described. Four distinct bioassay systems were used to monitor bioactivity of the P. piscicida extracts, including a high throughput cell cytotoxicity assay and a reporter gene assay as well as assays using brine shrimp and fish. Using these bioassays to guide fractionation, we have isolated two distinct, active fractions from Pfiesteria culture medium and cell mass extracts on the basis of their solubility characteristics. We have identified and characterized a bioactive lipophilic substance from Pfiesteria-derived extracts as di(2-ethylhexyl)phthalate, a commonly used plasticizer. The source of this typically man-made substance has been identified as originating from Instant Ocean (Aquarium Systems, Mentor, OH, USA), a commercially available seawater salt mixture used to prepare our mass culture growth medium. We have developed chromatographic methodology to isolate a bioactive polar compound isolated from extracts of Pfiesteria culture and presently report the characterization of the activity of this substance. The molecular structural analysis of the polar active component(s) using mass spectrometry and nuclear magnetic resonance spectroscopy is currently under way. PMID:11677183

Magnetic phase transitions and magnetic structures in RTxX2, RSn1+xGe1-x and RSn2 compounds

NASA Astrophysics Data System (ADS)

Gil, Alina

2018-02-01

The work presents the review of magnetic properties of the RTxX2, RSn1+xGe1-x and RSn2 compounds. The RTxX2 (where R - rare earth, T - 3d-metal, X - p-electron element: Si, Ge, Sn, and 1 ≥ x > 0) and RSn1+xGe1-x compounds (where x ≈ 0.1) crystallize in the orthorhombic crystal structure of CeNiSi2-type and RSn2 compounds crystallize in ZrSi2-type structure. Both structures are described by the space group Cmcm. The RSn1+xGe1-x compounds seem to be interesting due to the replacement of d-metal to p-electron element. The non-stoichiometric CeNiSi2-type of RTxX2 compounds may be regarded as partially filled ZrSi2-type compounds. The transitions from paramagnetic to antiferromagnetic or ferromagnetic states are observed at low temperatures and there are lots of variants of magnetic structures ranging from simple collinear to the sine-modulated structures with commensurate or incommensurate propagation vector. The comparison of magnetic properties of these compounds may help to find answers to questions concerning mechanisms of interaction between the magnetic moments.

Structural stability and electronic structure of transition metal compound: HfN

NASA Astrophysics Data System (ADS)

Sarwan, Madhu; Shukoor, V. Abdul; Singh, Sadhna

2018-05-01

The structural stability of transition metal nitride (HfN) has been investigated using density functional theory (DFT) with the help of Quantum-espresso codes. Our calculations confirm that the hafnium nitride (HfN) is stable in zinc-blende (B3) and rock-salt (B1) type structure. We have also reported the structural and electronic properties of HfN compound. These structural properties have been compared with experimental and theoretical data available on this compound.

Identification of Novel Anti-mycobacterial Compounds by Screening a Pharmaceutical Small-Molecule Library against Nonreplicating Mycobacterium tuberculosis.

PubMed

Warrier, Thulasi; Martinez-Hoyos, Maria; Marin-Amieva, Manuel; Colmenarejo, Gonzalo; Porras-De Francisco, Esther; Alvarez-Pedraglio, Ana Isabel; Fraile-Gabaldon, Maria Teresa; Torres-Gomez, Pedro Alfonso; Lopez-Quezada, Landys; Gold, Ben; Roberts, Julia; Ling, Yan; Somersan-Karakaya, Selin; Little, David; Cammack, Nicholas; Nathan, Carl; Mendoza-Losana, Alfonso

2015-12-11

Identification of compounds that target metabolically diverse subpopulations of Mycobacterium tuberculosis (Mtb) may contribute to shortening the course of treatment for tuberculosis. This study screened 270,000 compounds from GlaxoSmithKline's collection against Mtb in a nonreplicating (NR) state imposed in vitro by a combination of four host-relevant stresses. Evaluation of 166 confirmed hits led to detailed characterization of 19 compounds for potency, specificity, cytotoxicity, and stability. Compounds representing five scaffolds depended on reactive nitrogen species for selective activity against NR Mtb, and two were stable in the assay conditions. Four novel scaffolds with activity against replicating (R) Mtb were also identified. However, none of the 19 compounds was active against Mtb in both NR and R states. There was minimal overlap between compounds found active against NR Mtb and those previously identified as active against R Mtb, supporting the hypothesis that NR Mtb depends on distinct metabolic pathways for survival.

Ferrocenylaniline based amide analogs of methoxybenzoic acids: Synthesis, structural characterization and butyrylcholinesterase (BChE) inhibition studies

NASA Astrophysics Data System (ADS)

Altaf, Ataf Ali; Kausar, Samia; Hamayun, Muhammad; Lal, Bhajan; Tahir, Muhammad Nawaz; Badshah, Amin

2017-10-01

Three new ferrocene based amides were synthesized with slight structural difference. The general formula of the amides is C5H5FeC5H4C6H4NHCOC6H4(OCH3). The synthesized compounds were characterized by instrumental techniques like elemental analysis, FTIR and NMR spectroscopy. Structure of the two compounds was also studied by single crystal X-rays diffraction analysis. Structural studies provide the evidence that pMeO (one of the synthesized compounds) is an example of amides having no intermolecular hydrogen bonding in solid structure. In the BChE inhibition assay, compound (oMeO) having strong intermolecular force in the solid structure is less active than the compound (pMeO) with weak intermolecular forces in the solid structure. The docking studies proved that hydrogen bonding between inhibitor and BChE enzyme is of more importance for the activity, rather than intermolecular hydrogen bonding in the solid structure of inhibitor.

Novel consortium of Klebsiella variicola and Lactobacillus species enhances the functional potential of fermented dairy products by increasing the availability of branched-chain amino acids and the amount of distinctive volatiles.

PubMed

Rosales-Bravo, H; Morales-Torres, H C; Vázquez-Martínez, J; Molina-Torres, J; Olalde-Portugal, V; Partida-Martínez, L P

2017-11-01

Identify novel bacterial taxa that could increase the availability of branched-chain amino acids and the amount of distinctive volatiles during skim milk fermentation. We recovered 344 bacterial isolates from stool samples of healthy and breastfed infants. Five were selected based on their ability to produce branched-chain amino acids. Three strains were identified as Escherichia coli, one as Klebsiella pneumoniae and other as Klebsiella variicola by molecular and biochemical methods. HPLC and solid-phase microextraction with GC-MS were used for the determination of free amino acids and volatile compounds respectively. The consortium formed by K. variicola and four Lactobacillus species showed the highest production of Leu and Ile in skim milk fermentation. In addition, the production of volatile compounds, such as acetoin, ethanol, 2-nonanone, and acetic, hexanoic and octanoic acids, increased in comparison to commercial yogurt, Emmental and Gouda cheese. Also, distinctive volatiles, such as 2,3-butanediol, 4-methyl-2- hexanone and octanol, were identified. The use of K. variicola in combination with probiotic Lactobacillus species enhances the availability of Leu and Ile and the amount of distinctive volatiles during skim milk fermentation. The identified consortium increases the functional potential of fermented dairy products. © 2017 The Society for Applied Microbiology.

Tradeoff between robustness and elaboration in carotenoid networks produces cycles of avian color diversification.

PubMed

Badyaev, Alexander V; Morrison, Erin S; Belloni, Virginia; Sanderson, Michael J

2015-08-20

Resolution of the link between micro- and macroevolution calls for comparing both processes on the same deterministic landscape, such as genomic, metabolic or fitness networks. We apply this perspective to the evolution of carotenoid pigmentation that produces spectacular diversity in avian colors and show that basic structural properties of the underlying carotenoid metabolic network are reflected in global patterns of elaboration and diversification in color displays. Birds color themselves by consuming and metabolizing several dietary carotenoids from the environment. Such fundamental dependency on the most upstream external compounds should intrinsically constrain sustained evolutionary elongation of multi-step metabolic pathways needed for color elaboration unless the metabolic network gains robustness - the ability to synthesize the same carotenoid from an additional dietary starting point. We found that gains and losses of metabolic robustness were associated with evolutionary cycles of elaboration and stasis in expressed carotenoids in birds. Lack of metabolic robustness constrained lineage's metabolic explorations to the immediate biochemical vicinity of their ecologically distinct dietary carotenoids, whereas gains of robustness repeatedly resulted in sustained elongation of metabolic pathways on evolutionary time scales and corresponding color elaboration. The structural link between length and robustness in metabolic pathways may explain periodic convergence of phylogenetically distant and ecologically distinct species in expressed carotenoid pigmentation; account for stasis in carotenoid colors in some ecological lineages; and show how the connectivity of the underlying metabolic network provides a mechanistic link between microevolutionary elaboration and macroevolutionary diversification.

The Curious Case of Orthographic Distinctiveness: Disruption of Categorical Processing

ERIC Educational Resources Information Center

McDaniel, Mark A.; Cahill, Michael J.; Bugg, Julie M.

2016-01-01

How does orthographic distinctiveness affect recall of structured (categorized) word lists? On one theory, enhanced item-specific information (e.g., more distinct encoding) in concert with robust relational information (e.g., categorical information) optimally supports free recall. This predicts that for categorically structured lists,…

High pressure phase transitions in tetrahedrally coordinated semiconducting compounds

NASA Technical Reports Server (NTRS)

Yu, S. C.; Spain, I. L.; Skelton, E. F.

1978-01-01

New experimental results are reported for structural transitions at high pressure in several III-V compounds and two II-VI compounds. These data, together with earlier results, are then compared with the predictions of model calculations of Van Vechten. Experimental transition pressures are often at variance with calculated values. However, his calculation assumes that the high pressure phase is metallic, with the beta-Sn structure. The present results show that several compounds assume an ionic NaCl structure at high pressure, while others have neither the beta-Sn nor NaCl structure.

Structure-guided statistical textural distinctiveness for salient region detection in natural images.

PubMed

Scharfenberger, Christian; Wong, Alexander; Clausi, David A

2015-01-01

We propose a simple yet effective structure-guided statistical textural distinctiveness approach to salient region detection. Our method uses a multilayer approach to analyze the structural and textural characteristics of natural images as important features for salient region detection from a scale point of view. To represent the structural characteristics, we abstract the image using structured image elements and extract rotational-invariant neighborhood-based textural representations to characterize each element by an individual texture pattern. We then learn a set of representative texture atoms for sparse texture modeling and construct a statistical textural distinctiveness matrix to determine the distinctiveness between all representative texture atom pairs in each layer. Finally, we determine saliency maps for each layer based on the occurrence probability of the texture atoms and their respective statistical textural distinctiveness and fuse them to compute a final saliency map. Experimental results using four public data sets and a variety of performance evaluation metrics show that our approach provides promising results when compared with existing salient region detection approaches.

Synthesis, structural characterization and density functional studies of ethyl 4-(biphenyl-4-yl)-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate A non-merohedral twinned structure

NASA Astrophysics Data System (ADS)

Yıdırım, Sema Öztürk; Büyükmumcu, Zeki; Butcher, Ray J.; Çetin, Gökalp; Şimşek, Rahime; Şafak, Cihat

2018-07-01

1,4-Dihydropyridine (1,4-DHP) derivatives have the reducing effect of extracellular Ca2+ ions influx on the L-type calcium channel. Because of this effect many 1,4-DHP derivatives are potent calcium channel blockers and antihypertensive agents. The biphenyl group is present in the structures of the most biologically active compounds and thus is an important group. By introducing this moiety into the structure of various compounds, active compounds are obtained. Thus, pharmacologically active structures can be condensed with the biphenyl structure to achieve novel biologically active compounds or compounds with increased activity. In this study, to achieve an active calcium channel blocker compound, the biphenyl group was introduced into the 1,4-DHP structure. The structure of the compound is proved by IR, 1H NMR, Mass spectroscopy, X-ray crystallography and elemental analysis. The cytotoxic activity assays have continued and positive results have been obtained. The phenyl rings [C16-C21 and C22-C27] make dihedral angles of 84.4 (1) and 87.5 (1)°, respectively, with the 1,4-dihydropyridine ring [N1/C1/C4-C9]. In the crystal, adjacent molecules are linked by Nsbnd H … O and Csbnd H … O hydrogen bonds into chains parallel to [010].

Actions of 3-[2′-phosphonomethyl[1,1′-biphenyl]-3-yl]alanine (PMBA) on cloned glycine receptors

PubMed Central

Hosie, Alastair M; Akagi, Hiroyuki; Ishida, Michiko; Shinozaki, Haruhiko

1999-01-01

PMBA is a novel antagonist of strychnine-sensitive glycine receptors in the rat spinal cord, however, its mode of action is unknown. The actions of PMBA on rat glycine receptor α1 and α2 homomers in Xenopus oocytes were studied under two-electrode voltage-clamp. Co-application of PMBA and glycine to both α1 and α2 homomers yielded inward currents which decayed to a steady-state. Responses rose slowly to the same steady-state amplitude following a 2 min pre-incubation in PMBA. Strychnine, but not picrotoxinin, showed similar antagonism to PMBA. The potency of PMBA was independent of membrane potential between −100 and 0 mV. When tested against EC50 concentrations of glycine, PMBA was almost equally potent on α1 (IC50, 406±41 nM: Hill coefficient, 1.5±0.2) and α2 (IC50, 539±56 nM; Hill coefficient, 1.4±0.2) homomers. PMBA (1–10 μM) and strychnine (200 nM) reduced the potency of glycine and the amplitude of the maximal agonist response of α1 and α2 homomers. In 10 μM PMBA, two distinct classes of glycine response were observed on α2, only a single class of responses were observed on α1. There are similarities in PMBA and strychnine antagonism, although these compounds are structurally distinct. The possibility that PMBA interacts at two binding sites which differ in α1 and α2 subunits is discussed. PMBA may provide a lead structure for novel antagonists with which to investigate structural differences in glycine receptor at α1 and α2 subunits. PMID:10205013

Boron-containing organic pigments from a Jurassic red alga

PubMed Central

Wolkenstein, Klaus; Gross, Jürgen H.; Falk, Heinz

2010-01-01

Organic biomolecules that have retained their basic chemical structures over geological periods (molecular fossils) occur in a wide range of geological samples and provide valuable paleobiological, paleoenvironmental, and geochemical information not attainable from other sources. In rare cases, such compounds are even preserved with their specific functional groups and still occur within the organisms that produced them, providing direct information on the biochemical inventory of extinct organisms and their possible evolutionary relationships. Here we report the discovery of an exceptional group of boron-containing compounds, the borolithochromes, causing the distinct pink coloration of well-preserved specimens of the Jurassic red alga Solenopora jurassica. The borolithochromes are characterized as complicated spiroborates (boric acid esters) with two phenolic moieties as boron ligands, representing a unique class of fossil organic pigments. The chiroptical properties of the pigments unequivocally demonstrate a biogenic origin, at least of their ligands. However, although the borolithochromes originated from a fossil red alga, no analogy with hitherto known present-day red algal pigments was found. The occurrence of the borolithochromes or their possible diagenetic products in the fossil record may provide additional information on the classification and phylogeny of fossil calcareous algae. PMID:20974956

Boron-containing organic pigments from a Jurassic red alga.

PubMed

Wolkenstein, Klaus; Gross, Jürgen H; Falk, Heinz

2010-11-09

Organic biomolecules that have retained their basic chemical structures over geological periods (molecular fossils) occur in a wide range of geological samples and provide valuable paleobiological, paleoenvironmental, and geochemical information not attainable from other sources. In rare cases, such compounds are even preserved with their specific functional groups and still occur within the organisms that produced them, providing direct information on the biochemical inventory of extinct organisms and their possible evolutionary relationships. Here we report the discovery of an exceptional group of boron-containing compounds, the borolithochromes, causing the distinct pink coloration of well-preserved specimens of the Jurassic red alga Solenopora jurassica. The borolithochromes are characterized as complicated spiroborates (boric acid esters) with two phenolic moieties as boron ligands, representing a unique class of fossil organic pigments. The chiroptical properties of the pigments unequivocally demonstrate a biogenic origin, at least of their ligands. However, although the borolithochromes originated from a fossil red alga, no analogy with hitherto known present-day red algal pigments was found. The occurrence of the borolithochromes or their possible diagenetic products in the fossil record may provide additional information on the classification and phylogeny of fossil calcareous algae.

Molecular Cloning and Characterization of a Xanthone Prenyltransferase from Hypericum calycinum Cell Cultures.

PubMed

Fiesel, Tobias; Gaid, Mariam; Müller, Andreas; Bartels, Joana; El-Awaad, Islam; Beuerle, Till; Ernst, Ludger; Behrends, Sönke; Beerhues, Ludger

2015-08-27

In plants, prenylation of metabolites is widely distributed to generate compounds with efficient defense potential and distinct pharmacological activities profitable to human health. Prenylated compounds are formed by members of the prenyltransferase (PT) superfamily, which catalyze the addition of prenyl moieties to a variety of acceptor molecules. Cell cultures of Hypericum calycinum respond to elicitor treatment with the accumulation of the prenylated xanthone hyperxanthone E. A cDNA encoding a membrane-bound PT (HcPT) was isolated from a subtracted cDNA library and transcript preparations of H. calycinum. An increase in the HcPT transcript level preceded hyperxanthone E accumulation in cell cultures of H. calycinum treated with elicitor. The HcPT cDNA was functionally characterized by expression in baculovirus-infected insect cells. The recombinant enzyme catalyzed biosynthesis of 1,3,6,7-tetrahydroxy-8-prenylxanthone through regiospecific C-8 prenylation of 1,3,6,7-tetrahydroxyxanthone, indicating its involvement in hyperxanthone E formation. The enzymatic product shared significant structural features with the previously reported cholinesterase inhibitor γ-mangostin. Thus, our findings may offer a chance for semisynthesis of new active agents to be involved in the treatment of Alzheimer's disease.

Corona[5]arenes Accessed by a Macrocycle-to-Macrocycle Transformation Route and a One-Pot Three-Component Reaction.

PubMed

Wu, Zhi-Chen; Guo, Qing-Hui; Wang, Mei-Xiang

2017-06-12

Corona[5]arenes, a novel type of macrocyclic compound that is composed of alternating heteroatoms and para-arylenes, were synthesized efficiently by two distinct methods. In a macrocycle-to-macrocycle transformation approach, S 6 -corona[3]arene[3]tetrazine underwent sequential S N Ar reactions with HS-C 6 H 4 -X-C 6 H 4 -SH (X=S, CH 2 , CMe 2 , SO 2 , and O) to produce the corresponding corona[3]arene[2]tetrazines. Different corona[3]arene[2]tetrazine compounds were also constructed in a straightforward manner by a one-pot three-component reaction of HS-C 6 H 4 -X-C 6 H 4 -SH (X=S, CH 2 , CMe 2 , SO 2 , and O) with diethyl 2,5-dimercaptoterephthalate and 2 equiv of 3,6-dichlorotetrazine under very mild conditions. All corona[5]arenes adopted 1,2,4-alternate conformational structures in the crystalline state yielding similar nearly regular pentagonal cavities. Both the cavity size and the electronic property of the acquired macrocycles were fine-tuned by the nature of the bridging element X. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The sympathetic postganglionic fibre and the block by bretylium; the block prevented by hexamethonium and imitated by mecamylamine

PubMed Central

Burn, J. H.; Gibbons, W. R.

1964-01-01

Acetylcholine, in the presence of atropine, has an action like that of sympathetic stimulation. When injected into the splenic artery it causes contraction of the spleen, but this action is blocked by hexamethonium; stimulation of the splenic nerves, however, is still effective. Thus hexamethonium distinguishes between sympathetic nerve stimulation and the action of acetylcholine. If bretylium is used instead of hexamethonium, there is no such distinction, for bretylium blocks the response to nerve stimulation as well as that to acetylcholine. It appeared that hexamethonium might block the action of acetylcholine by preventing its entry into the sympathetic fibre. Acetylcholine has some structural similarity to bretylium, since acetylcholine is a derivative of trimethylammonium and bretylium is a derivative of dimethylethylammonium. It has been found that hexamethonium, pentolinium and hemicholinium (HC-3), which are all bis-quaternary compounds, block the action of bretylium, presumably by preventing its entry into the fibre. Consistent with the view that ability to enter the fibre is important is the observation that mecamylamine and pempidine, which are ganglion-blocking agents, but not either mono- or bis-quaternary compounds, often abolish the response to stimulation of the sympathetic postganglionic fibre. PMID:14211685

Comparative Study of Essential Oils Extracted from Algerian Myrtus communis L. Leaves Using Microwaves and Hydrodistillation

PubMed Central

Berka-Zougali, Baya; Ferhat, Mohamed-Amine; Hassani, Aicha; Chemat, Farid; Allaf, Karim S.

2012-01-01

Two different extraction methods were used for a comparative study of Algerian Myrtle leaf essential oils: solvent-free-microwave-extraction (SFME) and conventional hydrodistillation (HD). Essential oils analyzed by GC and GC-MS presented 51 components constituting 97.71 and 97.39% of the total oils, respectively. Solvent-Free-Microwave-Extract Essential oils SFME-EO were richer in oxygenated compounds. Their major compounds were 1,8-cineole, followed by α-pinene as against α-pinene, followed by 1,8-cineole for HD. Their antimicrobial activity was investigated on 12 microorganisms. The antioxidant activities were studied with the 2,2-diphenyl-1-picrylhydrazyl (DPPH•) radical scavenging method. Generally, both essential oils showed high antimicrobial and weak antioxidant activities. Microstructure analyses were also undertaken on the solid residue of myrtle leaves by Scanning Electronic Microscopy (SEM); it showed that the SFME-cellular structure undergoes significant modifications compared to the conventional HD residual solid. Comparison between hydrodistillation and SFME presented numerous distinctions. Several advantages with SFME were observed: faster kinetics and higher efficiency with similar yields: 0.32% dry basis, in 30 min as against 180 min for HD. PMID:22606003

Raman-atomic force microscopy of the ommatidial surfaces of Dipteran compound eyes.

PubMed

Anderson, Mark S; Gaimari, Stephen D

2003-06-01

The ommatidial lens surfaces of the compound eyes in several species of files (Insecta: Diptera) and a related order (Mecoptera) were analyzed using a recently developed Raman-atomic force microscope. We demonstrate in this work that the atomic force microscope (AFM) is a potentially useful instrument for gathering phylogenetic data and that the newly developed Raman-AFM may extend this application by revealing nanometer-scale surface chemistry. This is the first demonstration of apertureless near-field Raman spectroscopy on an intact biological surface. For Chrysopilus testaceipes Bigot (Rhagionidae), this reveals unique cerebral cortex-like surface ridges with periodic variation in height and surface chemistry. Most other Brachyceran flies, and the "Nematoceran" Sylvicola fenestralis (Scopoli) (Anisopodidae), displayed the same morphology, while other taxa displayed various other characteristics, such as a nodule-like (Tipula (Triplicitipula) sp. (Tipulidae)) or coalescing nodule-like (Tabanus punctifer Osten Sacken (Tabanidae)) morphology, a smooth morphology with distinct pits and grooves (Dilophus orbatus (Say) (Bibionidae)), or an entirely smooth surface (Bittacus chlorostigma MacLachlan (Mecoptera: Bittacidae)). The variation in submicrometer structure and surface chemistry provides a new information source of potential phylogenetic importance, suggesting the Raman-atomic force microscope could provide a new tool useful to systematic and evolutionary inquiry.

Anisotropic type-I superconductivity and anomalous superfluid density in OsB2

NASA Astrophysics Data System (ADS)

Bekaert, J.; Vercauteren, S.; Aperis, A.; Komendová, L.; Prozorov, R.; Partoens, B.; Milošević, M. V.

2016-10-01

We present a microscopic study of superconductivity in OsB2, and discuss the origin and characteristic length scales of the superconducting state. From first-principles we show that OsB2 is characterized by three different Fermi sheets, and we prove that this fermiology complies with recent quantum-oscillation experiments. Using the found microscopic properties, and experimental data from the literature, we employ Ginzburg-Landau relations to reveal that OsB2 is a distinctly type-I superconductor with a very low Ginzburg-Landau parameter κ —a rare property among compound materials. We show that the found coherence length and penetration depth corroborate the measured thermodynamic critical field. Moreover, our calculation of the superconducting gap structure using anisotropic Eliashberg theory and ab initio calculated electron-phonon interaction as input reveals a single but anisotropic gap. The calculated gap spectrum is shown to give an excellent account for the unconventional behavior of the superfluid density of OsB2 measured in experiments as a function of temperature. This reveals that gap anisotropy can explain such behavior, observed in several compounds, which was previously attributed solely to a two-gap nature of superconductivity.

Anisotropic type-I superconductivity and anomalous superfluid density in OsB 2

DOE PAGES

Bekaert, Jonas; Vercauteren, S.; Aperis, A.; ...

2016-10-12

Here, we present a microscopic study of superconductivity in OsB 2, and discuss the origin and characteristic length scales of the superconducting state. From first-principles we show that OsB 2 is characterized by three different Fermi sheets, and we prove that this fermiology complies with recent quantum-oscillation experiments. Using the found microscopic properties, and experimental data from the literature, we employ Ginzburg-Landau relations to reveal that OsB 2 is a distinctly type-I superconductor with a very low Ginzburg-Landau parameter κ—a rare property among compound materials. We show that the found coherence length and penetration depth corroborate the measured thermodynamic criticalmore » field. Moreover, our calculation of the superconducting gap structure using anisotropic Eliashberg theory and ab initio calculated electron-phonon interaction as input reveals a single but anisotropic gap. The calculated gap spectrum is shown to give an excellent account for the unconventional behavior of the superfluid density of OsB 2 measured in experiments as a function of temperature. This reveals that gap anisotropy can explain such behavior, observed in several compounds, which was previously attributed solely to a two-gap nature of superconductivity.« less

Role of dimensionality in the Kondo Ce T X2 family: The case of CeCd0.7Sb2

NASA Astrophysics Data System (ADS)

Rosa, P. F. S.; Bourg, R. J.; Jesus, C. B. R.; Pagliuso, P. G.; Fisk, Z.

2015-10-01

Motivated by the presence of competing magnetic interactions in the heavy fermion family Ce T X2 (T = transitionmetal, X =pnictogen), here we study the novel parent compound CeCd0.7Sb2 by combining magnetization, electrical resistivity, and heat-capacity measurements. Contrary to the antiferromagnetic (AFM) ground state observed in most members of this family, the magnetic properties of our CeCd0.7Sb2 single crystals revealed a ferromagnetic ordering at Tc=3 K with an unusual soft behavior. By using a mean field model including anisotropic nearest-neighbor interactions and the tetragonal crystalline electric field (CEF) Hamiltonian, a systematic analysis of our macroscopic data was obtained. Our fits allowed us to extract a simple but very distinct CEF scheme, as compared to the AFM counterparts. As in the previously studied ferromagnet CeAgSb2, a pure |±1 /2 > ground state is realized, hinting at a general trend within the ferromagnetic members. More generally, we propose a scenario for the understanding of the magnetism in this family of compounds based on the subtle changes of dimensionality in the crystal structure.

Abnormal XPD-induced nuclear receptor transactivation in DNA repair disorders: trichothiodystrophy and xeroderma pigmentosum.

PubMed

Zhou, Xiaolong; Khan, Sikandar G; Tamura, Deborah; Ueda, Takahiro; Boyle, Jennifer; Compe, Emmanuel; Egly, Jean-Marc; DiGiovanna, John J; Kraemer, Kenneth H

2013-08-01

XPD (ERCC2) is a DNA helicase involved in nucleotide excision repair and in transcription as a structural bridge tying the transcription factor IIH (TFIIH) core with the cdk-activating kinase complex, which phosphorylates nuclear receptors. Mutations in XPD are associated with several different phenotypes, including trichothiodystrophy (TTD), with sulfur-deficient brittle hair, bone defects, and developmental abnormalities without skin cancer, xeroderma pigmentosum (XP), with pigmentary abnormalities and increased skin cancer, or XP/TTD with combined features, including skin cancer. We describe the varied clinical features and mutations in nine patients examined at the National Institutes of Health who were compound heterozygotes for XPD mutations but had different clinical phenotypes: four TTD, three XP, and two combined XP/TTD. We studied TFIIH-dependent transactivation by nuclear receptor for vitamin D (VDR) and thyroid in cells from these patients. The vitamin D stimulation ratio of CYP24 and osteopontin was associated with specific pairs of mutations (reduced in 5, elevated in 1) but not correlated with distinct clinical phenotypes. Thyroid receptor stimulation ratio for KLF9 was not significantly different from normal. XPD mutations frequently were associated with abnormal VDR stimulation in compound heterozygote patients with TTD, XP, or XP/TTD.

Raman-atomic force microscopy of the ommatidial surfaces of Dipteran compound eyes

NASA Technical Reports Server (NTRS)

Anderson, Mark S.; Gaimari, Stephen D.

2003-01-01

The ommatidial lens surfaces of the compound eyes in several species of files (Insecta: Diptera) and a related order (Mecoptera) were analyzed using a recently developed Raman-atomic force microscope. We demonstrate in this work that the atomic force microscope (AFM) is a potentially useful instrument for gathering phylogenetic data and that the newly developed Raman-AFM may extend this application by revealing nanometer-scale surface chemistry. This is the first demonstration of apertureless near-field Raman spectroscopy on an intact biological surface. For Chrysopilus testaceipes Bigot (Rhagionidae), this reveals unique cerebral cortex-like surface ridges with periodic variation in height and surface chemistry. Most other Brachyceran flies, and the "Nematoceran" Sylvicola fenestralis (Scopoli) (Anisopodidae), displayed the same morphology, while other taxa displayed various other characteristics, such as a nodule-like (Tipula (Triplicitipula) sp. (Tipulidae)) or coalescing nodule-like (Tabanus punctifer Osten Sacken (Tabanidae)) morphology, a smooth morphology with distinct pits and grooves (Dilophus orbatus (Say) (Bibionidae)), or an entirely smooth surface (Bittacus chlorostigma MacLachlan (Mecoptera: Bittacidae)). The variation in submicrometer structure and surface chemistry provides a new information source of potential phylogenetic importance, suggesting the Raman-atomic force microscope could provide a new tool useful to systematic and evolutionary inquiry.

Anti-inflammatory drugs and prediction of new structures by comparative analysis.

PubMed

Bartzatt, Ronald

2012-01-01

Nonsteroidal anti-inflammatory drugs (NSAIDs) are a group of agents important for their analgesic, anti-inflammatory, and antipyretic properties. This study presents several approaches to predict and elucidate new molecular structures of NSAIDs based on 36 known and proven anti-inflammatory compounds. Based on 36 known NSAIDs the mean value of Log P is found to be 3.338 (standard deviation= 1.237), mean value of polar surface area is 63.176 Angstroms2 (standard deviation = 20.951 A2), and the mean value of molecular weight is 292.665 (standard deviation = 55.627). Nine molecular properties are determined for these 36 NSAID agents, including Log P, number of -OH and -NHn, violations of Rule of 5, number of rotatable bonds, and number of oxygens and nitrogens. Statistical analysis of these nine molecular properties provides numerical parameters to conform to in the design of novel NSAID drug candidates. Multiple regression analysis is accomplished using these properties of 36 agents followed with examples of predicted molecular weight based on minimum and maximum property values. Hierarchical cluster analysis indicated that licofelone, tolfenamic acid, meclofenamic acid, droxicam, and aspirin are substantially distinct from all remaining NSAIDs. Analysis of similarity (ANOSIM) produced R = 0.4947, which indicates low to moderate level of dissimilarity between these 36 NSAIDs. Non-hierarchical K-means cluster analysis separated the 36 NSAIDs into four groups having members of greatest similarity. Likewise, discriminant analysis divided the 36 agents into two groups indicating the greatest level of distinction (discrimination) based on nine properties. These two multivariate methods together provide investigators a means to compare and elucidate novel drug designs to 36 proven compounds and ascertain to which of those are most analogous in pharmacodynamics. In addition, artificial neural network modeling is demonstrated as an approach to predict numerous molecular properties of new drug designs that is based on neural training from 36 proven NSAIDs. Comprehensive and effective approaches are presented in this study for the design of new NSAID type agents which are so very important for inhibition of COX-2 and COX-1 isoenzymes.

Structure and Chemical Synthesis of a Biologically Active Form of Renilla (Sea Pansy) Luciferin*

PubMed Central

Hori, Kazuo; Cormier, Milton J.

1973-01-01

The structure of a biologically active form of Renilla (sea pansy) luciferin has been elucidated; this structure, confirmed by total chemical synthesis, is 3,7-dihydro-2-methyl-6-(p-hydroxyphenyl)-8-benzylimidazo [1,2-a] pyrazin-3-one. In the natural compound the methyl group at the 2 position is replaced by an unknown, more complex group. For this reason the synthetic compound is 10% as active as the natural compound in producing light with Renilla luciferase. However, the spectral properties of the two compounds are identical. In addition the rates of the luminescent reaction with both compounds are similar, and the color of the light produced is identical in each case. A compound isolated from the calcium-triggered photoprotein aequorin has been identified by Shimomura and Johnson [(1972) Biochemistry 11, 1602] to be 2-amino-3-benzyl-5-(p-hydroxyphenyl)pyrazine. This compound forms an integral part of the structure of Renilla luciferin. This, and other evidence, suggests that the structure elucidated for Renilla luciferin is a more general one associated with the luciferins of most, if not all, bioluminescent coelenterates. PMID:16592045

Strawberry flavor: diverse chemical compositions, a seasonal influence, and effects on sensory perception.

PubMed

Schwieterman, Michael L; Colquhoun, Thomas A; Jaworski, Elizabeth A; Bartoshuk, Linda M; Gilbert, Jessica L; Tieman, Denise M; Odabasi, Asli Z; Moskowitz, Howard R; Folta, Kevin M; Klee, Harry J; Sims, Charles A; Whitaker, Vance M; Clark, David G

2014-01-01

Fresh strawberries (Fragaria x ananassa) are valued for their characteristic red color, juicy texture, distinct aroma, and sweet fruity flavor. In this study, genetic and environmentally induced variation is exploited to capture biochemically diverse strawberry fruit for metabolite profiling and consumer rating. Analyses identify fruit attributes influencing hedonics and sensory perception of strawberry fruit using a psychophysics approach. Sweetness intensity, flavor intensity, and texture liking are dependent on sugar concentrations, specific volatile compounds, and fruit firmness, respectively. Overall liking is most greatly influenced by sweetness and strawberry flavor intensity, which are undermined by environmental pressures that reduce sucrose and total volatile content. The volatile profiles among commercial strawberry varieties are complex and distinct, but a list of perceptually impactful compounds from the larger mixture is better defined. Particular esters, terpenes, and furans have the most significant fits to strawberry flavor intensity. In total, thirty-one volatile compounds are found to be significantly correlated to strawberry flavor intensity, only one of them negatively. Further analysis identifies individual volatile compounds that have an enhancing effect on perceived sweetness intensity of fruit independent of sugar content. These findings allow for consumer influence in the breeding of more desirable fruits and vegetables. Also, this approach garners insights into fruit metabolomics, flavor chemistry, and a paradigm for enhancing liking of natural or processed products.

Strawberry Flavor: Diverse Chemical Compositions, a Seasonal Influence, and Effects on Sensory Perception

PubMed Central

Schwieterman, Michael L.; Colquhoun, Thomas A.; Jaworski, Elizabeth A.; Bartoshuk, Linda M.; Gilbert, Jessica L.; Tieman, Denise M.; Odabasi, Asli Z.; Moskowitz, Howard R.; Folta, Kevin M.; Klee, Harry J.; Sims, Charles A.; Whitaker, Vance M.; Clark, David G.

2014-01-01

Fresh strawberries (Fragaria x ananassa) are valued for their characteristic red color, juicy texture, distinct aroma, and sweet fruity flavor. In this study, genetic and environmentally induced variation is exploited to capture biochemically diverse strawberry fruit for metabolite profiling and consumer rating. Analyses identify fruit attributes influencing hedonics and sensory perception of strawberry fruit using a psychophysics approach. Sweetness intensity, flavor intensity, and texture liking are dependent on sugar concentrations, specific volatile compounds, and fruit firmness, respectively. Overall liking is most greatly influenced by sweetness and strawberry flavor intensity, which are undermined by environmental pressures that reduce sucrose and total volatile content. The volatile profiles among commercial strawberry varieties are complex and distinct, but a list of perceptually impactful compounds from the larger mixture is better defined. Particular esters, terpenes, and furans have the most significant fits to strawberry flavor intensity. In total, thirty-one volatile compounds are found to be significantly correlated to strawberry flavor intensity, only one of them negatively. Further analysis identifies individual volatile compounds that have an enhancing effect on perceived sweetness intensity of fruit independent of sugar content. These findings allow for consumer influence in the breeding of more desirable fruits and vegetables. Also, this approach garners insights into fruit metabolomics, flavor chemistry, and a paradigm for enhancing liking of natural or processed products. PMID:24523895

High-order nonlinear optical processes in ablated carbon-containing materials: Recent approaches in development of the nonlinear spectroscopy using harmonic generation in the extreme ultraviolet range

NASA Astrophysics Data System (ADS)

Ganeev, R. A.

2017-08-01

The nonlinear spectroscopy using harmonic generation in the extreme ultraviolet range became a versatile tool for the analysis of the optical, structural and morphological properties of matter. The carbon-contained materials have shown the advanced properties among other studied species, which allowed both the definition of the role of structural properties on the nonlinear optical response and the analysis of the fundamental features of carbon as the attractive material for generation of coherent short-wavelength radiation. We review the studies of the high-order harmonic generation by focusing ultrashort pulses into the plasmas produced during laser ablation of various organic compounds. We discuss the role of ionic transitions of ablated carbon-containing molecules on the harmonic yield. We also show the similarities and distinctions of the harmonic and plasma spectra of organic compounds and graphite. We discuss the studies of the generation of harmonics up to the 27th order (λ = 29.9 nm) of 806 nm radiation in the boron carbide plasma and analyze the advantages and disadvantages of this target compared with the ingredients comprising B4C (solid boron and graphite) by comparing plasma emission and harmonic spectra from three species. We also show that the coincidence of harmonic and plasma emission wavelengths in most cases does not cause the enhancement or decrease of the conversion efficiency of this harmonic.

Discovery of Platelet-Type 12-Human Lipoxygenase Selective Inhibitors by High-Throughput Screening of Structurally Diverse Libraries

PubMed Central

Deschamps, Joshua D.; Gautschi, Jeffrey T.; Whitman, Stephanie; Johnson, Tyler A.; Gassner, Nadine C.; Crews, Phillip; Holman, Theodore R.

2007-01-01

Human lipoxygenases (hLO) have been implicated in a variety of diseases and cancers and each hLO isozyme appears to have distinct roles in cellular biology. This fact emphasizes the need for discovering selective hLO inhibitors for both understanding the role of specific lipoxygenases in the cell and developing pharmaceutical therapeutics. To this end, we have modified a known lipoxygenase assay for high-throughput (HTP) screening of both the National Cancer Institute (NCI) and the UC Santa Cruz marine extract library (UCSC-MEL) in search of platelet-type 12-hLO (12-hLO) selective inhibitors. The HTP screen led to the characterization of five novel 12-hLO inhibitors from the NCI repository. One is the potent but non-selective michellamine B, a natural product, antiviral agent. The other four compounds were selective inhibitors against 12-hLO, with three being synthetic compounds and one being α-mangostin, a natural product, caspase-3 pathway inhibitor. In addition, a selective inhibitor was isolated from the UCSC-MEL (neodysidenin), which has a unique chemical scaffold for an hLO inhibitor. Due to the unique structure of neodysidenin, steady-state inhibition kinetics were performed and its mode of inhibition against 12-hLO was determined to be competitive (Ki = 17 µM) and selective over reticulocyte 15-hLO-1 (Ki 15-hLO-1/12-hLO > 30). PMID:17826100

Heteroaryldihydropyrimidine (HAP) and Sulfamoylbenzamide (SBA) Inhibit Hepatitis B Virus Replication by Different Molecular Mechanisms

PubMed Central

Zhou, Zheng; Hu, Taishan; Zhou, Xue; Wildum, Steffen; Garcia-Alcalde, Fernando; Xu, Zhiheng; Wu, Daitze; Mao, Yi; Tian, Xiaojun; Zhou, Yuan; Shen, Fang; Zhang, Zhisen; Tang, Guozhi; Najera, Isabel; Yang, Guang; Shen, Hong C.; Young, John A. T.; Qin, Ning

2017-01-01

Heteroaryldihydropyrimidine (HAP) and sulfamoylbenzamide (SBA) are promising non-nucleos(t)ide HBV replication inhibitors. HAPs are known to promote core protein mis-assembly, but the molecular mechanism of abnormal assembly is still elusive. Likewise, the assembly status of core protein induced by SBA remains unknown. Here we show that SBA, unlike HAP, does not promote core protein mis-assembly. Interestingly, two reference compounds HAP_R01 and SBA_R01 bind to the same pocket at the dimer-dimer interface in the crystal structures of core protein Y132A hexamer. The striking difference lies in a unique hydrophobic subpocket that is occupied by the thiazole group of HAP_R01, but is unperturbed by SBA_R01. Photoaffinity labeling confirms the HAP_R01 binding pose at the dimer-dimer interface on capsid and suggests a new mechanism of HAP-induced mis-assembly. Based on the common features in crystal structures we predict that T33 mutations generate similar susceptibility changes to both compounds. In contrast, mutations at positions in close contact with HAP-specific groups (P25A, P25S, or V124F) only reduce susceptibility to HAP_R01, but not to SBA_R01. Thus, HAP and SBA are likely to have distinctive resistance profiles. Notably, P25S and V124F substitutions exist in low-abundance quasispecies in treatment-naïve patients, suggesting potential clinical relevance. PMID:28205569

Neural correlates of processing sentences and compound words in Chinese

PubMed Central

Hung, Yi-Hui; Tzeng, Ovid; Wu, Denise H.

2017-01-01

Sentence reading involves multiple linguistic operations including processing of lexical and compositional semantics, and determining structural and grammatical relationships among words. Previous studies on Indo-European languages have associated left anterior temporal lobe (aTL) and left interior frontal gyrus (IFG) with reading sentences compared to reading unstructured word lists. To examine whether these brain regions are also involved in reading a typologically distinct language with limited morphosyntax and lack of agreement between sentential arguments, an FMRI study was conducted to compare passive reading of Chinese sentences, unstructured word lists and disconnected character lists that are created by only changing the order of an identical set of characters. Similar to previous findings from other languages, stronger activation was found in mainly left-lateralized anterior temporal regions (including aTL) for reading sentences compared to unstructured word and character lists. On the other hand, stronger activation was identified in left posterior temporal sulcus for reading unstructured words compared to unstructured characters. Furthermore, reading unstructured word lists compared to sentences evoked stronger activation in left IFG and left inferior parietal lobule. Consistent with the literature on Indo-European languages, the present results suggest that left anterior temporal regions subserve sentence-level integration, while left IFG supports restoration of sentence structure. In addition, left posterior temporal sulcus is associated with morphological compounding. Taken together, reading Chinese sentences engages a common network as reading other languages, with particular reliance on integration of semantic constituents. PMID:29194453

Chemical structure of bismuth compounds determines their gastric ulcer healing efficacy and anti-Helicobacter pylori activity.

PubMed

Sandha, G S; LeBlanc, R; Van Zanten, S J; Sitland, T D; Agocs, L; Burford, N; Best, L; Mahoney, D; Hoffman, P; Leddin, D J

1998-12-01

The recognition of the role of Helicobacter pylori in the pathogenesis of peptic ulcer disease has led to renewed interest in bismuth pharmacology since bismuth compounds have both anti-Helicobacter pylori and ulcer healing properties. The precise chemical structure of current bismuth compounds is not known. This has hindered the development of new and potentially more efficacious formulations. We have created two new compounds, 2-chloro-1,3-dithia-2-bismolane (CDTB) and 1,2-[bis(1,3-dithia-2-bismolane)thio]ethane (BTBT), with known structure. In a rat model of gastric ulceration, BTBT was comparable to, and CDTB was significantly less effective than colloidal bismuth subcitrate in healing cryoprobe-induced ulcers. However, both BTBT and CDTB inhibited H. pylori growth in vitro at concentrations <1/10 that of colloidal bismuth subcitrate. The effects on ulcer healing are not mediated by suppression of acid secretion, pepsin inhibition, or prostaglandin production. Since all treated animals received the same amount of elemental bismuth, it appears that the efficacy of bismuth compounds varies with compound structure and is not simply dependent on the delivery of bismuth ion. Because the structure of the novel compounds is known, our understanding of the relationship of bismuth compound structure and to biologic activity will increase. In the future it may be possible to design other novel bismuth compounds with more potent anti-H. pylori and ulcer healing effects.

Distinct Effect of Benzalkonium Chloride on the Esterase and Aryl Acylamidase Activities of Butyrylcholinesterase.

PubMed

Jaganathan; Boopathy

2000-08-01

Acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) from vertebrates, other than their predominant acylcholine hydrolase (esterase) activity, display a genuine aryl acylamidase activity (AAA) capable of hydrolyzing the synthetic substrate o-nitroacetanilide to o-nitroaniline. This AAA activity is strongly inhibited by classical cholinesterase (ChE) inhibitors. In the present study, benzalkonium chloride (BAC), a cationic detergent widely used as a preservative in pharmaceutical preparations, has been shown to distinctly modulate the esterase and AAA activities of BChEs. The detergent BAC was able to inhibit the esterase activity of human serum and horse serum BChEs and AChEs from electric eel and human erythrocyte. The remarkable property of BAC was its ability to profoundly activate the AAA activity of human serum and horse serum BChEs but not the AAA activity of AChEs. Thus BAC seem to preferentially activate the AAA activity of BChEs alone. Results of the study using the ChE active site-specific inhibitor diisopropyl phosphorofluoridate indicated that BAC binds to the active site of ChEs. Furthermore, studies using a structural homolog of BAC indicated that the alkyl group of BAC is essential not only for its interaction with ChEs but also for its distinct effect on the esterase and AAA activities of BChEs. This is the first report of a compound that inhibits the esterase activity, while simultaneously activating the AAA activity, of BChEs. Copyright 2000 Academic Press.

Imaging Mercury's Polar Deposits during MESSENGER's Low-altitude Campaign.

PubMed

Chabot, Nancy L; Ernst, Carolyn M; Paige, David A; Nair, Hari; Denevi, Brett W; Blewett, David T; Murchie, Scott L; Deutsch, Ariel N; Head, James W; Solomon, Sean C

2016-09-28

Images obtained during MESSENGER's low-altitude campaign in the final year of the mission provide the highest-spatial-resolution views of Mercury's polar deposits. Images for distinct areas of permanent shadow within 35 north polar craters were successfully captured during the campaign. All of these regions of permanent shadow were found to have low-reflectance surfaces with well-defined boundaries. Additionally, brightness variations across the deposits correlate with variations in the biannual maximum surface temperature across the permanently shadowed regions, supporting the conclusion that multiple volatile organic compounds are contained in Mercury's polar deposits, in addition to water ice. A recent large impact event or ongoing bombardment by micrometeoroids could deliver water as well as many volatile organic compounds to Mercury. Either scenario is consistent with the distinctive reflectance properties and well-defined boundaries of Mercury's polar deposits and the presence of volatiles in all available cold traps.

Similarity of High-Resolution Tandem Mass Spectrometry Spectra of Structurally Related Micropollutants and Transformation Products

NASA Astrophysics Data System (ADS)

Schollée, Jennifer E.; Schymanski, Emma L.; Stravs, Michael A.; Gulde, Rebekka; Thomaidis, Nikolaos S.; Hollender, Juliane

2017-12-01

High-resolution tandem mass spectrometry (HRMS2) with electrospray ionization is frequently applied to study polar organic molecules such as micropollutants. Fragmentation provides structural information to confirm structures of known compounds or propose structures of unknown compounds. Similarity of HRMS2 spectra between structurally related compounds has been suggested to facilitate identification of unknown compounds. To test this hypothesis, the similarity of reference standard HRMS2 spectra was calculated for 243 pairs of micropollutants and their structurally related transformation products (TPs); for comparison, spectral similarity was also calculated for 219 pairs of unrelated compounds. Spectra were measured on Orbitrap and QTOF mass spectrometers and similarity was calculated with the dot product. The influence of different factors on spectral similarity [e.g., normalized collision energy (NCE), merging fragments from all NCEs, and shifting fragments by the mass difference of the pair] was considered. Spectral similarity increased at higher NCEs and highest similarity scores for related pairs were obtained with merged spectra including measured fragments and shifted fragments. Removal of the monoisotopic peak was critical to reduce false positives. Using a spectral similarity score threshold of 0.52, 40% of related pairs and 0% of unrelated pairs were above this value. Structural similarity was estimated with the Tanimoto coefficient and pairs with higher structural similarity generally had higher spectral similarity. Pairs where one or both compounds contained heteroatoms such as sulfur often resulted in dissimilar spectra. This work demonstrates that HRMS2 spectral similarity may indicate structural similarity and that spectral similarity can be used in the future to screen complex samples for related compounds such as micropollutants and TPs, assisting in the prioritization of non-target compounds. [Figure not available: see fulltext.

Subtype and pathway specific responses to anticancer compounds in breast cancer.

PubMed

Heiser, Laura M; Sadanandam, Anguraj; Kuo, Wen-Lin; Benz, Stephen C; Goldstein, Theodore C; Ng, Sam; Gibb, William J; Wang, Nicholas J; Ziyad, Safiyyah; Tong, Frances; Bayani, Nora; Hu, Zhi; Billig, Jessica I; Dueregger, Andrea; Lewis, Sophia; Jakkula, Lakshmi; Korkola, James E; Durinck, Steffen; Pepin, François; Guan, Yinghui; Purdom, Elizabeth; Neuvial, Pierre; Bengtsson, Henrik; Wood, Kenneth W; Smith, Peter G; Vassilev, Lyubomir T; Hennessy, Bryan T; Greshock, Joel; Bachman, Kurtis E; Hardwicke, Mary Ann; Park, John W; Marton, Laurence J; Wolf, Denise M; Collisson, Eric A; Neve, Richard M; Mills, Gordon B; Speed, Terence P; Feiler, Heidi S; Wooster, Richard F; Haussler, David; Stuart, Joshua M; Gray, Joe W; Spellman, Paul T

2012-02-21

Breast cancers are comprised of molecularly distinct subtypes that may respond differently to pathway-targeted therapies now under development. Collections of breast cancer cell lines mirror many of the molecular subtypes and pathways found in tumors, suggesting that treatment of cell lines with candidate therapeutic compounds can guide identification of associations between molecular subtypes, pathways, and drug response. In a test of 77 therapeutic compounds, nearly all drugs showed differential responses across these cell lines, and approximately one third showed subtype-, pathway-, and/or genomic aberration-specific responses. These observations suggest mechanisms of response and resistance and may inform efforts to develop molecular assays that predict clinical response.

Structural diversity of three Cu(II) compounds based on a new tripodal zwitterionic ligand: Syntheses, structures and properties

NASA Astrophysics Data System (ADS)

Zhou, Jie; Zhao, Jing-Song; Feng, Jing; Zhang, Xiao-Feng; Xu, Jian; Du, Lin; Xie, Ming-Jin; Zhao, Qi-Hua

2018-03-01

An exploration of reactions of 1,1‧,1″-(benzene-1,3,5-triyltris(methylene))tris(4-carboxypyridinium)-tribromide (H3LBr3) with Cu(II) salt under different pH conditions has led to the formation of three complexes, [Cu(HL)2(H2O)3]·4(ClO4)·3H2O (1), [Cu2(HL)(μ3-OH)(μ2-H2O)(H2O)2]·4(ClO4)·6H2O (2), and [Cu3(L)2Cl6(H2O)4]·4H2O (3). Single-crystal X-ray analyses revealed that complex 1 displays a discrete mononuclear structure with the ligand in a bowl-shaped configuration. Complex 2 possesses a tetranuclear 1D beaded chain structure. While complex 3 features a discrete trinuclear 'H-type' structure with the ligand in a chair-like configuration. The distinct compositions and structures of 1-3 are mainly ascribed to the different pH values of the reaction solution, the influences of anions, as well as the configurations which the zwitterion ligands adopt. The magnetic properties of 2, and the photoluminescence properties of 2, and 3 have been investigated. Moreover, powder X-ray diffraction, infrared spectroscopy, and elemental analysis were also performed.

Tuning the formations of metal-1,3,5-benzenetricarboxylate frameworks via the assistance of amino acids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lei, Xiao-Ping; Lian, Ting-Ting; Chen, Shu-Mei, E-mail: csm@fzu.edu.cn

Seven new metal-1,3,5-benzenetricarboxylate coordination polymers have been synthesized by modification of auxiliary components during the assembly reactions. Their structures have been determined by single-crystal X-ray diffraction analyses and further characterized by XRD and TGA. Interestingly, they show fascinating topological structures. Compounds 1 and 2 possess the undulating layer structure with 3-connected hcb network and (3,6)-connected kgd network. Compound 3 possesses three-dimensional (3D) pillared-layer structure with 3-connected 2-fold interpenetrating srs net. Compound 4 also has the 3D 2-fold interpenetrating pillared-layer structure; however, it has (3,5)-connected hms topology because the Cd(II) center is 5-connected. Compound 5 possess 3D structure through hydrogen bondingmore » interactions between ladder-like layers. Compounds 6 and 7 have the similar 3D frameworks with 4-connected umc net and (3,7)-connected (3.4.5)(3{sup 2}.4{sup 6}.5{sup 5}.6{sup 8}) topology, respectively. The photoluminescent properties of compounds 2–7 were also investigated. - Graphical abstract: Presented here are seven new metal-1,3,5-benzenetricarboxylate coordination polymers with diverse structures from 2D layers to 3D open frameworks. The synthesis and structural diversity of these compounds are determined by the additional amino acids as unusual buffering agents. - Highlights: • Structural diversity of metal-1,3,5-benzenetricarboxylate frameworks. • Tuning structural topologies of MOFs via the assistance of amino acids. • Amino acids as unusual buffering agents for the synthesis of MOFs.« less

Assessing the chemotaxis behavior of Physarum polycephalum to a range of simple volatile organic chemicals.

PubMed

de Lacy Costello, Ben P J; Adamatzky, Andrew I

2013-09-01

The chemotaxis behavior of the plasmodial stage of the true slime mold Physarum Polycephalum was assessed when given a binary choice between two volatile organic chemicals (VOCs) placed in its environment. All possible binary combinations were tested between 19 separate VOCs selected due to their prevalence and biological activity in common plant and insect species. The slime mold exhibited positive chemotaxis toward a number of VOCs with the following order of preference:   Farnesene > β-myrcene > tridecane > limonene > p-cymene > 3-octanone > β-pinene > m-cresol > benzylacetate > cis-3-hexenylacetate. For the remaining compounds, no positive chemotaxis was observed in any of the experiments, and for most compounds there was an inhibitory effect on the growth of the slime mold. By assessing this lack of growth or failure to propagate, it was possible to produce a list of compounds ranked in terms of their inhibitory effect: nonanal > benzaldehyde > methylbenzoate > linalool > methyl-p-benzoquinone > eugenol > benzyl alcohol > geraniol > 2-phenylethanol. This analysis shows a distinct preference of the slime mold for non-oxygenated terpene and terpene-like compounds (farnesene, β-myrcene, limonene, p-cymene and β-pinene). In contrast, terpene-based alcohols such as geraniol and linalool were found to have a strong inhibitory effect on the slime mold. Both the aldehydes utilized in this study had the strongest inhibitory effect on the slime mold of all the 19 VOCs tested. Interestingly, 3-octanone, which has a strong association with a "fungal odor," was the only compound with an oxygenated functionality where Physarum Polycephalum exhibits distinct positive chemotaxis.

Assessing the chemotaxis behavior of Physarum polycephalum to a range of simple volatile organic chemicals

PubMed Central

de Lacy Costello, Ben P.J.; Adamatzky, Andrew I.

2013-01-01

The chemotaxis behavior of the plasmodial stage of the true slime mold Physarum Polycephalum was assessed when given a binary choice between two volatile organic chemicals (VOCs) placed in its environment. All possible binary combinations were tested between 19 separate VOCs selected due to their prevalence and biological activity in common plant and insect species. The slime mold exhibited positive chemotaxis toward a number of VOCs with the following order of preference:   Farnesene > β-myrcene > tridecane > limonene > p-cymene > 3-octanone > β-pinene > m-cresol > benzylacetate > cis-3-hexenylacetate. For the remaining compounds, no positive chemotaxis was observed in any of the experiments, and for most compounds there was an inhibitory effect on the growth of the slime mold. By assessing this lack of growth or failure to propagate, it was possible to produce a list of compounds ranked in terms of their inhibitory effect: nonanal > benzaldehyde > methylbenzoate > linalool > methyl-p-benzoquinone > eugenol > benzyl alcohol > geraniol > 2-phenylethanol. This analysis shows a distinct preference of the slime mold for non-oxygenated terpene and terpene-like compounds (farnesene, β-myrcene, limonene, p-cymene and β-pinene). In contrast, terpene-based alcohols such as geraniol and linalool were found to have a strong inhibitory effect on the slime mold. Both the aldehydes utilized in this study had the strongest inhibitory effect on the slime mold of all the 19 VOCs tested. Interestingly, 3-octanone, which has a strong association with a “fungal odor,” was the only compound with an oxygenated functionality where Physarum Polycephalum exhibits distinct positive chemotaxis. PMID:24265848

Site preferences of actinide cations in [NZP] compounds

NASA Astrophysics Data System (ADS)

Hawkins, H. T.; Spearing, D. R.; Smith, D. M.; Hampel, F. G.; Veirs, D. K.; Scheetz, B. E.

2000-07-01

Compounds adopting the sodium dizirconium tris(phosphate) (NaZr2(PO4)3) structure type belong to the [NZP] structural family of compounds. [NZP] compounds possess desirable properties that would permit their application as hosts for the actinides. These properties include compositional flexibility (i.e., three structural sites that can accommodate a variety of different cations), high thermal stability, negligible thermal expansion, and resistance to radiation damage. Experimental data indicate that [NZP] compounds resist dissolution and release of constituents over a wide range of experimental conditions. Moreover, [NZP] compounds may be synthesized by both conventional and novel methods and may be heat treated or sintered at modest temperatures (800 °C-1350 °C) in open or restricted systems.

Differential inhibition of Ca2+ channels in mature rat cerebellar Purkinje cells by sFTX-3.3 and FTX-3.3.

PubMed

Dupere, J R; Moya, E; Blagbrough, I S; Usowicz, M M

1996-01-01

Synthetic funnel web spider toxin (sFTX-3.3) is a polyamine amide analogue of FTX, a toxin fraction isolated from the venom of the funnel web spider, Agelenopsis aperta, that blocks P-type Ca2+ channels. The structures of these polyamine containing compounds are not identical: sFTX-3.3 contains an amide carbonyl oxygen that is absent from the predicted structure of native FTX. Recently, a compound called FTX-3.3 was synthesized with the structure predicted for native FTX. We have compared the effects of polyamine amide sFTX-3.3 and polyamine FTX-3.3, on Ca2+ channel currents in the soma of mature rat cerebellar Purkinje neurons, in which the predominant Ca2+ channels are defined as P-type. Differential inhibition by sFTX-3.3 and FTX-3.3 revealed three populations of Ca2+ channels. One group, mediating approximately 66% of the current, was blocked by sFTX-3.3 with an IC50 (concentration producing half maximal inhibition) of 33 nM or by FTX-3.3 with an IC50 of 55 pM. A second population (5-25% of the total current) was inhibited by sFTX-3.3 with an IC50 of 33 nM, but was insensitive to FTX-3.3, while a third (10-30%) was blocked by FTX-3.3 with an IC50 of 125 nM and was resistant to sFTX-3.3. These channels also showed distinctive current-voltage relationships. Our results suggest that P-type Ca2+ channels in mature rat cerebellar Purkinje cells may be subdivided according to pharmacological and biophysical properties.