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Sample records for key structural analogues

  1. Structural Analogues of Selfotel.

    PubMed

    Dziuganowska, Zofia A; Ślepokura, Katarzyna; Volle, Jean-Noël; Virieux, David; Pirat, Jean-Luc; Kafarski, Paweł

    2016-06-17

    A small library of phosphonopiperidylcarboxylic acids, analogues of NMDA antagonist selfotel (CGS 19755), was synthesized. First, the series of aromatic esters was obtained via a palladium-catalyzed cross-coupling reaction (Hirao coupling) of dialkyl phosphites with bromopyridinecarboxylates, followed by their hydrolysis. Then, hydrogenation of the resulting phosphonopyridylcarboxylic acids over PtO2 yielded the desired phosphonopiperidylcarboxylic acids. NMR studies indicated that the hydrogenation reaction proceeds predominantly by cis addition. Several compounds were obtained as monocrystal structures. Preliminary biological studies performed on cultures of neurons suggest that the obtained compounds possess promising activity toward NMDA receptors. PMID:27187758

  2. Materials analogue of zero-stiffness structures

    NASA Astrophysics Data System (ADS)

    Kumar, Arun; Subramaniam, Anandh

    2011-04-01

    Anglepoise lamps and certain tensegrities are examples of zero-stiffness structures. These structures are in a state of neutral equilibrium with respect to changes in configuration of the system. Using Eshelby's example of an edge dislocation in a thin plate that can bend, we report the discovery of a non-trivial new class of material structures as an analogue to zero-stiffness structures. For extended positions of the edge dislocation in these structures, the dislocation experiences a zero image force. Salient features of these material structures along with the key differences from conventional zero-stiffness structures are pointed out.

  3. Total synthesis of vinblastine, related natural products, and key analogues and development of inspired methodology suitable for the systematic study of their structure-function properties.

    PubMed

    Sears, Justin E; Boger, Dale L

    2015-03-17

    Biologically active natural products composed of fascinatingly complex structures are often regarded as not amenable to traditional systematic structure-function studies enlisted in medicinal chemistry for the optimization of their properties beyond what might be accomplished by semisynthetic modification. Herein, we summarize our recent studies on the Vinca alkaloids vinblastine and vincristine, often considered as prototypical members of such natural products, that not only inspired the development of powerful new synthetic methodology designed to expedite their total synthesis but have subsequently led to the discovery of several distinct classes of new, more potent, and previously inaccessible analogues. With use of the newly developed methodology and in addition to ongoing efforts to systematically define the importance of each embedded structural feature of vinblastine, two classes of analogues already have been discovered that enhance the potency of the natural products >10-fold. In one instance, remarkable progress has also been made on the refractory problem of reducing Pgp transport responsible for clinical resistance with a series of derivatives made accessible only using the newly developed synthetic methodology. Unlike the removal of vinblastine structural features or substituents, which typically has a detrimental impact, the additions of new structural features have been found that can enhance target tubulin binding affinity and functional activity while simultaneously disrupting Pgp binding, transport, and functional resistance. Already analogues are in hand that are deserving of full preclinical development, and it is a tribute to the advances in organic synthesis that they are readily accessible even on a natural product of a complexity once thought refractory to such an approach. PMID:25586069

  4. Stereocontrolled Synthesis of Key Advanced Intermediates toward Simplified Acetogenin Analogues.

    PubMed

    Le Huérou, Yvan; Doyon, Julien; Grée, René L.

    1999-09-01

    The stereo- and enantiocontrolled synthesis of substituted beta-hydroxy ethers based on glycol and catechol bearing an alkyne group and a series of substituents is reported. These substrates were designed to mimic the bis-THF array of annonaceous acetogenins and to provide an access to simplified and modified analogues. The key steps of the synthesis involve the condensation of the nonracemic mesylate of solketal with ethylene glycol and catechol, followed by an alkylation with a glycidyl derivative. Under appropriate conditions, the reaction is completely stereoselective and allows the synthesis of all the diastereomers. After the epoxide was opened with triethylsilylacetylene, the second epoxide was unmasked and reacted with a series of alkyl, aryl, amine, and alcohol reagents. A series of 28 analogues was prepared having a glycol or a catechol core, a stereodefined configuration of the flanking hydroxyl groups, and an acetylenic appendage suitable for a coupling to a lactone-bearing fragment. PMID:11674687

  5. The Relationship Between Water Structure and Blood Compatibility in Poly(2-methoxyethyl Acrylate) (PMEA) Analogues.

    PubMed

    Sato, Kazuhiro; Kobayashi, Shingo; Kusakari, Miho; Watahiki, Shogo; Oikawa, Masahiko; Hoshiba, Takashi; Tanaka, Masaru

    2015-09-01

    Six types of poly(2-methoxyethyl acrylate) (PMEA) analogues were synthesized and the water structure in the hydrated polymers was characterized using differential scanning calorimetry (DSC). The hydrated PMEA analogues exhibited the different amounts of intermediate water. Non-thrombogenicity evaluation was performed on PMEA analogues for platelet adhesion and protein adsorption. Platelet adhesion was suppressed on PMEA analogues. In addition, the protein adsorption and deformation were suppressed by increasing the amount of intermediate water. This study demonstrates that the amount of intermediate water might play a key role in expressing the blood compatibility of polymeric materials. PMID:26017931

  6. Structural analogues of diosgenyl saponins: synthesis and anticancer activity.

    PubMed

    Kaskiw, Matthew J; Tassotto, Mary Lynn; Mok, Mac; Tokar, Stacey L; Pycko, Roxanne; Th'ng, John; Jiang, Zi-Hua

    2009-11-15

    Saponins display various biological activities including anti-tumor activity. Recently intensive research has been focused on developing saponins for tumor therapies. The diosgenyl saponin dioscin is one of the most common steroidal saponins and exhibits potent anticancer activity in several human cancer cells through apoptosis-inducing pathways. In this paper, we describe the synthesis of several diosgenyl saponin analogues containing either a 2-amino-2-deoxy-beta-d-glucopyranosyl residue or an alpha-l-rhamnopyranosyl-(1-->4)-2-amino-2-deoxy-beta-d-glucopyranosyl residue with different acyl substituents on the amino group. The cytotoxic activity of these compounds was evaluated in MCF-7 breast cancer cells and HeLa cervical cancer cells. Structure-activity relationship studies show that the disaccharide saponin analogues are in general less active than their corresponding monosaccharide analogues. The incorporation of an aromatic nitro functionality into these saponin analogues does not exhibit significant effect on their cytotoxic activity. PMID:19819703

  7. Component-based syntheses of trioxacarcin A, DC-45-A1 and structural analogues

    NASA Astrophysics Data System (ADS)

    Magauer, Thomas; Smaltz, Daniel J.; Myers, Andrew G.

    2013-10-01

    The trioxacarcins are polyoxygenated, structurally complex natural products that potently inhibit the growth of cultured human cancer cells. Here we describe syntheses of trioxacarcin A, DC-45-A1 and structural analogues by late-stage stereoselective glycosylation reactions of fully functionalized, differentially protected aglycon substrates. Key issues addressed in this work include the identification of an appropriate means to activate and protect each of the two 2-deoxysugar components, trioxacarcinose A and trioxacarcinose B, as well as a viable sequencing of the glycosidic couplings. The convergent, component-based sequence we present allows for rapid construction of structurally diverse, synthetic analogues that would be inaccessible by any other means, in amounts required to support biological evaluation. Analogues that arise from the modification of four of five modular components are assembled in 11 steps or fewer. The majority of these are found to be active in antiproliferative assays using cultured human cancer cells.

  8. The International Space Analogue Rock Store (ISAR): A key tool for future planetary exploration.

    NASA Astrophysics Data System (ADS)

    Bost, N.; Westall, F.; Ramboz, C.; Foucher, F.

    2012-04-01

    In order to prepare the next in situ space missions we have created a « lithothèque » of analogue rocks for calibrating and testing future (and existing) space flight instruments. This rock collection is called the International Space Analogue Rockstore (ISAR) and is hosted in the CNRS and the Observatoire des Sciences de l'Univers en Region Centre (OSUC) in Orléans. For maximum science return, all instruments on a single mission should ideally be tested with the same suite of relevant analogue materials. The ISAR lithothéque aims to fulfill this role by providing suitable materials to instrument teams [1]. The lithothèque is accompanied by an online database of all relevant structural, textural, and geochemical data (www.isar.cnrs-orleans.fr).The data base will also be available during missions to aid interpretation of data obtained in situ. Mars is the immediate goal for MSL-2011 and the new international Mars 2018 mission. The lithothèque thus presently contains relevant Mars-analogue rock and mineral samples, a preliminary range of which is now available to the scientific community for instrument testing [2]. The preliminary group of samples covers a range of lithologies to be found on Mars, especially those in Noachain/Hesperian terrains where MSL will land (Gale Crater) and where the 2018 landing site will most likely be located. It includes a variety of basalts (tephrite, primitive basalt, silicified basalt; plus cumulates), komatiites, artificially synthesized martian basalts [3], volcanic sands, a banded iron formation, carbonates associated with volcanic lithologies and hydrothermalism, the clay Nontronite, and hydrothermal cherts. Some of the silicified volcanic sands contain traces of early life that are good analogues for potential martian life [4]. [1] Westall F. et al., LPI contribution 1608, 1346, 42nd LPSC, 2011; [2] Bost N. et al., in review (Icarus); [3] Bost N. et al., in review (Meteoritics); [4] Westall et al., 2011, Planetary and Space

  9. Polychlorinated biphenyls as hormonally active structural analogues

    SciTech Connect

    McKinney, J.D. ); Waller, C.L. )

    1994-03-01

    Among the environmental chemicals that may be able to disrupt the endocrine systems of animals and humans, the polychlorinated biphenyls (PCBs) are a chemical class of considerable concern. One possible mechanism by which PCBs may interfere with endocrine function is their ability to mimic natural hormones. These actions reflect a close relationship between the physicochemical properties encoded in the PCB molecular structure and the responses they evoke in biological systems. These physiocochemical properties determine the molecular reactivities of PCBs and are responsible for their recognition as biological acceptors and receptors, as well as for triggering molecular mechanisms that lead to tissue response. [open quotes]Coplanarity[close quotes] of PCB phenyl rings and [open quotes]laterality[close quotes] of chlorine atoms are important structural features determining specific binding behavior with proteins and certain toxic responses in biological systems. We compare qualitative structure-activity relationships for PCBs with the limited information on the related non-coplanar chlorinated diphenyl ethers, providing further insights into the nature of the molecular recognition processes and support for the structural relationship of PCBs to thyroid hormones. Steriodlike activity requires conformational restriction and possibility hydroxylation. We offer some simple molecular recognition models to account for the importance of these different structural features in the structure-activity relationships that permit one to express PCB reactivities in terms of dioxin, thyroxine, and estradiol equivalents. The available data support the involvement of PCBs as mimics of thyroid and other steroidal hormones. The potential for reproductive and developmental toxicity associated with human exposure to PCBs is of particular concern. 53 refs., 6 figs.

  10. A comparative study on the crystal structure of bicycle analogues to the natural phytotoxin helminthosporins

    NASA Astrophysics Data System (ADS)

    Barbosa, Luiz Cláudio de Almeida; Teixeira, Robson Ricardo; Nogueira, Leonardo Brandão; Maltha, Celia Regina Alvares; Doriguetto, Antônio Carlos; Martins, Felipe Terra

    2016-02-01

    Herein we described structural insights of a series of analogues to helminthosporin phytotoxins. The key reaction used to prepare the compounds corresponded to the [3 + 4] cycloaddition between the oxyallyl cation generated from 2,4-dibromopentan-3-one and different furans. Their structures were confirmed upon IR, NMR and X-ray diffraction analyses. While bicycles 7, 8 and 9 crystallize in the centrosymmetric monoclinic space group P21/c, compound 10 was solved in the noncentrosymmetric orthorhombic space group P212121. The solid materials obtained were shown to be racemic crystals (7, 8, 9) or racemic conglomerate (10). In all compounds, there is formation of a bicycle featured by fused tetrahydropyranone and 2,5-dihydrofuran rings. They adopt chair and envelope conformations, respectively. Crystal packing of all compounds is stabilized through C-H•••O contacts. Conformational aspects as well as similarities and differences among the crystal structures of the synthesized analogues are discussed.

  11. Structural Insights Lead to a Negamycin Analogue with Improved Antimicrobial Activity against Gram-Negative Pathogens.

    PubMed

    McKinney, David C; Basarab, Gregory S; Cocozaki, Alexis I; Foulk, Melinda A; Miller, Matthew D; Ruvinsky, Anatoly M; Scott, Clay W; Thakur, Kumar; Zhao, Liang; Buurman, Ed T; Narayan, Sridhar

    2015-08-13

    Negamycin is a natural product with antibacterial activity against a broad range of Gram-negative pathogens. Recent revelation of its ribosomal binding site and mode of inhibition has reinvigorated efforts to identify improved analogues with clinical potential. Translation-inhibitory potency and antimicrobial activity upon modification of different moieties of negamycin were in line with its observed ribosomal binding conformation, reaffirming stringent structural requirements for activity. However, substitutions on the N6 amine were tolerated and led to N6-(3-aminopropyl)-negamycin (31f), an analogue showing 4-fold improvement in antibacterial activity against key bacterial pathogens. This represents the most potent negamycin derivative to date and may be a stepping stone toward clinical development of this novel antibacterial class. PMID:26288696

  12. Structural Insights Lead to a Negamycin Analogue with Improved Antimicrobial Activity against Gram-Negative Pathogens

    PubMed Central

    2015-01-01

    Negamycin is a natural product with antibacterial activity against a broad range of Gram-negative pathogens. Recent revelation of its ribosomal binding site and mode of inhibition has reinvigorated efforts to identify improved analogues with clinical potential. Translation-inhibitory potency and antimicrobial activity upon modification of different moieties of negamycin were in line with its observed ribosomal binding conformation, reaffirming stringent structural requirements for activity. However, substitutions on the N6 amine were tolerated and led to N6-(3-aminopropyl)-negamycin (31f), an analogue showing 4-fold improvement in antibacterial activity against key bacterial pathogens. This represents the most potent negamycin derivative to date and may be a stepping stone toward clinical development of this novel antibacterial class. PMID:26288696

  13. Divergent regulation of the key enzymes of polyamine metabolism by chiral alpha-methylated polyamine analogues.

    PubMed

    Hyvönen, Mervi T; Howard, Michael T; Anderson, Christine B; Grigorenko, Nikolay; Khomutov, Alex R; Vepsäläinen, Jouko; Alhonen, Leena; Jänne, Juhani; Keinänen, Tuomo A

    2009-09-01

    The natural polyamines are ubiquitous multifunctional organic cations which play important roles in regulating cellular proliferation and survival. Here we present a novel approach to investigating polyamine functions by using optical isomers of MeSpd (alpha-methylspermidine) and Me2Spm (alpha,omega-bismethylspermine), metabolically stable functional mimetics of natural polyamines. We studied the ability of MeSpd and Me2Spm to alter the normal polyamine regulation pathways at the level of polyamine uptake and the major control mechanisms known to affect the key polyamine metabolic enzymes. These include: (i) ODC (ornithine decarboxylase), which catalyses the rate-limiting step of polyamine synthesis; (ii) ODC antizyme, an inhibitor of ODC and polyamine uptake; (iii) SSAT (spermidine/spermine N1-acetyltransferase), the major polyamine catabolic enzyme; and (iv) AdoMetDC (S-adenosyl-L-methionine decarboxylase), which is required for the conversion of putrescine into spermidine, and spermidine into spermine. We show that the stereoisomers differ in their cellular uptake and ability to downregulate ODC and AdoMetDC, and to induce SSAT. These effects are mediated by the ability of the enantiomers to induce +1 ribosomal frameshifting on ODC antizyme mRNA, to suppress the translation of AdoMetDC uORF (upstream open reading frame) and to regulate the alternative splicing of SSAT pre-mRNA. The unique effects of chiral polyamine analogues on polyamine metabolism may offer novel possibilities for studying the physiological functions, control mechanisms, and targets of the natural polyamines, as well as advance therapeutic drug development in cancer and other human health-related issues. PMID:19522702

  14. Solution structures of purine base analogues 9-deazaguanine and 9-deazahypoxanthine.

    PubMed

    Karnawat, Vishakha; Puranik, Mrinalini

    2016-03-01

    Deaza analogues of nucleobases are potential drugs against infectious diseases caused by parasites. A caveat is that apart from binding their target parasite enzymes, they also bind and inhibit enzymes of the host. In order to design derivatives of deaza analogues which specifically bind target enzymes, knowledge of their molecular structure, protonation state, and predominant tautomers at physiological conditions is essential. We have employed resonance Raman spectroscopy at an excitation wavelength of 260 nm, to decipher solution structure of 9-deazaguanine (9DAG) and 9-deazahypoxanthine (9DAH). These are analogues of guanine and hypoxanthine, respectively, and have been exploited to study static complexes of nucleobase binding enzymes. Such enzymes are known to perturb pKa of their ligands, and thus, we also determined solution structures of these analogues at two, acidic and alkaline, pH. Structure of each possible protonation state and tautomer was computed using density functional theoretical calculations. Species at various pHs were identified based on isotopic shifts in experimental wavenumbers and by comparing these shifts with corresponding computed isotopic shifts. Our results show that at physiological pH, N1 of pyrimidine ring in 9DAG and 9DAH bears a proton. At lower pH, N3 is place of protonation, and at higher pH, deprotonation occurs at N1 position. The proton at N7 of purine ring remains intact even at pH 12.5. We have further compared these results with naturally occurring nucleotides. Our results identify key vibrational modes which can report on hydrogen bonding interactions, protonation and deprotonation in purine rings upon binding to the active site of enzymes. PMID:25894214

  15. [Insulin analogues: modifications in the structure, molecular and metabolic consequences].

    PubMed

    de Luis, D A; Romero, E

    2013-01-01

    Recombinant DNA technology has provided insulin analogues for the treatment of diabetes mellitus, with an efficacy and safety that has improved the treatment of this disease. We briefly review the principal characteristics of the insulin analogues currently available. Both rapid-acting (lispro, aspart and glulisine) and long acting (glargine and determir) insulin analogues are included in this review. We describe the pharmacology of each insulin analogue, their differences with the human insulin, the administration, indication, efficacy and safety. In addition we discussed the main controversies of the use of these insulin analogues. In particular, those related with the risk of cancer and retinopathy, and their use in pregnant women. PMID:23517895

  16. 1'-Homonucleosides and their structural analogues: A review.

    PubMed

    Wróblewski, Andrzej E; Głowacka, Iwona E; Piotrowska, Dorota G

    2016-08-01

    Nucleoside analogues belong to an important class of antiviral and anticancer drugs. Insertion of a methylene fragment between the anomeric carbon and pyrimidine or purine bases transforms nucleosides into 1'-homonucleosides. When compared with nucleosides this modification lengthens the separation between HO-C5' of pentofuranoside fragments and nitrogen (N1 or N9) atoms of nucleobases, lowers the steric and electronic interactions between nucleobases and sugar rings, introduces greater flexibility around a CH2-Base bond and thus allows for more rotational freedom, and since the anomeric effect no longer operates any sugar or pseudosugar moiety exists in its unique conformation and experiences specific conformational mobility and hydrolysis of the C1'-CH2Base bond by cellular enzymes is no longer feasible. This review covers 1'-homonucleosides with a tetrahydrofuran ring and its nitrogen and sulfur analogues as well as those containing a cyclopentane moiety as a sugar replacer. Achievements in syntheses of sugar or pseudosugar scaffolds are of primary interest since pathways to install nucleobases are well recognized. Whenever possible, the biological activity, mostly antiviral and antitumor but sometimes as inhibitors of specific enzymes, will be presented and discussed to help identify structural features responsible for the particular mode of action and thus possible therapeutic significance. PMID:27128178

  17. Modern freshwater microbialite analogues for ancient dendritic reef structures

    NASA Technical Reports Server (NTRS)

    Laval, B.; Cady, S. L.; Pollack, J. C.; McKay, C. P.; Bird, J. S.; Grotzinger, J. P.; Ford, D. C.; Bohm, H. R.

    2000-01-01

    Microbialites are organosedimentary structures that can be constructed by a variety of metabolically distinct taxa. Consequently, microbialite structures abound in the fossil record, although the exact nature of the biogeochemical processes that produced them is often unknown. One such class of ancient calcareous structures, Epiphyton and Girvanella, appear in great abundance during the Early Cambrian. Together with Archeocyathids, stromatolites and thrombolites, they formed major Cambrian reef belts. To a large extent, Middle to Late Cambrian reefs are similar to Precambrian reefs, with the exception that the latter, including terminal Proterozoic reefs, do not contain Epiphyton or Girvanella. Here we report the discovery in Pavilion Lake, British Columbia, Canada, of a distinctive assemblage of freshwater calcite microbialites, some of which display microstructures similar to the fabrics displayed by Epiphyton and Girvanella. The morphologies of the modern microbialites vary with depth, and dendritic microstructures of the deep water (> 30 m) mounds indicate that they may be modern analogues for the ancient calcareous structures. These microbialites thus provide an opportunity to study the biogeochemical interactions that produce fabrics similar to those of some enigmatic Early Cambrian reef structures.

  18. Antithyroid drugs and their analogues: synthesis, structure, and mechanism of action.

    PubMed

    Manna, Debasish; Roy, Gouriprasanna; Mugesh, Govindasamy

    2013-11-19

    Thyroid hormones are essential for the development and differentiation of all cells of the human body. They regulate protein, fat, and carbohydrate metabolism. In this Account, we discuss the synthesis, structure, and mechanism of action of thyroid hormones and their analogues. The prohormone thyroxine (T4) is synthesized on thyroglobulin by thyroid peroxidase (TPO), a heme enzyme that uses iodide and hydrogen peroxide to perform iodination and phenolic coupling reactions. The monodeiodination of T4 to 3,3',5-triiodothyronine (T3) by selenium-containing deiodinases (ID-1, ID-2) is a key step in the activation of thyroid hormones. The type 3 deiodinase (ID-3) catalyzes the deactivation of thyroid hormone in a process that removes iodine selectively from the tyrosyl ring of T4 to produce 3,3',5'-triiodothyronine (rT3). Several physiological and pathological stimuli influence thyroid hormone synthesis. The overproduction of thyroid hormones leads to hyperthyroidism, which is treated by antithyroid drugs that either inhibit the thyroid hormone biosynthesis and/or decrease the conversion of T4 to T3. Antithyroid drugs are thiourea-based compounds, which include propylthiouracil (PTU), methimazole (MMI), and carbimazole (CBZ). The thyroid gland actively concentrates these heterocyclic compounds against a concentration gradient. Recently, the selenium analogues of PTU, MMI, and CBZ attracted significant attention because the selenium moiety in these compounds has a higher nucleophilicity than that of the sulfur moiety. Researchers have developed new methods for the synthesis of the selenium compounds. Several experimental and theoretical investigations revealed that the selone (C═Se) in the selenium analogues is more polarized than the thione (C═S) in the sulfur compounds, and the selones exist predominantly in their zwitterionic forms. Although the thionamide-based antithyroid drugs have been used for almost 70 years, the mechanism of their action is not completely

  19. Generation of crystal structures using known crystal structures as analogues

    PubMed Central

    Cole, Jason C.; Groom, Colin R.; Read, Murray G.; Giangreco, Ilenia; McCabe, Patrick; Reilly, Anthony M.; Shields, Gregory P.

    2016-01-01

    This analysis attempts to answer the question of whether similar molecules crystallize in a similar manner. An analysis of structures in the Cambridge Structural Database shows that the answer is yes – sometimes they do, particularly for single-component structures. However, one does need to define what we mean by similar in both cases. Building on this observation we then demonstrate how this correlation between shape similarity and packing similarity can be used to generate potential lattices for molecules with no known crystal structure. Simple intermolecular interaction potentials can be used to minimize these potential lattices. Finally we discuss the many limitations of this approach. PMID:27484374

  20. Total synthesis, stereochemical assignment, and biological activity of chamuvarinin and structural analogues.

    PubMed

    Florence, Gordon J; Morris, Joanne C; Murray, Ross G; Vanga, Raghava R; Osler, Jonathan D; Smith, Terry K

    2013-06-17

    A highly stereocontrolled synthesis of (+)-chamuvarinin has been completed in 1.5% overall yield over 20 steps. The key fragment coupling reactions were the addition of alkyne 8 to aldehyde 7 (under Felkin-Anh control), followed by the two step activation/cyclization to close the C20-C23 2,5-cis-substituted tetrahydrofuran ring and a Julia-Kocienski olefination at C8-C9 to introduce the terminal butenolide. The inherent flexibility of our coupling strategy led to a streamlined synthesis with 17 steps in the longest sequence (2.2% overall yield), in which the key bond couplings are reversed. In addition, a series of structural analogues of chamuvarinin have been prepared and screened for activity against HeLa cancer cell lines and both the bloodstream and insect forms of Trypanosoma brucei, the parasitic agent responsible for African sleeping sickness. PMID:23630031

  1. DNA information: from digital code to analogue structure.

    PubMed

    Travers, A A; Muskhelishvili, G; Thompson, J M T

    2012-06-28

    The digital linear coding carried by the base pairs in the DNA double helix is now known to have an important component that acts by altering, along its length, the natural shape and stiffness of the molecule. In this way, one region of DNA is structurally distinguished from another, constituting an additional form of encoded information manifest in three-dimensional space. These shape and stiffness variations help in guiding and facilitating the DNA during its three-dimensional spatial interactions. Such interactions with itself allow communication between genes and enhanced wrapping and histone-octamer binding within the nucleosome core particle. Meanwhile, interactions with proteins can have a reduced entropic binding penalty owing to advantageous sequence-dependent bending anisotropy. Sequence periodicity within the DNA, giving a corresponding structural periodicity of shape and stiffness, also influences the supercoiling of the molecule, which, in turn, plays an important facilitating role. In effect, the super-helical density acts as an analogue regulatory mode in contrast to the more commonly acknowledged purely digital mode. Many of these ideas are still poorly understood, and represent a fundamental and outstanding biological question. This review gives an overview of very recent developments, and hopefully identifies promising future lines of enquiry. PMID:22615471

  2. Antimicrobial Activity of Xanthohumol and Its Selected Structural Analogues.

    PubMed

    Stompor, Monika; Żarowska, Barbara

    2016-01-01

    The objective of this study was to evaluate the antimicrobial activity of structural analogues of xanthohumol 1, a flavonoid compound found in hops (Humulus lupulus). The agar-diffusion method using filter paper disks was applied. Biological tests performed for selected strains of Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria, fungi (Alternaria sp.), and yeasts (Rhodotorula rubra, Candida albicans) revealed that compounds with at least one hydroxyl group-all of them have it at the C-4 position-demonstrated good activity. Our research showed that the strain S. aureus was more sensitive to chalcones than to the isomers in which the heterocyclic ring C is closed (flavanones). The strain R. rubra was moderately sensitive to only one compound: 4-hydroxy-4'-methoxychalcone 8. Loss of the hydroxyl group in the B-ring of 4'-methoxychalcones or its replacement by a halogen atom (-Cl, -Br), nitro group (-NO₂), ethoxy group (-OCH₂CH₃), or aliphatic substituent (-CH₃, -CH₂CH₃) resulted in the loss of antimicrobial activity towards both R. rubra yeast and S. aureus bacteria. Xanthohumol 1, naringenin 5, and chalconaringenin 7 inhibited growth of S. aureus, whereas 4-hydroxy-4'-methoxychalcone 8 was active towards two strains: S. aureus and R. rubra. PMID:27187329

  3. Isolation and structural elucidation of a new tadalafil analogue in health supplements: bisprenortadalafil.

    PubMed

    Lee, Ji Hyun; Park, Han Na; Ganganna, Bogonda; Jeong, Ji Hye; Park, Sung-Kwan; Lee, Jongkook; Baek, Sun Young

    2016-06-01

    A new tadalafil analogue was found, along with nortadalafil, using HPLC-DAD during the inspection of a health product sold without official approval. The analogue was separated using a semi-preparative HPLC system and its structure was determined by a combination of mass spectrometry and NMR spectroscopy. The compound was identified as a tadalafil analogue in which the N-methyl group of tadalafil was replaced with a tadalafil precursor moiety. Nuclear Overhauser effect spectroscopy experiments suggested a cis-relationship between the substituents on a piperidine ring in the tadalafil moiety. PMID:27167568

  4. Preparing to return to the Moon: Lessons from science-driven analogue missions to the Mistastin Lake impact structure, Canada, a unique lunar analogue site

    NASA Astrophysics Data System (ADS)

    Osinski, G. R.; Barfoot, T.; Chanou, A.; Daly, M. G.; Francis, R.; Hodges, K. V.; Jolliff, B. L.; Mader, M. M.; McCullough, E. M.; Moores, J. E.; Pickersgill, A.; Pontefract, A.; Preston, L.; Shankar, B.; Singleton, A.; Sylvester, P.; Tornabene, L. L.; Young, K. E.

    2013-12-01

    Impact cratering is the dominant geological process on the Moon, Near Earth Asteroids (NEAs) and the moons of Mars - the objectives for the new Solar System Exploration Research Virtual Institute (SSERVI). Led by members of the Canadian Lunar Research Network (CLRN), funded by the Canadian Space Agency, and with participants from the U.S., we carried out a series of analogue missions on Earth in order to prepare and train for future potential robotic and human sample return missions. Critically, these analogue missions were driven by the paradigm that operational and technical objectives are conducted while conducting new science and addressing real overarching scientific objectives. An overarching operational goal was to assess the utility of a robotic field reconnaissance mission as a precursor to a human sortie sample return mission. Here, we focus on the results and lessons learned from a robotic precursor mission and follow on human-robotic mission to the Mistastin Lake impact structure in Labrador, northern Canada (55°53'N; 63°18'W). The Mistastin structure was chosen because it represents an exceptional analogue for lunar craters. This site includes both an anorthositic target, a central uplift, well-preserved impact melt rocks - mostly derived from melting anorthosite - and is (or was) relatively unexplored. This crater formed ~36 million years ago and has a diameter of ~28 km. The scientific goals for these analogue missions were to further our understanding of impact chronology, shock processes, impact ejecta and potential resources within impact craters. By combining these goals in an analogue mission campaign key scientific requirements for a robotic precursor were determined. From the outset, these analogue missions were formulated and executed like an actual space mission. Sites of interest were chosen using remote sensing imagery without a priori knowledge of the site through a rigorous site selection process. The first deployment occurred in

  5. Membrane structure and interactions of a short Lycotoxin I analogue.

    PubMed

    Adão, R; Seixas, R; Gomes, P; Pessoa, J Costa; Bastos, M

    2008-04-01

    Lycotoxin I and Lycotoxin II are natural anti-microbial peptides that were identified in the venom of the Wolf Spider Lycosa carolinensis. These peptides were found to be potent growth inhibitors for bacteria (Escherichia coli) and yeast (Candida glabrata) at micromolar concentrations. Recently, shortened analogues of LycoI and LycoII have been reported to have decreased haemolytic effects. A shorter Lyco-I analogue studied, LycoI 1-15 (H-IWLTALKFLGKHAAK-NH2), was active only above 10 microM, but was also the least haemolytic. On the basis of these findings, we became interested in obtaining a deeper insight into the membrane activity of LycoI 1-15, as this peptide may represent the first major step for the future development of selective, i.e. non-haemolytic, Lycotoxin-based antibiotics. The interaction of this peptide with liposomes of different composition was studied by microcalorimetry [differential scanning calorimetry (DSC) and isothermal titration calorimetry (ITC)] and CD. The results obtained from the calorimetric and spectroscopic techniques were jointly discussed in an attempt to further understand the interaction of this peptide with model membranes. PMID:18098329

  6. Dipolar Quinoidal Acene Analogues as Stable Isoelectronic Structures of Pentacene and Nonacene.

    PubMed

    Shi, Xueliang; Kueh, Weixiang; Zheng, Bin; Huang, Kuo-Wei; Chi, Chunyan

    2015-11-23

    Quinoidal thia-acene analogues, as the respective isoelectronic structures of pentacene and nonacene, were synthesized and an unusual 1,2-sulfur migration was observed during the Friedel-Crafts alkylation reaction. The analogues display a closed-shell quinoidal structure in the ground state with a distinctive dipolar character. In contrast to their acene isoelectronic structures, both compounds are stable because of the existence of more aromatic sextet rings, a dipolar character, and kinetic blocking. They exhibit unique packing in single crystals resulting from balanced dipole-dipole and [C-H⋅⋅⋅π]/[C-H⋅⋅⋅S] interactions. PMID:26447720

  7. Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch.

    PubMed

    Thore, Stéphane; Frick, Christian; Ban, Nenad

    2008-07-01

    The thiamine pyrophosphate (TPP)-sensing riboswitch is the only riboswitch found in eukaryotes. In plants, TPP regulates its own production by binding to the 3' untranslated region of the mRNA encoding ThiC, a critical enzyme in thiamine biosynthesis, which promotes the formation of an unstable splicing variant. In order to better understand the molecular basis of TPP-analogue binding to the eukaryotic TPP-responsive riboswitch, we have determined the crystal structures of the Arabidopsis thaliana TPP-riboswitch in complex with oxythiamine pyrophosphate (OTPP) and with the antimicrobial compound pyrithiamine pyrophosphate (PTPP). The OTPP-riboswitch complex reveals that the pyrimidine ring of OTPP is stabilized in its enol form in order to retain key interactions with guanosine 28 of the riboswitch previously observed in the TPP complex. The structure of PTPP in complex with the riboswitch shows that the base moiety of guanosine 60 undergoes a conformational change to cradle the pyridine ring of the PTPP. Structural information from these complexes has implications for the design of novel antimicrobials targeting TPP-sensing riboswitches. PMID:18533652

  8. Total Synthesis of Viridicatumtoxin B and Analogues Thereof: Strategy Evolution, Structural Revision, and Biological Evaluation

    PubMed Central

    2015-01-01

    The details of the total synthesis of viridicatumtoxin B (1) are described. Initial synthetic strategies toward this intriguing tetracycline antibiotic resulted in the development of key alkylation and Lewis acid-mediated spirocyclization reactions to form the hindered EF spirojunction, as well as Michael–Dieckmann reactions to set the A and C rings. The use of an aromatic A-ring substrate, however, was found to be unsuitable for the introduction of the requisite hydroxyl groups at carbons 4a and 12a. Applying these previous tactics, we developed stepwise approaches to oxidize carbons 12a and 4a based on enol- and enolate-based oxidations, respectively, the latter of which was accomplished after systematic investigations that revealed critical reactivity patterns. The herein described synthetic strategy resulted in the total synthesis of viridicatumtoxin B (1), which, in turn, formed the basis for the revision of its originally assigned structure. The developed chemistry facilitated the synthesis of a series of viridicatumtoxin analogues, which were evaluated against Gram-positive and Gram-negative bacterial strains, including drug-resistant pathogens, revealing the first structure–activity relationships within this structural type. PMID:25317739

  9. Structure activity relationship study of curcumin analogues toward the amyloid-beta aggregation inhibitor.

    PubMed

    Endo, Hitoshi; Nikaido, Yuri; Nakadate, Mamiko; Ise, Satomi; Konno, Hiroyuki

    2014-12-15

    Inhibition of the amyloid β aggregation process could possibly prevent the onset of Alzheimer's disease. In this article, we report a structure-activity relationship study of curcumin analogues for anti amyloid β aggregation activity. Compound 7, the ideal amyloid β aggregation inhibitor in vitro among synthesized curcumin analogues, has not only potent anti amyloid β aggregation effects, but also water solubility more than 160 times that of curcumin. In addition, new approaches to improve water solubility of curcumin-type compounds are proposed. PMID:25467149

  10. Natural and semisynthetic analogues of manadoperoxide B reveal new structural requirements for trypanocidal activity.

    PubMed

    Chianese, Giuseppina; Scala, Fernando; Calcinai, Barbara; Cerrano, Carlo; Dien, Henny A; Kaiser, Marcel; Tasdemir, Deniz; Taglialatela-Scafati, Orazio

    2013-09-01

    Chemical analysis of the Indonesian sponge Plakortis cfr. lita afforded two new analogues of the potent trypanocidal agent manadoperoxide B (1), namely 12-isomanadoperoxide B (2) and manadoperoxidic acid B (3). These compounds were isolated along with a new short chain dicarboxylate monoester (4), bearing some interesting relationships with the polyketide endoperoxides found in this sponge. Some semi-synthetic analogues of manadoperoxide B (6-8) were prepared and evaluated for antitrypanosomal activity and cytotoxicity. These studies revealed crucial structure-activity relationships that should be taken into account in the design of optimized and simplified endoperoxyketal trypanocidal agents. PMID:23989650

  11. Structural and Spectroscopic Characterizations of Amide-AlCl3-Based Ionic Liquid Analogues.

    PubMed

    Hu, Pengcheng; Zhang, Rui; Meng, Xianghai; Liu, Haiyan; Xu, Chunming; Liu, Zhichang

    2016-03-01

    Several amide-AlCl3-based ionic liquid (IL) analogues were synthesized through a one-step method using three different structure amides as donor molecules. The effects of the steric and inductive effects of the methyl group substituted on the N atom on the asymmetric splitting of AlCl3 and the coordination site of the amide were investigated by (27)Al NMR, Raman, in situ IR, and UV-vis spectra for these IL analogues. Bidentate coordination through both the O and N atoms was dominant in the N-methylacetamide-AlCl3- and N,N-dimethylacetamide-AlCl3-based IL analogues because of the inductive effect of the methyl group. By contrast, the acetamide-AlCl3-based IL analogue presented mainly in the form of monodentate coordination via the O atom. Compared with monodentate coordination, bidentate coordination was favorable to the asymmetric splitting of AlCl3 with the same amide-AlCl3 molar ratio. Under the influence of the steric and inductive effects of the methyl group, the ionic species percentages in these IL analogues ranked in the following order: N-methylacetamide > N,N-dimethylacetamide > acetamide. PMID:26848508

  12. Structure--antiadenoviral activity of nitrogen containing macroheterocycles and their analogues.

    PubMed

    Dyachenko, N S; Nosach, L N; Povnitsa, O Y; Kuz'min, V E; Artemenko, A G; Lozitskaya, R N; Basok, S S; Alexeeva, I V; Zhovnovataya, V L; Vanden Eynde, J J

    2006-01-01

    The search for the inhibitors of adenoviruses has been performed among the substances of new class NCM (nitrogen containing macroheterocycles) and their analogues that have high potential of pharmacological properties. We have found a number of NCM and their derivatives that inhibit the reproduction of adenoviruses to various degrees. For the prediction of NCM structure with antiadenoviral activity we have performed the computer modeling using QSAR approach on the basis of simplex representation of molecular structure (SiRMS). PMID:17388122

  13. The development of structures in analogue and natural debris avalanches

    NASA Astrophysics Data System (ADS)

    Paguican, Engielle Mae; van Wyk de Vries, Benjamin; Mahar Francisco Lagmay, Alfredo; Grosse, Pablo

    2010-05-01

    All types of rockslide-debris avalanches present a plethora of internal structures that are also well observed on the surface. Many of these are seen as faults and folds that can be used to determine deformation history and kinematics. We present two sets of simple and well-constrained experiments of reduced basal friction laboratory rockslides, equivalent to a highly deformed simple shear layer, with plug-flow. These follow the original ramp-slide work of Shea and van Wyk de Vries (Geosphere, 2008). The experiments used a curved ramp where materials accelerate until reaching a gently-sloped depositional surface and a constantly inclined ramp with a more regular slope and longer slides. A detailed description of deposit structures, their sequential formation and morphology is then used to investigate the transport type and deformation chronology from slide initiation to runout stopping of avalanches. Results using a curved ramp show accumulation and thickening at where the slope decreases. The thickened mass then further remobilises and advances by secondary collapse of the mass. Such a stop-start process may be important in many mountainous avalanches where there are rapid changes in slope. The constantly inclined ramp shows shearing and extensional structures at the levees and a set of compression and extension structures in the middle. We noted that frontal accumulation during flow occurs as materials at the front move slower relative to those in the medial and proximal zones. This also leads to secondary frontal collapse, and helps to maintain a thicker mass that can flow further. Descriptions and analyses of these structures are then applied to the kinematics and dynamics of natural examples. We study the 2006 Guinsaugon Rockslide event in the Philippines and find that frontal accumulation and secondary avalanching had also occurred and were important in determining the distribution and runout of the mass. Frontal bulking and collapse may also have occurred at

  14. The Beta Environmental Fine Structure (BEFS): The XAFS Nuclear Analogue

    SciTech Connect

    Monfardini, A.; Benedek, G.; Cremonesi, O.; Nucciotti, A.; Sisti, M.; Filipponi, A.

    2007-02-02

    The Beta Environmental Fine Structure (BEFS) effect is an oscillatory modulation on the otherwise smooth spectrum of electrons emitted by beta-decaying nuclei. The existence of this effect was theoretically proposed in 1991, for condensed emitters, in analogy with XAFS. In BEFS the electron, playing the role of the XAFS photoelectron, originates directly from the nucleus and an anti-neutrino is emitted at the same time. We present evidence for BEFS oscillations observed in Silver Perrhenate (AgReO4) low-temperature (0.1K) microbolometers, together with a XAFS-like analysis that allowed for the first time a direct measurement of the anti-neutrino angular momentum. We discuss the physical analogies and differences between BEFS and XAFS and the implications for the next generation experiments aimed at measuring the neutrino mass on purely kinematic grounds. Moreover, we briefly discuss the potential and the limits of BEFS-based techniques with respect to the classical XAFS.

  15. Structural Insights into 5-HT1A/D4 Selectivity of WAY-100635 Analogues: Molecular Modeling, Synthesis, and in Vitro Binding.

    PubMed

    Dilly, Sébastien; Liégeois, Jean-François

    2016-07-25

    The resurgence of interest in 5-HT1A receptors as a therapeutic target requires the existence of highly selective 5-HT1A ligands. To date, WAY-100635 has been the prototypical antagonist of these receptors. However, this compound also has significant affinity for and activity at D4 dopamine receptors. In this context, this work was aimed at better understanding the 5-HT1A/D4 selectivity of WAY-100635 and analogues from a structural point of view. In silico investigations revealed two key interactions for the 5-HT1A/D4 selectivity of WAY-100635 and analogues. First, a hydrogen bond only found with the Ser 7.36 of D4 receptor appeared to be the key for a higher D4 affinity for newly synthesized aza analogues. The role of Ser 7.36 was confirmed as the affinity of aza analogues for the mutant D4 receptor S7.36A was reduced. Then, the formation of another hydrogen bond with the conserved Ser 5.42 residue appeared to be also critical for D4 binding. PMID:27331407

  16. Structure of Mandelate Racemase with Bound Intermediate Analogues Benzohydroxamate and Cupferron

    SciTech Connect

    Lietzan, Adam D.; Nagar, Mitesh; Pellmann, Elise A.; Bourque, Jennifer R.; Bearne, Stephen L.; Maurice, Martin St.

    2012-05-09

    Mandelate racemase (MR, EC 5.1.2.2) from Pseudomonas putida catalyzes the Mg{sup 2+}-dependent interconversion of the enantiomers of mandelate, stabilizing the altered substrate in the transition state by 26 kcal/mol relative to the substrate in the ground state. To understand the origins of this binding discrimination, we determined the X-ray crystal structures of wild-type MR complexed with two analogues of the putative aci-carboxylate intermediate, benzohydroxamate and Cupferron, to 2.2-{angstrom} resolution. Benzohydroxamate is shown to be a reasonable mimic of the transition state and/or intermediate because its binding affinity for 21 MR variants correlates well with changes in the free energy of transition state stabilization afforded by these variants. Both benzohydroxamate and Cupferron chelate the active site divalent metal ion and are bound in a conformation with the phenyl ring coplanar with the hydroxamate and diazeniumdiolate moieties, respectively. Structural overlays of MR complexed with benzohydroxamate, Cupferron, and the ground state analogue (S)-atrolactate reveal that the para carbon of the substrate phenyl ring moves by 0.8-1.2 {angstrom} between the ground state and intermediate state, consistent with the proposal that the phenyl ring moves during MR catalysis while the polar groups remain relatively fixed. Although the overall protein structure of MR with bound intermediate analogues is very similar to that of MR with bound (S)-atrolactate, the intermediate-Mg{sup 2+} distance becomes shorter, suggesting a tighter complex with the catalytic Mg{sup 2+}. In addition, Tyr 54 moves closer to the phenyl ring of the bound intermediate analogues, contributing to an overall constriction of the active site cavity. However, site-directed mutagenesis experiments revealed that the role of Tyr 54 in MR catalysis is relatively minor, suggesting that alterations in enzyme structure that contribute to discrimination between the altered substrate in the

  17. The solution structure of a superpotent B-chain-shortened single-replacement insulin analogue.

    PubMed Central

    Kurapkat, G.; Siedentop, M.; Gattner, H. G.; Hagelstein, M.; Brandenburg, D.; Grötzinger, J.; Wollmer, A.

    1999-01-01

    This paper reports on an insulin analogue with 12.5-fold receptor affinity, the highest increase observed for a single replacement, and on its solution structure, determined by NMR spectroscopy. The analogue is [D-AlaB26]des-(B27-B30)-tetrapeptide-insulin-B26-amide. C-terminal truncation of the B-chain by four (or five) residues is known not to affect the functional properties of insulin, provided the new carboxylate charge is neutralized. As opposed to the dramatic increase in receptor affinity caused by the substitution of D-Ala for the wild-type residue TyrB26 in the truncated molecule, this very substitution reduces it to only 18% of that of the wild-type hormone when the B-chain is present in full length. The insulin molecule in solution is visualized as an ensemble of conformers interrelated by a dynamic equilibrium. The question is whether the "active" conformation of the hormone, sought after in innumerable structure/function studies, is or is not included in the accessible conformational space, so that it could be adopted also in the absence of the receptor. If there were any chance for the active conformation, or at least a predisposed state to be populated to a detectable extent, this chance should be best in the case of a superpotent analogue. This was the motivation for the determination of the three-dimensional structure of [D-AlaB26]des-(B27-B30)-tetrapeptide-insulin-B26-amide. However, neither the NMR data nor CD spectroscopic comparison of a number of related analogues provided a clue concerning structural features predisposing insulin to high receptor affinity. After the present study it seems more likely than before that insulin will adopt its active conformation only when exposed to the force field of the receptor surface. PMID:10091652

  18. Structural and Biochemical Studies of Actin in Complex with Synthetic Macrolide Tail Analogues

    SciTech Connect

    Pereira, Jose H.; Petchprayoon, Chutima; Hoepker, Alexander C.; Moriarty, Nigel W.; Fink, Sarah J.; Cecere, Giuseppe; Paterson, Ian; Adams, Paul D.; Marriott, Gerard

    2014-07-22

    The actin filament-binding and filament-severing activities of the aplyronine, kabiramide, and reidispongiolide families of marine macrolides are located within the hydrophobic tail region of the molecule. Two synthetic tail analogues of aplyronine C (SF-01 and GC-04) are shown to bind to G-actin with dissociation constants of (285±33) and (132±13) nM, respectively. The crystal structures of actin complexes with GC-04, SF-01, and kabiramide C reveal a conserved mode of tail binding within the cleft that forms between subdomains (SD) 1 and 3. Our studies support the view that filament severing is brought about by specific binding of the tail region to the SD1/SD3 cleft on the upper protomer, which displaces loop-D from the lower protomer on the same half-filament. With previous studies showing that the GC-04 analogue can sever actin filaments, it is argued that the shorter complex lifetime of tail analogues with F-actin would make them more effective at severing filaments compared with plasma gelsolin. In conclusion, structure-based analyses are used to suggest more reactive or targetable forms of GC-04 and SF-01, which may serve to boost the capacity of the serum actin scavenging system, to generate antibody conjugates against tumor cell antigens, and to decrease sputum viscosity in children with cystic fibrosis.

  19. Structural and Biochemical Studies of Actin in Complex with Synthetic Macrolide Tail Analogues

    DOE PAGESBeta

    Pereira, Jose H.; Petchprayoon, Chutima; Hoepker, Alexander C.; Moriarty, Nigel W.; Fink, Sarah J.; Cecere, Giuseppe; Paterson, Ian; Adams, Paul D.; Marriott, Gerard

    2014-07-22

    The actin filament-binding and filament-severing activities of the aplyronine, kabiramide, and reidispongiolide families of marine macrolides are located within the hydrophobic tail region of the molecule. Two synthetic tail analogues of aplyronine C (SF-01 and GC-04) are shown to bind to G-actin with dissociation constants of (285±33) and (132±13) nM, respectively. The crystal structures of actin complexes with GC-04, SF-01, and kabiramide C reveal a conserved mode of tail binding within the cleft that forms between subdomains (SD) 1 and 3. Our studies support the view that filament severing is brought about by specific binding of the tail region tomore » the SD1/SD3 cleft on the upper protomer, which displaces loop-D from the lower protomer on the same half-filament. With previous studies showing that the GC-04 analogue can sever actin filaments, it is argued that the shorter complex lifetime of tail analogues with F-actin would make them more effective at severing filaments compared with plasma gelsolin. In conclusion, structure-based analyses are used to suggest more reactive or targetable forms of GC-04 and SF-01, which may serve to boost the capacity of the serum actin scavenging system, to generate antibody conjugates against tumor cell antigens, and to decrease sputum viscosity in children with cystic fibrosis.« less

  20. Characterization of electronic structure and physicochemical properties of antiparasitic nifurtimox analogues: A theoretical study

    NASA Astrophysics Data System (ADS)

    Soriano-Correa, Catalina; Raya, A.; Esquivel, Rodolfo O.

    American trypanosomiasis, also known as Chagas' disease, is caused by Trypanosoma cruzi (T. cruzi). It is well known that trypanosomes, and particularly T. cruzi, are highly sensitive towards oxidative stress, i.e., to compounds than are able to produce free radicals. Generally, nifurtimox (NFX) and benznidazol are most effective in the acute phase of the disease; therefore, nitroheterocycles constitute good models to design other nitrocompounds with specific biological characteristics. Thus, we have performed an ab initio study at the Hartree-Fock and Density Functional Theory levels of theory of several NFX analogues recently synthesized, to characterize them by obtaining their electronic, structural, and physicochemical properties, which might be linked to the observed antichagasic activity. The antitrypanosomal activity scale previously reported for the NFX analogues studied in this work is in good agreement with our theoretical results, from which we can conclude that the activity seems to be related to the reactivity along with the acidity observed for the most active molecules.

  1. Antihyperglycemic activities of cryptolepine analogues: an ethnobotanical lead structure isolated from Cryptolepis sanguinolenta.

    PubMed

    Bierer, D E; Dubenko, L G; Zhang, P; Lu, Q; Imbach, P A; Garofalo, A W; Phuan, P W; Fort, D M; Litvak, J; Gerber, R E; Sloan, B; Luo, J; Cooper, R; Reaven, G M

    1998-07-16

    Cryptolepine (1) is a rare example of a natural product whose synthesis was reported prior to its isolation from nature. In the previous paper we reported the discovery of cryptolepine's antihyperglycemic properties. As part of a medicinal chemistry program designed to optimize natural product lead structures originating from our ethnobotanical and ethnomedical field research, a series of substituted and heterosubstituted cryptolepine analogues was synthesized. Antihyperglycemic activity was measured in vitro and in an NIDDM mouse model to generate the first structure-bioactivity study about the cryptolepine nucleus. PMID:9667966

  2. Topographic modelling of caldera analogues using Structure from Motion - Multiview stereo-photogrammetry

    NASA Astrophysics Data System (ADS)

    Ulusoy, İnan; Aydın, Eda; Evren Çubukçu, H.

    2016-04-01

    Analogue caldera models have long been used in volcanology to investigate structural evolution of volcanoes during tumescence and collapse periods. Influence of tectonic forces on volcanic features are also in the scope of those experiments. As well as interior modelling of the caldera experiments, topographic modelling is essential for digital monitoring and quantification purposes. Topographic modelling of those sandbox models is possible using laser scanning techniques. Particle tracking using still images is another way to demonstrate and quantify the structure and movement during the experiment. The quantum leap in the digital photography and computation tools and ease of access to both, provides the use of a new modelling technique in various scales and applications in Geology. Although the roots are older, Structure from Motion - Multiview stereo-photogrammetry (SfM-MVS) is a relatively new technique for surface modelling via several high resolution photographs. We have used SfM-MVS to digitally model the elevation of the tumescence and collapse cycles in analogue caldera experiments. Several sandbox experiments have been modelled using SfM-MVS technique stage by stage during tumescence and collapse periods. It has been possible to evaluate the structural evolution of the collapse models. Additionally, using particle tracking via still images acquired during the experiments, we have modelled the superficial evolution of the caldera structure. SfM-MVS is an effective low budget method for modelling in decimetric scale down to millimetre/micrometre precision.

  3. Geometry, Electronic Structure, and Pseudo Jahn-Teller Effect in Tetrasilacyclobutadiene Analogues.

    PubMed

    Liu, Yang; Wang, Ya; Bersuker, Isaac B

    2016-01-01

    We revealed the origin of the structural features of a series of tetrasilacyclobutadiene analogues based on a detailed study of their electronic structure and the pseudo Jahn-Teller effect (PJTE). Starting with the D4h symmetry of the Si4R4 system with a square four-membered silicon ring as a reference geometry, and employing ab initio calculations of energy profiles along lower-symmetry nuclear displacements in the ground and several excited states, we show that the ground-state boat-like and chair-like equilibrium configurations are produced by the PJT interaction with appropriate excited sates. For Si4F4 a full two-mode b1g-b2g adiabatic potential energy surface is calculated showing explicitly the way of transformation from the unstable D4h geometry to the two equilibrium C2h configurations via the D2h saddle point. The PJTE origin of these structural features is confirmed also by estimates of the vibronic coupling parameters. For Si4R4 with large substituents the origin of their structure is revealed by analyzing the PJT interaction between the frontier molecular orbitals. The preferred chair-like structures of Si4R4 analogues with amido substituents, and heavier germanium-containing systems Ge4R4 (potential precursors for semiconducting materials) are predicted. PMID:26996445

  4. Geometry, Electronic Structure, and Pseudo Jahn-Teller Effect in Tetrasilacyclobutadiene Analogues

    NASA Astrophysics Data System (ADS)

    Liu, Yang; Wang, Ya; Bersuker, Isaac B.

    2016-03-01

    We revealed the origin of the structural features of a series of tetrasilacyclobutadiene analogues based on a detailed study of their electronic structure and the pseudo Jahn-Teller effect (PJTE). Starting with the D4h symmetry of the Si4R4 system with a square four-membered silicon ring as a reference geometry, and employing ab initio calculations of energy profiles along lower-symmetry nuclear displacements in the ground and several excited states, we show that the ground-state boat-like and chair-like equilibrium configurations are produced by the PJT interaction with appropriate excited sates. For Si4F4 a full two-mode b1g‑b2g adiabatic potential energy surface is calculated showing explicitly the way of transformation from the unstable D4h geometry to the two equilibrium C2h configurations via the D2h saddle point. The PJTE origin of these structural features is confirmed also by estimates of the vibronic coupling parameters. For Si4R4 with large substituents the origin of their structure is revealed by analyzing the PJT interaction between the frontier molecular orbitals. The preferred chair-like structures of Si4R4 analogues with amido substituents, and heavier germanium-containing systems Ge4R4 (potential precursors for semiconducting materials) are predicted.

  5. Geometry, Electronic Structure, and Pseudo Jahn-Teller Effect in Tetrasilacyclobutadiene Analogues

    PubMed Central

    Liu, Yang; Wang, Ya; Bersuker, Isaac B.

    2016-01-01

    We revealed the origin of the structural features of a series of tetrasilacyclobutadiene analogues based on a detailed study of their electronic structure and the pseudo Jahn-Teller effect (PJTE). Starting with the D4h symmetry of the Si4R4 system with a square four-membered silicon ring as a reference geometry, and employing ab initio calculations of energy profiles along lower-symmetry nuclear displacements in the ground and several excited states, we show that the ground-state boat-like and chair-like equilibrium configurations are produced by the PJT interaction with appropriate excited sates. For Si4F4 a full two-mode b1g−b2g adiabatic potential energy surface is calculated showing explicitly the way of transformation from the unstable D4h geometry to the two equilibrium C2h configurations via the D2h saddle point. The PJTE origin of these structural features is confirmed also by estimates of the vibronic coupling parameters. For Si4R4 with large substituents the origin of their structure is revealed by analyzing the PJT interaction between the frontier molecular orbitals. The preferred chair-like structures of Si4R4 analogues with amido substituents, and heavier germanium-containing systems Ge4R4 (potential precursors for semiconducting materials) are predicted. PMID:26996445

  6. Photoelectron spectra and electronic structure of nitrogen analogues of boron β-diketonates

    NASA Astrophysics Data System (ADS)

    Tikhonov, Sergey A.; Vovna, Vitaliy I.; Borisenko, Aleksandr V.

    2016-07-01

    The electronic structure of the valence levels of seven nitrogen-containing boron complexes was investigated using methods of ultraviolet photoelectron spectroscopy and density functional theory. The ionization energies of π- and σ-levels were obtained from photoelectron spectra. The electronic structure of nitrogen-containing compounds was compared with the electronic structure of β-diketonates. It was shown the influence of various substituents on carbon and nitrogen atoms of six-membered ring on the electronic structure of complexes. The changes in the electronic structure after the substitution of atoms in condensed cycles have been identified. In order to compare the experimental vertical ionization energies IEi with Kohn-Sham orbital energies εi we used the analogue of Koopmans theorem and average amendment to the orbital energy of the electrons (δbari). For 26 electronic levels of seven studied complexes, the calculated values are in good accordance with experimental energy intervals between electron levels.

  7. Synthesis of Silicate Zeolite Analogues Using Organic Sulfonium Compounds as Structure-Directing Agents.

    PubMed

    Jo, Changbum; Lee, Sungjune; Cho, Sung June; Ryoo, Ryong

    2015-10-19

    A microporous crystalline silica zeolite of the MEL structure type and three other zeolite analogues composed of germanosilicate frameworks were synthesized using tributylsulfonium, triphenylsulfonium, or tri(para-tolyl)sulfonium as the structure-directing agent. The germanosilicates thus obtained had ISV, ITT, or a new zeolite structure depending on the synthesis conditions. The structure of the new germanosilicate was solved using X-ray powder diffraction data with the aid of a charge-flipping method. The solution indicated a crystal structure belonging to the P63/mmc space group with cell parameters of a=16.2003 Å and c=21.8579 Å. After calcination, the new germanosilicate material exhibited two types of accessible micropores with diameters of 0.61 and 0.78 nm. PMID:26302889

  8. Synthesis and glutathione S-transferase structure-affinity relationships of nonpeptide and peptidase-stable glutathione analogues.

    PubMed

    Klotz, P; Slaoui-Hasnaoui, A; Banères, J L; Duckert, J F; Rossi, J C; Kerbal, A

    1998-06-18

    A series of nonpeptidic glutathione analogues where the peptide bonds were replaced by simple carbon-carbon bonds or isosteric E double bonds were prepared. The optimal length for the two alkyl chains on either side of the mercaptomethyl group was evaluated using structure-affinity relationships. Affinities of the analogues 14a-f, 23, and 25 were evaluated for a recombinant GST enzyme using a new affinity chromatography method previously developed in our laboratory. Analysis of these analogues gives an additional understanding for GST affinity requirements: (a) the carbon skeleton must conserve that of glutathione since analogue 14a showed the best affinity (IC50 = 5.2 microM); (b) the GST G site is not able to accommodate a chain length elongation of one methylene group (no affinity for analogues 14c,f); (c) a one-methylene group chain length reduction is tolerated, much more for the "Glu side" (14d, IC50 = 10.1 microM) than for the "Gly side" (14b, IC50 = 1800 microM); (d) the mercaptomethyl group must remain at position 5 as shown from the null affinity of the 6-mercaptomethyl analogue 14e; (e) the additional peptide isosteric E double bond (25) or hydroxyl derivative (23) in 14e did not help to retrieve affinity. This work reveals useful information for the design of new selective nonpeptidic and peptidase-stable glutathione analogues. PMID:9632361

  9. Relationship between structure of phenothiazine analogues and their activity on platelet calcium fluxes.

    PubMed Central

    Enouf, J.; Lévy-Toledano, S.

    1984-01-01

    Phenothiazine analogues have been tested for their effect on calcium uptake into platelet membrane vesicles and on ionophore-induced platelet activation, both phenomena being Ca2+-dependent. Both calcium uptake into membrane vesicles and ionophore-induced platelet activation were inhibited by the drugs. Evidence for two inhibitors as potent as chlorpromazine and trifluoperazine was found. These drugs are apparently competitive inhibitors of calcium uptake. A structure-activity relationship has been established. The data suggest that the phenothiazines are able to inhibit calmodulin-insensitive calcium uptake of platelet membrane vesicles and that therefore they cannot be assumed to be selective inhibitors of calmodulin interactions under all circumstances. PMID:6697061

  10. Analogue and numerical models coupled with structural analysis to investigate the runout of dry granular flows.

    NASA Astrophysics Data System (ADS)

    Céline, Longchamp; Irène, Manzella; Abellan, Antonio; Caspar, Olivier; Podladchikov, Yury; Jaboyedoff, Michel

    2016-04-01

    The objective of this research is to better understand the propagation of dry granular flows by coupling analogue modelling, structural analysis of deposit and numerical modelling, as follows: (a) The analogue modelling use laboratory experiments to investigate both the fluid-like flow of a granular mass falling down a slope and the influence of certain parameters such as the basal roughness, mobilized volume and slope angle. The experimental setup allows unconfined flow which spreads freely on a horizontal surface. Different grainsizes (115, 545 and 2605 μm) and substratum roughness (simulates by aluminium and sandpapers with grainsize from 16 to 425 μm) were used in order to understand their influence on the motion of a granular mass. During our experiments, the runout varied between 4.5cm and 11cm, with an increase of the basal roughness. When the volume varied between 300 and 600cm3 the runout was comprised between 9.2cm and 11.7cm. Finally when the slope angle was increased from 35° to 60°, the observed runout was between 5.3cm and 20cm. (b) Rock avalanche dynamic is analysed by means of a detailed structural analysis of the analogue modelling deposits. A series of 3D measurements were carried out on the deposit and a median filter and a gradient operator along the direction of propagation were applied to the 3D datasets. Treatment yield a more precise mapping of the longitudinal and transversal displacement features observed at the surface of the deposits. (c) The numerical modelling performed during this research is based both on continuum mechanics approach and on solving the shallow water equations. The avalanche was described from an Eulerian point of view within a continuum framework as single phase of incompressible granular material following Mohr-Coulomb friction law. The results obtained with the numerical model resemble those observed with the analogue modelling mentioned above. By coupling these three approaches, we obtained a complete scheme

  11. Design, structure activity relationship, cytotoxicity and evaluation of antioxidant activity of curcumin derivatives/analogues.

    PubMed

    Sahu, Pramod K

    2016-10-01

    New fourteen 3,4-dihydropyrimidine derivatives/analogues of curcumin (2a-2n) were designed, synthesized and biologically evaluated for their cytotoxicity and antioxidant activity. Cytotoxicity effect has been evaluated against three cell lines HeLa, HCT-116 and QG-56 by MTT assay method. From SAR study, it has been revealed that particularly, compound 2e and 2j (IC50 value 12.5 μM) have shown better cytotoxicity effect against three cell lines. According to results of SAR study, it was found that 3,4-dihydropyrimidines of curcumin, 2c, 2d, 2j and 2n exhibited better antioxidant activity than curcumin. A correlation of structure and activities relationship of these compounds with respect to drug score profiles and other physico-chemical properties of drugs are described and verified experimentally. Therefore, we conclude that physico-chemical analyses may prove structural features of curcumin analogues with their promising combined cytotoxicity/antioxidant activity and it is also concluded from virtual and practical screening that the compounds were varied to possess a broad range of lipophilic character, revealed by Log P values. PMID:27318975

  12. Implications for the active form of human insulin based on the structural convergence of highly active hormone analogues

    PubMed Central

    Jiráček, Jiří; Žáková, Lenka; Antolíková, Emília; Watson, Christopher J.; Turkenburg, Johan P.; Dodson, Guy G.; Brzozowski, Andrzej M.

    2010-01-01

    Insulin is a key protein hormone that regulates blood glucose levels and, thus, has widespread impact on lipid and protein metabolism. Insulin action is manifested through binding of its monomeric form to the Insulin Receptor (IR). At present, however, our knowledge about the structural behavior of insulin is based upon inactive, multimeric, and storage-like states. The active monomeric structure, when in complex with the receptor, must be different as the residues crucial for the interactions are buried within the multimeric forms. Although the exact nature of the insulin’s induced-fit is unknown, there is strong evidence that the C-terminal part of the B-chain is a dynamic element in insulin activation and receptor binding. Here, we present the design and analysis of highly active (200–500%) insulin analogues that are truncated at residue 26 of the B-chain (B26). They show a structural convergence in the form of a new β-turn at B24-B26. We propose that the key element in insulin’s transition, from an inactive to an active state, may be the formation of the β-turn at B24-B26 associated with a trans to cis isomerisation at the B25-B26 peptide bond. Here, this turn is achieved with N-methylated L-amino acids adjacent to the trans to cis switch at the B25-B26 peptide bond or by the insertion of certain D-amino acids at B26. The resultant conformational changes unmask previously buried amino acids that are implicated in IR binding and provide structural details for new approaches in rational design of ligands effective in combating diabetes. PMID:20133841

  13. Structural correlation of some heterocyclic chalcone analogues and evaluation of their antioxidant potential.

    PubMed

    Kumar, C S Chidan; Loh, Wan-Sin; Ooi, Chin Wei; Quah, Ching Kheng; Fun, Hoong-Kun

    2013-01-01

    A series of six novel heterocyclic chalcone analogues 4(a-f) has been synthesized by condensing 2-acetyl-5-chlorothiophene with benzaldehyde derivatives in methanol at room temperature using a catalytic amount of sodium hydroxide. The newly synthesized compounds are characterized by IR, mass spectra, elemental analysis and melting point. Subsequently; the structures of these compounds were determined using single crystal X-ray diffraction. All the synthesized compounds were screened for their antioxidant potential by employing various in vitro models such as DPPH free radical scavenging assay, ABTS radical scavenging assay, ferric reducing antioxidant power and cupric ion reducing antioxidant capacity. Results reflect the structural impact on the antioxidant ability of the compounds. The IC₀ values illustrate the mild to good antioxidant activities of the reported compounds. Among them, 4f with a p-methoxy substituent was found to be more potent as antioxidant agent. PMID:24077177

  14. Band gap and chemically ordered domain structure of a graphene analogue BCN

    NASA Astrophysics Data System (ADS)

    Venu, K.; Kanuri, S.; Raidongia, K.; Hembram, K. P. S. S.; Waghmare, U. V.; Datta, R.

    2010-12-01

    Chemically synthesized few layer graphene analogues of B xC yN z are characterized by aberration corrected transmission electron microscopy and high resolution electron energy loss spectroscopy (HREELS) to determine the local phase, electronic structure and band gap. HREELS band gap studies of a B xC yN z composition reveal absorption edges at 2.08, 3.43 and 6.01 eV, indicating that the B xC yN z structure may consist of domains of different compositions. The K-absorption edge energy position of the individual elements in B xC yN z is determined and compared with h-BN and graphite. An understanding of these experimental findings is developed with complementary first-principles based calculations of the various ordered configurations of B xC yN z.

  15. Isolated magnetic field structures in Mercury's magnetosheath as possible analogues for terrestrial magnetosheath plasmoids and jets

    NASA Astrophysics Data System (ADS)

    Karlsson, Tomas; Liljeblad, Elisabet; Kullen, Anita; Raines, Jim M.; Slavin, James A.; Sundberg, Torbjörn

    2016-09-01

    We have investigated MESSENGER magnetic field data from the Mercury magnetosheath and near solar wind, to identify isolated magnetic field structures (defined as clear, isolated changes in the field magnitude). Their properties are studied in order to determine if they may be considered as analogues to plasmoids and jets known to exist in Earth's magnetosheath. Both isolated decreases of the magnetic field absolute value ('negative magnetic field structures') and increases ('positive structures') are found in the magnetosheath, whereas only negative structures are found in the solar wind. The similar properties of the solar wind and magnetosheath negative magnetic field structures suggests that they are analogous to diamagnetic plasmoids found in Earth's magnetosheath and near solar wind. The latter have earlier been identified with solar wind magnetic holes. Positive magnetic field structures are only found in the magnetosheath, concentrated to a region relatively close to the magnetopause. Their proximity to the magnetopause, their scale sizes, and the association of a majority of the structures with bipolar magnetic field signatures identify them as flux transfer events (which generally are associated with a decrease of plasma density in the magnetosheath). The positive magnetic field structures are therefore not likely to be analogous to terrestrial paramagnetic plasmoids but possibly to a sub-population of magnetosheath jets. At Earth, a majority of magnetosheath jets are associated with the quasi-parallel bow shock. We discuss some consequences of the findings of the present investigation pertaining to the different nature of the quasi-parallel bow shock at Mercury and Earth.

  16. Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins

    SciTech Connect

    Ho, Meng-Chiao; Sturm, Matthew B.; Almo, Steven C.; Schramm, Vern L.

    2010-01-12

    Ricin A-chain (RTA) and saporin-L1 (SAP) catalyze adenosine depurination of 28S rRNA to inhibit protein synthesis and cause cell death. We present the crystal structures of RTA and SAP in complex with transition state analogue inhibitors. These tight-binding inhibitors mimic the sarcin-ricin recognition loop of 28S rRNA and the dissociative ribocation transition state established for RTA catalysis. RTA and SAP share unique purine-binding geometry with quadruple {pi}-stacking interactions between adjacent adenine and guanine bases and 2 conserved tyrosines. An arginine at one end of the {pi}-stack provides cationic polarization and enhanced leaving group ability to the susceptible adenine. Common features of these ribosome-inactivating proteins include adenine leaving group activation, a remarkable lack of ribocation stabilization, and conserved glutamates as general bases for activation of the H{sub 2}O nucleophile. Catalytic forces originate primarily from leaving group activation evident in both RTA and SAP in complex with transition state analogues.

  17. Structural Basis for Recognition of Guanosine by a Synthetic Tricyclic Cytosine Analogue: Guanidinium G-Clamp

    SciTech Connect

    Wilds, C.J.; Maier, M.A.; Manoharan, M.; Egli, M.

    2010-03-08

    An oligonucleotide analogue containing a novel heterocyclic analogue, the guanidinium G-clamp, was designed to allow formation of five H-bonds to guanosine. The guanidinium group was introduced postsynthetically by treatment of the deprotected oligonucleotide containing a free amino group with a solution of 1H-pyrazole-1-carboxamidine and purified by a combination of size-exclusion chromatography and reversed-phase HPLC. A single incorporation of this modification into an oligodeoxynucleotide sequence was found to increase duplex stability by 13{sup o} and 16{sup o} per modification to RNA and DNA, respectively. Crystals of a self-complementary decamer sequence containing this modification were grown and diffracted to 1-{angstrom} resolution. The structure was solved by molecular replacement and revealed that the modification forms additional H-bonds to O(6) and N(7) of guanosine through the amino and imino N-atoms, respectively. The origins of enhanced duplex stability are also attributed to increased stacking interactions mediated by the phenoxazine moiety of the G-clamp and formation of H-bond networks between the positively charged guanidinium group, H{sub 2}O molecules, and negatively charged O-atoms from phosphates on the adjacent strand.

  18. Electronic structure and vibrational spectra of cis-diammine(orotato)platinum(II), a potential cisplatin analogue: DFT and experimental study

    NASA Astrophysics Data System (ADS)

    Wysokiński, Rafał; Hernik, Katarzyna; Szostak, Roman; Michalska, Danuta

    2007-03-01

    Orotic acid (vitamin B 13) is a key intermediate in biosynthesis of the pyrimidine nucleotides in living organisms, moreover, it may serve as the biological carrier for some metal ions. cis-Diammine(orotato)platinum(II), cis-[Pt(C 5H 2N 2O 4)(NH 3) 2] can be considered as a new potential cisplatin analogue. The FT-Raman and FT-IR spectra of the title complex are reported, for the first time. The molecular structure, vibrational frequencies, and the theoretical infrared and Raman intensities have been calculated by the density functional mPW1PW91 method. The detailed vibrational assignment has been made on the basis of the calculated potential energy distribution. The theoretically predicted IR and Raman spectra show very good agreement with experiment. Natural bond orbital (NBO) analyses were performed for cisplatin, carboplatin and the title complex. The results provided new data on the nature of platinum-ligand bonding in these compounds. Strong intramolecular hydrogen bond between the orotate ligand and the coordinated ammonia group stabilizes the structure of the platinum(II) complex. Thus, it is suggested that the orotate ligand in the title complex is more inert to the substitution reactions than the chloride ligands in cisplatin.

  19. Inhibition of Mycobacterium tuberculosis dihydrodipicolinate synthase by alpha-ketopimelic acid and its other structural analogues

    PubMed Central

    Shrivastava, Priyanka; Navratna, Vikas; Silla, Yumnam; Dewangan, Rikeshwer P.; Pramanik, Atreyi; Chaudhary, Sarika; Rayasam, GeethaVani; Kumar, Anuradha; Gopal, Balasubramanian; Ramachandran, Srinivasan

    2016-01-01

    The Mycobacterium tuberculosis dihydrodipicolinate synthase (Mtb-dapA) is an essential gene. Mtb-DapA catalyzes the aldol condensation between pyruvate and L-aspartate-beta-semialdehyde (ASA) to yield dihydrodipicolinate. In this work we tested the inhibitory effects of structural analogues of pyruvate on recombinant Mtb-DapA (Mtb-rDapA) using a coupled assay with recombinant dihydrodipicolinate reductase (Mtb-rDapB). Alpha-ketopimelic acid (α-KPA) showed maximum inhibition of 88% and IC50 of 21 μM in the presence of pyruvate (500 μM) and ASA (400 μM). Competition experiments with pyruvate and ASA revealed competition of α-KPA with pyruvate. Liquid chromatography-mass spectrometry (LC-MS) data with multiple reaction monitoring (MRM) showed that the relative abundance peak of final product, 2,3,4,5-tetrahydrodipicolinate, was decreased by 50%. Thermal shift assays showed 1 °C Tm shift of Mtb-rDapA upon binding α-KPA. The 2.4 Å crystal structure of Mtb-rDapA-α-KPA complex showed the interaction of critical residues at the active site with α-KPA. Molecular dynamics simulations over 500 ns of pyruvate docked to Mtb-DapA and of α-KPA-bound Mtb-rDapA revealed formation of hydrogen bonds with pyruvate throughout in contrast to α-KPA. Molecular descriptors analysis showed that ligands with polar surface area of 91.7 Å2 are likely inhibitors. In summary, α-hydroxypimelic acid and other analogues could be explored further as inhibitors of Mtb-DapA. PMID:27501775

  20. Inhibition of Mycobacterium tuberculosis dihydrodipicolinate synthase by alpha-ketopimelic acid and its other structural analogues.

    PubMed

    Shrivastava, Priyanka; Navratna, Vikas; Silla, Yumnam; Dewangan, Rikeshwer P; Pramanik, Atreyi; Chaudhary, Sarika; Rayasam, GeethaVani; Kumar, Anuradha; Gopal, Balasubramanian; Ramachandran, Srinivasan

    2016-01-01

    The Mycobacterium tuberculosis dihydrodipicolinate synthase (Mtb-dapA) is an essential gene. Mtb-DapA catalyzes the aldol condensation between pyruvate and L-aspartate-beta-semialdehyde (ASA) to yield dihydrodipicolinate. In this work we tested the inhibitory effects of structural analogues of pyruvate on recombinant Mtb-DapA (Mtb-rDapA) using a coupled assay with recombinant dihydrodipicolinate reductase (Mtb-rDapB). Alpha-ketopimelic acid (α-KPA) showed maximum inhibition of 88% and IC50 of 21 μM in the presence of pyruvate (500 μM) and ASA (400 μM). Competition experiments with pyruvate and ASA revealed competition of α-KPA with pyruvate. Liquid chromatography-mass spectrometry (LC-MS) data with multiple reaction monitoring (MRM) showed that the relative abundance peak of final product, 2,3,4,5-tetrahydrodipicolinate, was decreased by 50%. Thermal shift assays showed 1 °C Tm shift of Mtb-rDapA upon binding α-KPA. The 2.4 Å crystal structure of Mtb-rDapA-α-KPA complex showed the interaction of critical residues at the active site with α-KPA. Molecular dynamics simulations over 500 ns of pyruvate docked to Mtb-DapA and of α-KPA-bound Mtb-rDapA revealed formation of hydrogen bonds with pyruvate throughout in contrast to α-KPA. Molecular descriptors analysis showed that ligands with polar surface area of 91.7 Å(2) are likely inhibitors. In summary, α-hydroxypimelic acid and other analogues could be explored further as inhibitors of Mtb-DapA. PMID:27501775

  1. Extrapolating surface structures to depth in transpressional systems: the role of rheology and convergence angle deduced from analogue experiments

    NASA Astrophysics Data System (ADS)

    Hsieh, Shang Yu; Neubauer, Franz; Cloetingh, Sierd; Willingshofer, Ernst; Sokoutis, Dimitrios

    2014-05-01

    The internal structure of major strike-slip faults is still poorly understood, particularly how the deep structure could be inferred from its surface expression (Molnar and Dayem, 2011 and references therein). Previous analogue experiments suggest that the convergence angle is the most influential factor (Leever et al., 2011). Further analogue modeling may allow a better understanding how to extrapolate surface structures to the subsurface geometry of strike-slip faults. Various scenarios of analogue experiments were designed to represent strike-slip faults in nature from different geological settings. As such key parameters, which are investigated in this study include: (a) the angle of convergence, (b) the thickness of brittle layer, (c) the influence of a rheological weak layer within the crust, and (d) influence of a thick and rheologically weak layer at the base of the crust. The latter aimed to simulate the effect of a hot metamorphic core complex or an alignment of uprising plutons bordered by a transtensional/transpressional strike-slip fault. The experiments are aimed to explain first order structures along major transcurrent strike-slip faults such as the Altyn, Kunlun, San Andrea and Greendale (Darfield earthquake 2010) faults. The preliminary results show that convergence angle significantly influences the overall geometry of the transpressive system with greater convergence angles resulting in wider fault zones and higher elevation. Different positions, densities and viscosities of weak rheological layers have not only different surface expressions but also affect the fault geometry in the subsurface. For instance, rheological weak material in the bottom layer results in stretching when experiment reaches a certain displacement and a buildup of a less segmented, wide positive flower structure. At the surface, a wide fault valley in the middle of the fault zone is the reflection of stretching along the velocity discontinuity at depth. In models with a

  2. Structural Insight into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues

    SciTech Connect

    Cedervall, Peder E.; Dey, Mishtu; Pearson, Arwen R.; Ragsdale, Stephen W.; Wilmot, Carrie M.

    2010-09-07

    Methyl-coenzyme M reductase (MCR) catalyzes the final and rate-limiting step in methane biogenesis: the reduction of methyl-coenzyme M (methyl-SCoM) by coenzyme B (CoBSH) to methane and a heterodisulfide (CoBS-SCoM). Crystallographic studies show that the active site is deeply buried within the enzyme and contains a highly reduced nickel-tetrapyrrole, coenzyme F430. Methyl-SCoM must enter the active site prior to CoBSH, as species derived from methyl-SCoM are always observed bound to the F430 nickel in the deepest part of the 30 {angstrom} long substrate channel that leads from the protein surface to the active site. The seven-carbon mercaptoalkanoyl chain of CoBSH binds within a 16 {angstrom} predominantly hydrophobic part of the channel close to F430, with the CoBSH thiolate lying closest to the nickel at a distance of 8.8 {angstrom}. It has previously been suggested that binding of CoBSH initiates catalysis by inducing a conformational change that moves methyl-SCoM closer to the nickel promoting cleavage of the C-S bond of methyl-SCoM. In order to better understand the structural role of CoBSH early in the MCR mechanism, we have determined crystal structures of MCR in complex with four different CoBSH analogues: pentanoyl, hexanoyl, octanoyl, and nonanoyl derivatives of CoBSH (CoB5SH, CoB6SH, CoB8SH, and CoB9SH, respectively). The data presented here reveal that the shorter CoB5SH mercaptoalkanoyl chain overlays with that of CoBSH but terminates two units short of the CoBSH thiolate position. In contrast, the mercaptoalkanoyl chain of CoB6SH adopts a different conformation, such that its thiolate is coincident with the position of the CoBSH thiolate. This is consistent with the observation that CoB6SH is a slow substrate. A labile water in the substrate channel was found to be a sensitive indicator for the presence of CoBSH and HSCoM. The longer CoB8SH and CoB9SH analogues can be accommodated in the active site through exclusion of this water. These analogues

  3. The action of structural analogues of ethidium bromide on the mitochondrial genome of yeast.

    PubMed

    Hall, R M; Mattick, J S; Nagley, P; Cobon, G S; Eastwood, F W; Linnane, A W

    1977-12-01

    We have studied the effects on the yeast mitochondrial genome of four analogues of ethidium bromide, in which the phenyl moieyt has been replaced by linear alkyl chains of lengths varying from seven to fifteen carbon atoms. These analogues are more efficient than ethidium bromide in inducing petite mutants in Saccharomyces cervisiae. The drugs also cause a loss of mtDNA from the cells in vivo; however these analogues are in fact less effective inhibitors of mitochondrial DNA replication per se, as shown by direct in vitro studies. It is concluded that these analogues are more efficient than ethidium bromide in causing the fragmentation of mitochondrial DNA in S. cervisiae. PMID:339057

  4. Adherence to RIASEC Structure as a Key Career Decision Construct

    ERIC Educational Resources Information Center

    Tracey, Terence J. G.

    2008-01-01

    The present study examined the relation between individual cognitive structure and several key career decision variables. Specifically, in a sample of college students enrolled in a career development class, the usage of the RIASEC (Realistic, Investigative, Artistic, Social, Enterprising, and Conventional) circumplex (adherence) was examined as…

  5. Morpho-structural criteria for the identification of volcano deformation processes from analogue modeling

    NASA Astrophysics Data System (ADS)

    Rincon, Marta; Marquez, Alvaro; van Wyk de Vries, Benjamin; Herrera, Raquel; Granja Bruña, Jose Luis; Llanes, Pilar

    2014-05-01

    The morphology of volcanoes provides important information about edifice evolution. Volcanoes can deform by gravitational instability and intrusions. This deformation can compromise volcano structural stability, promoting flank collapse even at dormant edifices. Identification of past/active deformation processes is therefore important not only for the understanding of volcano evolution but also for volcanic hazards. Both deformation due to the flank spreading of a volcano over its weak core and due to the intrusion of a cryptodome in the volcano edifice can produce faulting and changes in the morphology of volcano flanks. These morpho-structural changes in the volcano open the possibility to identify potential deformed and unstable volcanoes using remote sensing techniques and DEMs. We have used analogue models of flank spreading and intrusion processes to make progress in the morpho-structural identification of deformation features which can provide criteria for distinguishing processes. We have geometrically and mechanically scaled two different sets of experiments using a sand-plaster mixture for volcano materials, silicone putty for weak core rocks and Golden Syrup for magma intrusions. For monitoring changes in the volcano morphology we have used a Kinect sensor (Microsoft), which provides us vertical displacements of volcano flanks several times per second with a 1 mm precision. We have synchronized the Kinect sensor with a digital camera for monitoring the spatio-temporal evolution of tectonic structures together with morphology. All experiments produce asymmetrical changes in volcano morphology, developing convex-concave geometries in the deformed flank. However, the spatial relationships of structures with changes in volcano flank curvature are different for the two processes, as noted by previous authors. The morphometric tools developed for analyzing volcano topography allow us to identify intrusion processes due to volcano volume increase. We have

  6. Combretastatin A-4 analogues with benzoxazolone scaffold: Synthesis, structure and biological activity.

    PubMed

    Gerova, Mariana S; Stateva, Silviya R; Radonova, Elena M; Kalenderska, Rositsa B; Rusew, Rusi I; Nikolova, Rositsa P; Chanev, Christo D; Shivachev, Boris L; Apostolova, Margarita D; Petrov, Ognyan I

    2016-09-14

    In order to design and synthesize a new class of heterocyclic analogues of natural combretastatin A-4 and its synthetic derivative AVE8062, the benzoxazolone ring was selected as a scaffold for a bioisosteric replacement of the ring B of both molecules. A library of 28 cis- and trans-styrylbenzoxazolones was obtained by a modified Wittig reaction under Boden's conditions. Structures of the newly synthesized compounds bearing the 3,4,5-trimethoxy-, 3,4-dimethoxy-, 3,5-dimethoxy-, and 4-methoxystyryl fragment at position 4, 5, 6 or 7 of benzoxazolone core were determined on the basis of spectral and X ray data. The in vitro cytotoxicity of styrylbenzoxazolones against different cell lines was examined. Stilbene derivative 16Z, (Z)-3-methyl-6-(3,4,5-trimethoxystyryl)-2(3H)-benzoxazolone, showed highest antiproliferative potential of the series, with IC50 of 0.25 μM against combretastatin resistant cell line HT-29, 0.19 μM against HepG2, 0.28 μM against EA.hy926 and 0.73 μM against K562 cells. Furthermore, the results of flow cytometric analysis confirmed that 16Z induced cell cycle arrest in G2/M phase in the cell lines like combretastatin A-4. This arrest is followed by an abnormal exit of cells from mitosis without cytokinesis into a pseudo G1-like multinucleate state leading to late apoptosis and cell death. Accordingly, synthetic analogue 16Z was identified as the most promising potential anticancer agent in present study, and was selected as lead compound for further detailed investigations. PMID:27187864

  7. An NHC-Stabilized Silicon Analogue of Acylium Ion: Synthesis, Structure, Reactivity, and Theoretical Studies.

    PubMed

    Ahmad, Syed Usman; Szilvási, Tibor; Irran, Elisabeth; Inoue, Shigeyoshi

    2015-05-01

    The silicon analogues of an acylium ion, namely, sila-acylium ions 2a and 2b [RSi(O)(NHC)2]Cl stabilized by two N-heterocyclic carbenes (NHC = 1,3,4,5-tetramethylimidazol-2-ylidene), and having chloride as a countercation were successfully synthesized by the reduction of CO2 using the donor stabilized silyliumylidene cations 1a and 1b [RSi(NHC)2]Cl (1a, 2a; R = m-Ter = 2,6-Mes2C6H3, Mes = 2,4,6-Me3C6H2 and 1b, 2b; R = Tipp = 2,4,6-iPr3C6H2). Structurally, compound 2a features a four coordinate silicon center together with a double bond between silicon and oxygen atoms. The reaction of sila-acylium ions 2a and 2b with water afforded different products which depend on the bulkiness of aryl substituents. Although the exposure of 2a to H2O afforded a stable silicon analogue of carboxylate anion as a dimer form, [m-TerSi(O)O]2(2-)·2[NHC-H](+) (3), the same reaction with the less bulkier triisopropylphenyl substituted sila-acylium ion 2b afforded cyclotetrasiloxanediol dianion [{TippSi(O)}4{(O)OH}2](2-)·2[NHC-H](+) (4). Metric and DFT (Density Functional Theory) evidence support that 2a and 2b possess strong Si═O double bond character, while 3 and 4 contain more ionic terminal Si-O bonds. Mechanistic details of the formation of different (SiO)n (n = 2, 3, 4) core rings were explored using DFT to explain the experimentally characterized products and a proposed stable intermediate was identified with mass spectrometry. PMID:25871835

  8. Nano-Self-Assemblies Based on Synthetic Analogues of Mycobacterial Monomycoloyl Glycerol and DDA: Supramolecular Structure and Adjuvant Efficacy.

    PubMed

    Martin-Bertelsen, Birte; Korsholm, Karen S; Roces, Carla B; Nielsen, Maja H; Christensen, Dennis; Franzyk, Henrik; Yaghmur, Anan; Foged, Camilla

    2016-08-01

    The mycobacterial cell-wall lipid monomycoloyl glycerol (MMG) is a potent immunostimulator, and cationic liposomes composed of a shorter synthetic analogue (MMG-1) and dimethyldioctadecylammonium (DDA) bromide represent a promising adjuvant that induces strong antigen-specific Th1 and Th17 responses. In the present study, we investigated the supramolecular structure and in vivo adjuvant activity of dispersions based on binary mixtures of DDA and an array of synthetic MMG-1 analogues (MMG-2/3/5/6) displaying longer (MMG-2) or shorter (MMG-3) alkyl chain lengths, or variations in stereochemistry of the polar headgroup (MMG-5) or of the hydrophobic moiety (MMG-6). Synchrotron small-angle X-ray scattering experiments and cryo transmission electron microscopy revealed that DDA:MMG-1/2/5/6 dispersions consisted of unilamellar and multilamellar vesicles (ULVs/MLVs), whereas a coexistence of both ULVs and hexosomes was observed for DDA:MMG-3, depending on the DDA:MMG molar ratio. The studies also showed that ULVs were formed, regardless of the structural characteristics of the neat MMG analogues in excess buffer [lamellar (MMG-1/2/5) or inverse hexagonal (MMG-3/6) phases]. Immunization of mice with a chlamydia antigen surface-adsorbed to DDA:MMG-1/3/6 dispersions revealed that all tested adjuvants were immunoactive and induced strong Th1 and Th17 responses with a potential for a central effector memory profile. The MMG-1 and MMG-6 analogues were equally immunoactive in vivo upon incorporation into DDA liposomes, despite the reported highly different immunostimulatory properties of the neat analogues in vitro, which were attributed to the different nanostructural characteristics. This clearly demonstrates that optimal formulation and delivery of MMG analogues to the immune system is of major importance and challenges the use of in vitro screening assays with nondispersed compounds to identify potential new vaccine adjuvants. PMID:27377146

  9. Experimental and Theoretical Studies of the Structures and Interactions of Vancomycin Antibiotics with Cell Wall Analogues

    SciTech Connect

    Yang, Zhibo; Vorpagel, Erich R.; Laskin, Julia

    2008-10-01

    Surface-induced dissociation (SID) of the singly protonated complex of vancomycin antibiotic with cell wall peptide analogue (Nα,Nε-diacetyl-L-Lys-D-Ala-D-Ala) was studied using a 6 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FT-ICR MS) specially configured for SID experiments. The binding energy between the vancomycin and the peptide was obtained from the RRKM modeling of the time- and energy resolved fragmentation efficiency curves (TFECs) of the precursor ion and its fragments. Electronic structure calculations of the geometries, proton affinities and binding energies were performed for several model systems including vancomycin (V), vancomycin aglycon (VA), Nα,Nε-diacetyl-L-Lys-D-Ala-D-Ala, and non-covalent complexes of VA with N-acetyl-D-Ala-D-Ala and Nα,Nε-diacetyl-L-Lys-D-Ala-D-Ala at the B3LYP/6-31G(d) level of theory. Comparison between the experimental and computational results suggests that the most probable structure of the complex observed in our experiments corresponds to the neutral peptide bound to the vancomycin protonated at the secondary amino group of the N-methyl-leucine residue. The experimental binding energy of 30.9 ± 1.8 kcal/mol is in good agreement with the binding energy of 29.3 ± 2.5 kcal/mol calculated for the model system representing the preferred structure of the complex.

  10. Structure and Properties of a Synthetic Analogue of Bacterial Iron-Sulfur Proteins

    PubMed Central

    Herskovitz, T.; Averill, B. A.; Holm, R. H.; Ibers, James A.; Phillips, W. D.; Weiher, J. F.

    1972-01-01

    The compound (Et4N)2[Fe4S4(SCH2Ph)4] has been prepared and its structure determined by x-ray diffraction. The Fe4S4 core of the anion possesses a configuration of D2d symmetry that is closely related to the Fe4S4 active-site structures of the high-potential iron protein from Chromatium and the ferredoxin from Micrococcus aerogenes. Electronic properties of the tetrameric anion have been partially characterized by measurement of proton magnetic resonance, Mössbauer, photoelectron, and electronic spectra, and magnetic susceptibility. Comparison of corresponding properties of [Fe4S4(SCH2Ph)4]2- and the proteins implies that the oxidation levels of the synthetic tetramer, the reduced form of the high-potential protein, and the oxidized form of the 8-Fe ferredoxins are equivalent. The tetramer possesses the one-electron redox capacity associated with the 4-Fe centers of the ferredoxins. The structural and collective electronic features of [Fe4S4(SCH2Ph)4]2- reveal it to be the first well-defined synthetic analogue of the active site of an iron-sulfur protein. PMID:4506765

  11. Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues.

    PubMed

    Toyoshima, Chikashi; Nomura, Hiromi; Tsuda, Takeo

    2004-11-18

    P-type ion transporting ATPases are ATP-powered ion pumps that establish ion concentration gradients across biological membranes. Transfer of bound cations to the lumenal or extracellular side occurs while the ATPase is phosphorylated. Here we report at 2.3 A resolution the structure of the calcium-ATPase of skeletal muscle sarcoplasmic reticulum, a representative P-type ATPase that is crystallized in the absence of Ca2+ but in the presence of magnesium fluoride, a stable phosphate analogue. This and other crystal structures determined previously provide atomic models for all four principal states in the reaction cycle. These structures show that the three cytoplasmic domains rearrange to move six out of ten transmembrane helices, thereby changing the affinity of the Ca2+-binding sites and the gating of the ion pathway. Release of ADP triggers the opening of the lumenal gate and release of phosphate its closure, effected mainly through movement of the A-domain, the actuator of transmembrane gates. PMID:15448704

  12. Structural organisation and phase behaviour of a stratum corneum lipid analogue: ceramide 3A.

    PubMed

    Garidel, Patrick

    2006-05-21

    The thermotropic phase behaviour and structural organisation of ceramide N-linoeoyl-phytosphingosine (ceramide 3A) is investigated by means of differential scanning calorimetry (DSC) and Fourier transform infrared spectroscopy (FTIR). Its polymorphism and structural properties are compared with two ceramides of the type III class with various hydrocarbon chain saturation degrees. After hydration the main phase transition temperature of ceramide 3A is found at 76 degrees C with a phase transition enthalpy of +29 kJ mol(-1). Analysing the frequency of methylene stretching vibrations (by infrared spectroscopy) reveals that the fluidity (amount of trans-gauche isomers) is strongly increased for ceramide 3A compared to its stearoyl ceramide type III analogue. After lipid hydration, the acyl chains of all investigated phytosphingosine ceramides of type III adopt a hexagonal-like chain packing. The amide I and amide II vibrations are quite sensitive to the phase transition of the ceramide. The corresponding band analysis reveals strong inter- and intramolecular hydrogen bonds between the amide and hydroxyl groups in the ceramide head groups. The H-bonding network and conformation of the head group of ceramide 3A is only slightly influenced by hydration. The water penetration capacity of ceramide 3A is, however, considerably larger compared to other phytosphingosine derivatives. The structural and organisational properties of ceramides of type III class are discussed with respect to their physiological relevancies for the stratum corneum lipid barrier property of the skin. PMID:16688309

  13. Conformational studies of synthetic lipid A analogues and partial structures by infrared spectroscopy.

    PubMed

    Brandenburg, K; Kusumoto, S; Seydel, U

    1997-10-01

    Synthetic lipid A analogues and partial structures were analyzed and compared with natural hexaacyl lipid A from E. coli applying Fourier transform infrared spectroscopy. The investigations comprised (i) the measurement of the beta <=> alpha phase transition of the acyl chains via monitoring of the symmetric stretching vibration of the methylene groups, (ii) an estimation of the supramolecular aggregate structures evaluating vibrations from the interface like ester carbonyl and applying theoretical calculations (iii) a determination of the inter- and intramolecular conformations monitoring functional groups from the interface and the diglucosamine backbone (ester carbonyl, phosphate). The phase transition temperature Tc was found to be nearly a linear function of the number of acyl chains for most bisphosphoryl compounds indicating comparable packing density, whereas the deviating behaviour of some samples indicated a higher packing density. From the determination of the supramolecular aggregate structures (cubic, HII) of natural hexaacyl lipid A by X-ray small-angle diffraction, the existence of the same aggregate structures also for the synthetic hexaacyl lipid A was deduced from the nearly identical thermotropism of the ester carbonyl band. From this, a good approximation of the supramolecular structures of all synthetic samples was possible on the basis of the theory of Israelachvili. The analysis of the main phosphate band, together with that of the Tc data and former colorimetric results, allowed the establishment of a model of the intermolecular conformations of neighbouring lipid A/LPS molecules. The biological relevance of the findings is discussed in terms of the strongly varying biological activity (between high and no activity) of the samples. PMID:9370256

  14. Energetics, electronic structures and geometries of naphthalene, quinoline and isoquinoline analogues of 1,2-didehydrobenzene

    NASA Astrophysics Data System (ADS)

    Cioslowski, Jerzy; Szarecka, Agnieszka; Moncrieff, David

    2003-01-01

    B3LYP/cc-pVTZ electronic structure calculations employed in conjunction with additive corrections derived from experimental data for 1,2-didehydrobenzene predict the standard enthalpies of formation of 1,2- and 2,3-didehydronaphthalenes to be equal to 121.0 and 123.7 kcal mol -1 , respectively. The corresponding singlet-triplet splittings amount to 40.1 and 35.4 kcal mol -1 . The positional dependence of both of these quantities is preserved in those didehydroquinolines and didehydroisoquinolines in which the didehydrogenation sites are separated by at least one carbon from the heteroatoms. The effect of the adjacent heteroatoms on the singlet-triplet splittings is significantly more pronounced than that on the standard enthalpies of formation. Test G3 calculations on 2,3-didehydronaphthalene confirm the reliability of the additive correction scheme in the prediction of properties of annelated analogues of 1,2-didehydrobenzene. Such a scheme opens an avenue to facile electronic structure calculations on didehydrogenation reactions of polycondensed heterocyclic compounds with six-membered rings.

  15. XAFS and XEOL of tetramesityldigermene - An electronic structure study of a heavy group 14 ethylene analogue

    SciTech Connect

    Ward, Matthew J.; Rupar, Paul A.; Murphy, Michael W.; Yiu, Yun-Mui; Baines, Kim M.; Sham, Tsun-Kong

    2013-05-29

    Digermene, the germanium analogue of ethylene, has a multiple bonding motif that differs greatly from that of alkenes and exhibits no pure σ or π type bonds. The electronic structure of digermenes is difficult to study experimentally due to their reactivity, and is computationally challenging because of their shallow potential energy surfaces. Using X-ray absorption near edge structures at both the germanium K and L edges we have been able to directly probe the unoccupied electronic states, or the lowest unoccupied molecular orbital (LUMO), and LUMO+ etc. in the Ge=Ge bond of tetramesityldigermene. We have demonstrated that the LUMO, LUMO+, etc. are composed of hybrid Ge 4s and 4p orbitals. Additionally, our data suggest that the LUMO exhibits relatively more Ge 4s character, whereas the LUMO+ and LUMO+2 exhibit relatively more Ge 4p character. An X-ray excited optical luminescence study of Ge2Mes4 revealed one broad optical emission band at 620 nm, which is significantly red shifted compared to the known energy gap of this molecular germanium compound.

  16. How oblique extension and structural inheritance control rift segment linkage: Insights from 4D analogue models

    NASA Astrophysics Data System (ADS)

    Zwaan, Frank; Schreurs, Guido

    2016-04-01

    INTRODUCTION During the early stages of rifting, rift segments may form along non-continuous and/or offset pre-existing weaknesses. It is important to understand how these initial rift segments interact and connect to form a continuous rift system. A previous study of ours (Zwaan et al., in prep) investigated the influence of dextral oblique extension and rift offset on rift interaction. Here we elaborate upon our previous work by using analogue models to assess the added effects of 1) sinistral oblique extension as observed along the East African Rift and 2) the geometry of linked and non-linked inherited structures. METHODS Our set-up involves a base of foam and plexiglass that forces distributed extension in the overlying model materials: a sand layer for the brittle upper crust and a viscous sand/silicone mixture for ductile lower crust. A mobile base plate allows lateral motion for oblique extension. We create inherited structures, along which rift segments develop, with right-stepping offset lines of silicone (seeds) on top of the basal viscous layer. These seeds can be connected by an additional weak seed that represents a secondary inherited structural grain (model series 1) or disconnected and laterally discontinuous (over/underlap, model series 2). Selected models are run in an X-ray computer topographer (CT) to reveal the 3D evolution of internal structures with time that can be quantified with particle image velocitmetry (PIV) techniques. RESULTS Models in both series show that rift segments initially form along the main seeds and then generally propagate approximately perpendicular to the extension direction: with orthogonal extension they propagate in a parallel fashion, dextral oblique extension causes them to grow towards each other and connect, while with sinistral oblique extension they grow away from each other. However, sinistral oblique extension can also promote rift linkage through an oblique- or strike-slip zone oriented almost parallel to

  17. Structure-based approach to the identification of a novel group of selective glucosamine analogue inhibitors of Trypanosoma cruzi glucokinase.

    PubMed

    D'Antonio, Edward L; Deinema, Mason S; Kearns, Sean P; Frey, Tyler A; Tanghe, Scott; Perry, Kay; Roy, Timothy A; Gracz, Hanna S; Rodriguez, Ana; D'Antonio, Jennifer

    2015-12-01

    Glucokinase and hexokinase from pathogenic protozoa Trypanosoma cruzi are potential drug targets for antiparasitic chemotherapy of Chagas' disease. These glucose kinases phosphorylate d-glucose with co-substrate ATP and yield glucose 6-phosphate and are involved in essential metabolic pathways, such as glycolysis and the pentose phosphate pathway. An inhibitor class was conceived that is selective for T. cruzi glucokinase (TcGlcK) using structure-based drug design involving glucosamine having a linker from the C2 amino that terminates with a hydrophobic group either being phenyl, p-hydroxyphenyl, or dioxobenzo[b]thiophenyl groups. The synthesis and characterization for two of the four compounds are presented while the other two compounds were commercially available. Four high-resolution X-ray crystal structures of TcGlcK inhibitor complexes are reported along with enzyme inhibition constants (Ki) for TcGlcK and Homo sapiens hexokinase IV (HsHxKIV). These glucosamine analogue inhibitors include three strongly selective TcGlcK inhibitors and a fourth inhibitor, benzoyl glucosamine (BENZ-GlcN), which is a similar variant exhibiting a shorter linker. Carboxybenzyl glucosamine (CBZ-GlcN) was found to be the strongest glucokinase inhibitor known to date, having a Ki of 0.71±0.05μM. Also reported are two biologically active inhibitors against in vitro T. cruzi culture that were BENZ-GlcN and CBZ-GlcN, with intracellular amastigote growth inhibition IC50 values of 16.08±0.16μM and 48.73±0.69μM, respectively. These compounds revealed little to no toxicity against mammalian NIH-3T3 fibroblasts and provide a key starting point for further drug development with this class of compound. PMID:26778112

  18. Structure-activity studies on the potentiation of benzodiazepine receptor binding by ethylenediamine analogues and derivatives.

    PubMed Central

    Morgan, P. F.; Stone, T. W.

    1983-01-01

    The effect of ethylenediamine analogues on in vitro binding of [3H]-diazepam to crude cerebral cortical synaptosomal membranes in the rat was studied. Ethylenediamine significantly increased [3H]-diazepam binding to a maximum potentiation of 154% control (EC50 = 1.8 X 10(-4) M) and was the most active compound studied in terms of both potency and the maximum potentiation observed. Potentiation of [3H]-diazepam binding by ethylenediamine analogues is dependent on carbon-chain length, appears to require two terminal amino groups, and is not observed in the rigid analogues studied. Potentiation of [3H]-diazepam binding by ethylenediamine analogues is mediated largely by a change in receptor number and not receptor affinity. Results are discussed in terms of the possible nature of the ethylenediamine binding site. PMID:6317124

  19. Exogenous ceramide-1-phosphate (C1P) and phospho-ceramide analogue-1 (PCERA-1) regulate key macrophage activities via distinct receptors

    PubMed Central

    Katz, Sebastián; Ernst, Orna; Avni, Dorit; Athamna, Muhammad; Philosoph, Amir; Arana, Lide; Ouro, Alberto; Hoeferlin, L. Alexis; Meijler, Michael M.; Chalfant, Charles E.; Gómez-Muñoz, Antonio; Zor, Tsaffrir

    2016-01-01

    Inflammation is an ensemble of tightly regulated steps, in which macrophages play an essential role. Previous reports showed that the natural sphingolipid ceramide 1-phosphate (C1P) stimulates macrophages migration, while the synthetic C1P mimic, phospho-ceramide analogue-1 (PCERA-1), suppresses production of the key pro-inflammatory cytokine TNFα and amplifies production of the key anti-inflammatory cytokine IL-10 in LPS-stimulated macrophages, via one or more unidentified G-protein coupled receptors. We show that C1P stimulated RAW264.7 macrophages migration via the NFκB pathway and MCP-1 induction, while PCERA-1 neither mimicked nor antagonized these activities. Conversely, PCERA-1 synergistically elevated LPS-dependent IL-10 expression in RAW264.7 macrophages via the cAMP-PKA-CREB signaling pathway, while C1P neither mimicked nor antagonized these activities. Interestingly, both compounds have the capacity to additively inhibit TNFα secretion; PCERA-1, but not C1P, suppressed LPS-induced TNFα expression in macrophages in a CREB-dependent manner, while C1P, but not PCERA-1, directly inhibited recombinant TNFα converting enzyme (TACE). Finally, PCERA-1 failed to interfere with binding of C1P to either the cell surface receptor or to TACE. These results thus indicate that the natural sphingolipid C1P and its synthetic analog PCERA-1 bind and activate distinct receptors expressed in RAW264.7 macrophages. Identification of these receptors will be instrumental for elucidation of novel activities of extra-cellular sphingolipids, and may pave the way for the design of new sphingolipid mimics for the treatment of inflammatory diseases, and pathologies which depend on cell migration, as in metastatic tumors. PMID:26656944

  20. Structural and Biochemical Characterization of the Interaction of Tubulin with Potent Natural Analogues of Podophyllotoxin.

    PubMed

    Antúnez-Mojica, Mayra; Rodríguez-Salarichs, Javier; Redondo-Horcajo, Mariano; León, Alejandra; Barasoain, Isabel; Canales, Ángeles; Cañada, F J; Jiménez-Barbero, Jesús; Alvarez, Laura; Díaz, J Fernando

    2016-08-26

    Four natural analogues of podophyllotoxin obtained from the Mexican medicinal plant Bursera fagaroides, namely, acetyl podophyllotoxin (2), 5'-desmethoxy-β-peltatin A methyl ether (3), 7',8'-dehydro acetyl podophyllotoxin (4), and burseranin (5), have been characterized, and their interactions with tubulin have been investigated. Cytotoxic activity measurements, followed by immunofluorescence microscopy and flow cytometry studies, demonstrated that these compounds disrupt microtubule networks in cells and cause cell cycle arrest in the G2/M phase in the A549 cell line. A tubulin binding assay showed that compounds 1-4 were potent assembly inhibitors, displaying binding to the colchicine site with Kb values ranging from 11.75 to 185.0 × 10(5) M(-1). In contrast, burseranin (5) was not able to inhibit tubulin assembly. From the structural perspective, the ligand-binding epitopes of compounds 1-3 have been mapped using STD-NMR, showing that B and E rings are the major points for interaction with the protein. The obtained results indicate that the inhibition of tubulin assembly of this family of compounds is more effective when there are at least two methoxyl groups at the E ring, along with a trans configuration of the lactone ring in the aryltetralin lignan core. PMID:27518758

  1. Intraparticle mass transfer kinetics on molecularly imprinted polymers of structural analogues of a template

    SciTech Connect

    Kim, Hyunjung; Kaczmarski, Krzysztof; Guiochon, Georges A

    2005-09-01

    The intraparticle mass transfer kinetics of the structural analogues of a template on a Fmoc-L-Tryptophan (Fmoc-L-Trp) imprinted polymer (MIP) and on the corresponding non-imprinted polymer (NIP) were quantitatively studied using the lumped pore diffusion model (POR) of chromatography. The best equilibrium isotherm models of these compounds were used to calculate the high-concentration band profiles of different substrates on the MIP and the NIP with the POR model. These profiles were compared to experimental band profiles. The numerical values of the intraparticle pore and surface diffusion coefficients were adjusted to determine those that minimized the differences between calculated and experimental profiles. The results of this exercise show that surface diffusion is the dominant intraparticle mass transfer process for the substrates on the polymers and that the energetic heterogeneity of the surface should be considered in accounting for the surface diffusion of the L-enantiomers on the MIP. The surface diffusion coefficient increases with decreasing overall affinity of each substrate for the polymers.

  2. Structural analysis of specificity: alpha-lytic protease complexes with analogues of reaction intermediates.

    PubMed

    Bone, R; Frank, D; Kettner, C A; Agard, D A

    1989-09-19

    To better understand the structural basis of enzyme specificity, the structures of complexes formed between alpha-lytic protease, an extracellular serine protease of Lysobacter enzymogenes, and five inhibitory peptide boronic acids (R2-boroX, where R2 is methoxysuccinyl-Ala-Ala-Pro- and boroX is the alpha-aminoboronic acid analogue of Ala, Val, Ile, Norleu, or Phe) have been studied at high resolution by X-ray crystallography. The enzyme has primary specificity for Ala in the P1 position of peptide substrates with catalytic efficiency decreasing with increasing side-chain volume. Enzyme affinity for inhibitors with boroVal, boroIle, and boroPhe residues is much higher than expected on the basis of the catalytic efficiencies of homologous substrates. Covalent tetrahedral adducts are formed between the active-site serine and the boronic acid moieties of R2-boroAla, R2-boroVal R2-boroIle, and R2-boroNorleu. Though R2-boroVal is a slowly bound inhibitor and R2-boroAla is rapidly bound [Kettner, C. A., Bone, R., Agard, D. A., & Bachovchin, W. W. (1988) Biochemistry 27, 7682-7688], there appear to be no structural differences that could account for slow binding. The removal from solution of 20% more hydrophobic surface on binding accounts for the improved affinity of alpha-lytic protease for R2-boroVal relative to R2-boroAla. The high affinity of the enzyme for R2-boroIle derives from the selective binding of the L-allo stereoisomer of the boroIle residue, which can avoid bad steric interactions in the binding pocket.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2611204

  3. Mutagenicity and DNA damage of bisphenol A and its structural analogues in HepG2 cells.

    PubMed

    Fic, Anja; Žegura, Bojana; Sollner Dolenc, Marija; Filipič, Metka; Peterlin Mašič, Lucija

    2013-06-01

    Environmental oestrogen bisphenol A (BPA) and its analogues are widespread in our living environment. Because their production and use are increasing, exposure of humans to bisphenols is becoming a significant issue. We evaluated the mutagenic and genotoxic potential of eight BPA structural analogues (BPF, BPAF, BPZ, BPS, DMBPA, DMBPS, BP-1, and BP-2) using the Ames and comet assay, respectively. None of the tested bisphenols showed a mutagenic effect in Salmonella typhimurium strains TA98 and TA100 in either the presence or absence of external S9-mediated metabolic activation (Aroclor 1254-induced male rat liver). Potential genotoxicity of bisphenols was determined in the human hepatoma cell line (HepG2) at non-cytotoxic concentrations (0.1 μmol L(-1) to 10 μmol L(-1)) after 4-hour and 24-hour exposure. In the comet assay, BPA and its analogue BPS induced significant DNA damage only after the 24-hour exposure, while analogues DMBPS, BP-1, and BP-2 induced a transient increase in DNA strand breaks. PMID:23819927

  4. Elucidation of Structural Elements for Selectivity across Monoamine Transporters: Novel 2-[(Diphenylmethyl)sulfinyl]acetamide (Modafinil) Analogues

    PubMed Central

    2015-01-01

    2-[(Diphenylmethyl)sulfinyl]acetamide (modafinil, (±)-1) is a unique dopamine uptake inhibitor that binds the dopamine transporter (DAT) differently than cocaine and may have potential for the treatment of psychostimulant abuse. To further investigate structural requirements for this divergent binding mode, novel thio- and sulfinylacetamide and ethanamine analogues of (±)-1 were synthesized wherein (1) the diphenyl rings were substituted with methyl, trifluoromethyl, and halogen substituents and (2) substituents were added to the terminal amide/amine nitrogen. Halogen substitution of the diphenyl rings of (±)-1 gave several amide analogues with improved binding affinity for DAT and robust selectivity over the serotonin transporter (SERT), whereas affinity improved at SERT over DAT for the p-halo-substituted amine analogues. Molecular docking studies, using a subset of analogues with DAT and SERT homology models, and functional data obtained with DAT (A480T) and SERT (T497A) mutants defined a role for TM10 in the substrate/inhibitor S1 binding sites of DAT and SERT. PMID:24494745

  5. Solution-phase parallel synthesis of a pharmacophore library of HUN-7293 analogues: a general chemical mutagenesis approach to defining structure-function properties of naturally occurring cyclic (depsi)peptides.

    PubMed

    Chen, Yan; Bilban, Melitta; Foster, Carolyn A; Boger, Dale L

    2002-05-15

    HUN-7293 (1), a naturally occurring cyclic heptadepsipeptide, is a potent inhibitor of cell adhesion molecule expression (VCAM-1, ICAM-1, E-selectin), the overexpression of which is characteristic of chronic inflammatory diseases. Representative of a general approach to defining structure-function relationships of such cyclic (depsi)peptides, the parallel synthesis and evaluation of a complete library of key HUN-7293 analogues are detailed enlisting solution-phase techniques and simple acid-base liquid-liquid extractions for isolation and purification of intermediates and final products. Significant to the design of the studies and unique to solution-phase techniques, the library was assembled superimposing a divergent synthetic strategy onto a convergent total synthesis. An alanine scan and N-methyl deletion of each residue of the cyclic heptadepsipeptide identified key sites responsible for or contributing to the biological properties. The simultaneous preparation of a complete set of individual residue analogues further simplifying the structure allowed an assessment of each structural feature of 1, providing a detailed account of the structure-function relationships in a single study. Within this pharmacophore library prepared by systematic chemical mutagenesis of the natural product structure, simplified analogues possessing comparable potency and, in some instances, improved selectivity were identified. One potent member of this library proved to be an additional natural product in its own right, which we have come to refer to as HUN-7293B (8), being isolated from the microbial strain F/94-499709. PMID:11996584

  6. Reworking of structural inheritance at strike-slip restraining-bends: templates from sandbox analogue models

    NASA Astrophysics Data System (ADS)

    Nestola, Yago; Storti, Fabrizio; Cavozzi, Cristian; Magistroni, Corrado; Meda, Marco; Piero Righetti, Fabrizio

    2016-04-01

    Structural inheritance plays a fundamental role during crustal deformation because pre-existing fault and shear zones typically provide weakness zone suitable to fail again when affected by a new regional stress field. Re-activation of structural inheritance is expected to unavoidably increase the complexity of structural architectures, whose geometric and kinematic patterns can significantly deviate from what expected in newly deformed crustal sectors. Availability of templates from analogue models can provide a very effective tool to help unraveling such a structural complexity. For this purpose, we simulated the reworking of a set of basement hosted pre-existing fault zones at strike-slip restraining fault bends. In the models, the mechanical stratigraphy consists of a basement, made of a mixture of dry kaolin and sand to slightly increase cohesion, and a sedimentary cover made by pure dry sand. Inherited fault zones are confined to the basement and coated by a thin veneer of silicone putty. In the experimental programme, the geometry of the left-lateral restraining bend is maintained the same, with a bending angle of 30° of the restraining fault segment. The strike of the inherited fault zones, measured counterclockwise with respect to that of the master strike-slip fault zone outside the restraining bend, was 0°, 30°, and 60° in different experiments, respectively. An end member experiment without inheritance was also run for comparison. Our experimental results show that the angle that the inherited fault zones make with the restraining bend plays a fundamental role in governing the deformation pattern. When structural inheritance is near parallel to the master strike-slip fault zone, synthetic shears form and severely compartmentalize the transpressional pop-up anticline growing on top of the restraining bend. Fault-bounded blocks undergo sinistral escape during transpression. On the other hand, when structural inheritance makes a high angle to the

  7. Biofunctional constituent isolated from Citrullus colocynthis fruits and structure-activity relationships of its analogues show acaricidal and insecticidal efficacy.

    PubMed

    Jeon, Ju-Hyun; Lee, Hoi-Seon

    2014-08-27

    The acaricidal and insecticidal potential of the active constituent isolated from Citrullus colocynthis fruits and its structurally related analogues was evaluated by performing leaf disk, contact toxicity, and fumigant toxicity bioassays against Tetranychus urticae, Sitophilus oryzae, and Sitophilus zeamais adults. The active constituent of C. colocynthis fruits was isolated by chromatographic techniques and was identified as 4-methylquinoline on the basis of spectroscopic analyses. To investigate the structure-activity relationships, 4-methylquinoline and its structural analogues were tested against mites and two insect pests. On the basis of the LC50 values, 7,8-benzoquinoline was the most effective against T. urticae. Quinoline, 8-hydroxyquinoline, 2-methylquinoline, 4-methylquinoline, 6-methylquinoline, 8-methylquinoline, and 7,8-benzoquinoline showed high insecticidal activities against S. oryzae and S. zeamais regardless of the application method. These results indicate that introduction of a functional group into the quinoline skeleton and changing the position of the group have an important influence on the acaricidal and insecticidal activities. Furthermore, 4-methylquinoline isolated from C. colocynthis fruits, along with its structural analogues, could be effective natural pesticides for managing spider mites and stored grain weevils. PMID:25110971

  8. Adsorption on molecularly imprinted polymers of structural analogues of a template. Single-component adsorption isotherm data

    SciTech Connect

    Kim, Hyunjung; Guiochon, Georges A

    2005-10-01

    The equilibrium adsorption isotherms on two otherwise identical polymers, one imprinted with Fmoc-L-tryptophan (Fmoc-L-Trp) (MIP), the other nonimprinted (NIP), of compounds that are structural analogues of the template were acquired by frontal analysis (FA) in an acetonitrile/acetic acid (99/1 v/v) mobile phase, over a wide concentration range (from 0.005 to 50 mM). These analogues were Fmoc-L-tyrosine, Fmoc-L-serine, Fmoc-L-phenyalanine, Fmoc-glycine (Fmoc-Gly), Fmoc-L-tryptophan pentafluorophenyl ester (Fmoc-L-Trp(OPfp)), and their antipodes. These substrates have different numbers of functional groups able to interact with the 4-vinylpyridine groups of the polymer. For a given number of the functional groups, these substrates have different hydrophobicities of their side groups (as indicated by their partition coefficients (log P{sub ow}) in the octanol-water system (e.g., from 4.74 for Fmoc-Trp to 2.53 for Fmoc-Gly)). Statistical results from the fitting of the FA data to Langmuirian isotherm models, the calculation of the affinity energy distribution, and the comparison of calculated and experimental band profiles show that all these sets of FA data are best accounted for by a tri-Langmuir isotherm model, except for the data of Fmoc-L-Trp(OPfp) that are best modeled by a simple Langmuir isotherm. So, all compounds but Fmoc-L-Trp(OPfp) find three different types of adsorption sites on both the MIP and the NIP. The properties of these different types of sites were studied systematically. The results show that the affinity of the structural analogues for the NIP is controlled mostly by the number of the functional groups on the substrates and somewhat by the hydrophobicity of their side groups. These two factors control also the MIP affinity toward the enantiomers of the structural analogues that have a stereochemistry different from that of the template. In contrast, the affinity of the highest affinity sites of the MIP toward the enantiomers of these

  9. Formation of dome and basin structures: Results from scaled experiments using non-linear rock analogues

    NASA Astrophysics Data System (ADS)

    Zulauf, J.; Zulauf, G.; Zanella, F.

    2016-09-01

    Dome and basin folds are structures with circular or slightly elongate outcrop patterns, which can form during single- and polyphase deformation in various tectonic settings. We used power-law viscous rock analogues to simulate single-phase dome-and-basin folding of rocks undergoing dislocation creep. The viscosity ratio between a single competent layer and incompetent matrix was 5, and the stress exponent of both materials was 7. The samples underwent layer-parallel shortening under bulk pure constriction. Increasing initial layer thickness resulted in a decrease in the number of domes and basins and an increase in amplitude, A, arc-length, L, wavelength, λ, and layer thickness, Hf. Samples deformed incrementally show progressive development of domes and basins until a strain of eY=Z = -30% is attained. During the dome-and-basin formation the layer thickened permanently, while A, L, and λ increased. A dominant wavelength was not attained. The normalized amplitude (A/λ) increased almost linearly reaching a maximum of 0.12 at eY=Z = -30%. During the last increment of shortening (eY=Z = -30 to -40%) the domes and basins did not further grow, but were overprinted by a second generation of non-cylindrical folds. Most of the geometrical parameters of the previously formed domes and basins behaved stable or decreased during this phase. The normalized arc-length (L/Hf) of domes and basins is significantly higher than that of 2D cylindrical folds. For this reason, the normalized arc length can probably be used to identify domes and basins in the field, even if these structures are not fully exposed in 3D.

  10. Inhibition and structure of Trichomonas vaginalis purine nucleoside phosphorylase with picomolar transition state analogues.

    PubMed

    Rinaldo-Matthis, Agnes; Wing, Corin; Ghanem, Mahmoud; Deng, Hua; Wu, Peng; Gupta, Arti; Tyler, Peter C; Evans, Gary B; Furneaux, Richard H; Almo, Steven C; Wang, Ching C; Schramm, Vern L

    2007-01-23

    Trichomonas vaginalis is a parasitic protozoan purine auxotroph possessing a unique purine salvage pathway consisting of a bacterial type purine nucleoside phosphorylase (PNP) and a purine nucleoside kinase. Thus, T. vaginalis PNP (TvPNP) functions in the reverse direction relative to the PNPs in other organisms. Immucillin-A (ImmA) and DADMe-Immucillin-A (DADMe-ImmA) are transition state mimics of adenosine with geometric and electrostatic features that resemble early and late transition states of adenosine at the transition state stabilized by TvPNP. ImmA demonstrates slow-onset tight-binding inhibition with TvPNP, to give an equilibrium dissociation constant of 87 pM, an inhibitor release half-time of 17.2 min, and a Km/Kd ratio of 70,100. DADMe-ImmA resembles a late ribooxacarbenium ion transition state for TvPNP to give a dissociation constant of 30 pM, an inhibitor release half-time of 64 min, and a Km/Kd ratio of 203,300. The tight binding of DADMe-ImmA supports a late SN1 transition state. Despite their tight binding to TvPNP, ImmA and DADMe-ImmA are weak inhibitors of human and P. falciparum PNPs. The crystal structures of the TvPNP x ImmA x PO4 and TvPNP x DADMe-ImmA x PO4 ternary complexes differ from previous structures with substrate analogues. The tight binding with DADMe-ImmA is in part due to a 2.7 A ionic interaction between a PO4 oxygen and the N1' cation of the hydroxypyrrolidine and is weaker in the TvPNP x ImmA x PO4 structure at 3.5 A. However, the TvPNP x ImmA x PO4 structure includes hydrogen bonds between the 2'-hydroxyl and the protein that are not present in TvPNP x DADMe-ImmA x PO4. These structures explain why DADMe-ImmA binds tighter than ImmA. Immucillin-H is a 12 nM inhibitor of TvPNP but a 56 pM inhibitor of human PNP. And this difference is explained by isotope-edited difference infrared spectroscopy with [6-18O]ImmH to establish that O6 is the keto tautomer in TvPNP x ImmH x PO4, causing an unfavorable leaving-group interaction

  11. Nucleic acid-like structures II. Polynucleotide analogues as possible primitive precursors of nucleic acids

    NASA Astrophysics Data System (ADS)

    Schwartz, Alan W.; Visscher, J.; Bakker, C. G.; Niessen, J.

    1987-09-01

    Activated derivatives of purine-containing deoxynucleoside- diphosphates spontaneously oligomerize to produce pyrophosphate- linked oligodeoxynucleotide analogues. These analogues are of potential interest as models of primitive, polynucleotide precursors. The efficiency of oligomerization (ImpdGpIm and ImpdApIm much greater than ImpdIpIm) appears to reflect a combination of stacking forces and the specific geometric orientations of the stacked units. Under favorable conditions, chain lengths greater than 20 have been obtained for oligomers containing pdGp in the absence of a template. In the presence of a complementary template, the activated derivatives of pdGp and pdAp oligomerize much more extensively. An acyclo-analogue of G has also been shown to undergo template-directed oligomerization on poly(C). These observations suggest the possibility that primitive information transfer might have evolved in much simpler systems and that this function was taken over by polynucleotides at a later stage in evolution.

  12. Extracellular cellobiose lipid from yeast and their analogues: structures and fungicidal activities.

    PubMed

    Kulakovskaya, Tatyana; Shashkov, Alexander; Kulakovskaya, Ekaterina; Golubev, Wladyslav; Zinin, Alexander; Tsvetkov, Yury; Grachev, Alexey; Nifantiev, Nikolay

    2009-01-01

    Basidiomycetous yeasts Cryptococcus humicola and Pseudozyma fusiformata secrete cellobiose lipids into the culture broth. In the case of Cr. humicola, 16-(tetra-O-acetyl-beta-cellobiosyloxy)-2-hydroxyhexadecanoic acid was defined as major product and 16-(tetra-O-acetyl-beta-cellobiosyloxy)-2,15-dihydrohexadecanoic acid was defined as minor product, while Ps. fusiformata secreted mainly 16-[6-O-acetyl-2'-O-(3-hydroxyhexanoyl)-beta-cellobiosyloxy)-2,15-dihydroxyhexadecanoic acid. These compounds exhibit similar fungicidal activities against different yeasts including pathogenic Cryptococcus and Candida species. The cells of Filobasidiella neoformans causing systemic cryptococcosis completely died after 30-min incubation with 0.02 mg mL(-1) of cellobiose lipids. The same effect on ascomycetous yeast, including pathogenic Candida species, is achieved at 0.1-0.3 mg mL(-1) of cellobiose lipids depending on the test culture used. Cellobiose lipid of Ps. fusiformata inhibits the growth of phytopathogenic fungi Sclerotinia sclerotiorum and Phomopsis helianthi more efficiently than cellobiose lipids from Cr. humicola. Fully O-deacylated analogue, namely 16-(beta-cellobiosyloxy)-2-hydroxyhexadecanoic acid, and totally synthetic compound, 16-(beta-cellobiosyloxy)-hexadecanoic acid, do not inhibit the growth of F. neoformans and Saccharomyces cerevisiae, while 16-(beta-cellobiosyloxy)-2,15-dihydroxyhexadecanoic acid inhibits the growth of both test cultures but at higher concentrations than cellobiose lipids of Cr. humicola and Ps. fusiformata. The amide of 16-(beta-cellobiosyloxy)-2,15-dihydroxyhexadecanoic acid possessed no fungicide activity. Thus, the structures of both the carbohydrate part and fatty acid aglycon moiety are important for the fungicidal activity of cellobiose lipids. PMID:19202311

  13. Carbocyclic nucleoside analogues: classification, target enzymes, mechanisms of action and synthesis

    NASA Astrophysics Data System (ADS)

    Matyugina, E. S.; Khandazhinskaya, A. P.; Kochetkov, Sergei N.

    2012-08-01

    Key biological targets (S-adenosyl-L-homocysteine hydrolase, telomerase, human immunodeficiency virus reverse transcriptase, herpes virus DNA polymerase and hepatitis B virus DNA polymerase) and the mechanisms of action of carbocyclic nucleoside analogues are considered. Structural types of analogues are discussed. Methods of synthesis for the most promising compounds and the spectrum of their biological activities are described. The bibliography includes 126 references.

  14. New Atglistatin closely related analogues: Synthesis and structure-activity relationship towards adipose triglyceride lipase inhibition.

    PubMed

    Roy, Pierre-Philippe; D'Souza, Kenneth; Cuperlovic-Culf, Miroslava; Kienesberger, Petra C; Touaibia, Mohamed

    2016-08-01

    Adipose Triglyceride Lipase (ATGL) performs the first and rate-limiting step in lipolysis by hydrolyzing triacylglycerols stored in lipid droplets to diacylglycerols. By mediating lipolysis in adipose and non-adipose tissues, ATGL is a major regulator of overall energy metabolism and plasma lipid levels. Since chronically high levels of plasma lipids are linked to metabolic disorders including insulin resistance and type 2 diabetes, ATGL is an interesting therapeutic target. In the present study, fourteen closely related analogues of Atglistatin (1), a newly discovered ATGL inhibitor, were synthesized, and their ATGL inhibitory activity was evaluated. The effect of these analogues on lipolysis in 3T3-L1 adipocytes clearly shows that inhibition of the enzyme by Atglistatin (1) is due to the presence of the carbamate and N,N-dimethyl moieties on the biaryl central core at meta and para position, respectively. Mono carbamate-substituted analogue C2, in which the carbamate group was in the meta position as in Atglistatin (1), showed slight inhibition. Low dipole moment of Atglistatin (1) compared to the synthesized analogues possibly explains the lower inhibitory activities. PMID:27155760

  15. [Peculiarities of the Brevundimonas diminuta Gl7ACA-Acylase quaternary structure formation and obtaining stable enzyme analogues].

    PubMed

    2013-01-01

    The physicochemical and enzymatic properties of hybrid analogues of the Brevundimonas diminuta Gl7ACA-acylase (BrdGIA), containing the N-terminal chitin-binding domain of the bacterial chitinase (BrdG1A/NmChBD) or the C-terminal oligohistidine sequence (BrdGIA/H), were studied. An enhanced thermostability level of BrdG1A/NmChBD could suggest the stabilizing effect of the chitin-binding domain. An analysis of pH profiles of the enzymatic activity of recombinat BrdGIA analogues did not reveal significant differences: the catalytic activity of both variants changed slightly in the.interval ofpH values from 6.0 to 9.0 but drastically decreased at lower pH values. Both analogues demonstrated similar sensitivity towards denaturing agents: addition of 2.0 M ofguanidine chloride resulted in the complete inactivation of both enzymes. A scheme was developed for obtaining isolated recombinant alpha- and beta-subunits of BrdGLA. In vitro enzyme reconstructions indicated that the alpha-subunit was necessary for the formation of a correct spatial structure of the beta-subunit and for the formation of a functionally active enzyme. PMID:25507777

  16. [Peculiarities of the Brevundimonas diminuta Gl7ACA-Acylase quaternary structure formation and obtaining stable enzyme analogues].

    PubMed

    Zakirova, S A; Mikhaĭlova, T V; Él'darov, M A

    2013-01-01

    The physicochemical and enzymatic properties of hybrid analogues of the Brevundimonas diminuta Gl7ACA-acylase (BrdGIA), containing the N-terminal chitin-binding domain of the bacterial chitinase (BrdG1A/NmChBD) or the C-terminal oligohistidine sequence (BrdGIA/H), were studied. An enhanced thermostability level of BrdG1A/NmChBD could suggest the stabilizing effect of the chitin-binding domain. An analysis of pH profiles of the enzymatic activity of recombinat BrdGIA analogues did not reveal significant differences: the catalytic activity of both variants changed slightly in the.interval ofpH values from 6.0 to 9.0 but drastically decreased at lower pH values. Both analogues demonstrated similar sensitivity towards denaturing agents: addition of 2.0 M ofguanidine chloride resulted in the complete inactivation of both enzymes. A scheme was developed for obtaining isolated recombinant alpha- and beta-subunits of BrdGLA. In vitro enzyme reconstructions indicated that the alpha-subunit was necessary for the formation of a correct spatial structure of the beta-subunit and for the formation of a functionally active enzyme. PMID:25434179

  17. Synthesis, properties and structures of NbOF3 complexes and comparisons with NbOCl3 analogues.

    PubMed

    Levason, William; Reid, Gillian; Trayer, Jonathan; Zhang, Wenjian

    2014-03-01

    The first series of complexes of niobium(v) oxide trifluoride, [NbOF3(OPR3)2] (R = Me or Ph), [NbOF3(dppmO2)] (dppmO2 = Ph2P(O)CH2P(O)Ph2), [NbOF3(dmso)2], [NbOF3(tmeda)] (tmeda = Me2N(CH2)2NMe2) and [NbOF3(diimine)] (diimine = 2,2'-bipy, 1,10-phen) have been prepared, either by reaction of the corresponding complexes of NbF5 and hexamethyldisiloxane (HMDSO) in CH2Cl2-MeCN solution, or directly from NbF5, ligand and HMDSO. They were characterised by IR, (1)H, (31)P{(1)H} and (19)F{(1)H} NMR spectroscopy, and X-ray crystal structures are reported for [NbOF3(OPR3)2] (R = Me or Ph) and [NbOF3(dppmO2)]. Complexes of NbOCl3, [NbOCl3(OPPh3)2], [NbOCl3(dppmO2)], [NbOCl3(dppeO2)] (dppeO2 = Ph2P(O)(CH2)2P(O)Ph2), [NbOCl3(tmeda)] and [NbOCl3(diimine)] were made from NbCl5 and HMDSO in MeCN (which forms [NbOCl3(MeCN)2] in situ), followed by addition of the neutral ligand. Their properties are compared with the oxide fluoride analogues. X-ray structures are reported for [NbOCl3(dppmO2)], [NbOCl3(dppeO2)], [NbOCl3(tmeda)] and [NbOCl3(2,2'-bipy)]. The synthesis and spectroscopic characterisation of [MF5L] (M = Nb or Ta; L = OPR3, OAsPh3) and [MF4(diimine)2][MF6] are also described, and the key properties of the four series of complexes compared. PMID:24413623

  18. Structural bisphenol analogues differentially target steroidogenesis in murine MA-10 Leydig cells as well as the glucocorticoid receptor.

    PubMed

    Roelofs, Maarke J E; van den Berg, Martin; Bovee, Toine F H; Piersma, Aldert H; van Duursen, Majorie B M

    2015-03-01

    Although much information on the endocrine activity of bisphenol A (BPA) is available, a proper human hazard assessment of analogues that are believed to have a less harmful toxicity profile is lacking. Here the possible effects of BPA, bisphenol F (BPF), bisphenol S (BPS), as well as the brominated structural analogue and widely used flame retardant tetrabromobisphenol A (TBBPA) on human glucocorticoid and androgen receptor (GR and AR) activation were assessed. BPA, BPF, and TBBPA showed clear GR and AR antagonism with IC50 values of 67 μM, 60 μM, and 22 nM for GR, and 39 μM, 20 μM, and 982 nM for AR, respectively, whereas BPS did not affect receptor activity. In addition, murine MA-10 Leydig cells exposed to the bisphenol analogues were assessed for changes in secreted steroid hormone levels. Testicular steroidogenesis was altered by all bisphenol analogues tested. TBBPA effects were more directed towards the male end products and induced testosterone synthesis, while BPF and BPS predominantly increased the levels of progestagens that are formed in the beginning of the steroidogenic pathway. The MA-10 Leydig cell assay shows added value over the widely used H295R steroidogenesis assay because of its fetal-like characteristics and specificity for the physiologically more relevant testicular Δ4 steroidogenic pathway. Therefore, adding an in vitro assay covering fetal testicular steroidogenesis, such as the MA-10 cell line, to the panel of tests used to screen potential endocrine disruptors, is highly recommendable. PMID:25576683

  19. Insights into the electronic structure of Cu(II) bound to an imidazole analogue of westiellamide.

    PubMed

    Comba, Peter; Dovalil, Nina; Hanson, Graeme R; Harmer, Jeffrey R; Noble, Christopher J; Riley, Mark J; Seibold, Bjoern

    2014-12-01

    Three synthetic analogues of westiallamide, H3L(wa), have previously been synthesized (H3L(1-3)) that have a common backbone (derived from l-valine) with H3L(wa) but differ in their heterocyclic rings (imidazole, oxazole, thiazole, and oxazoline). Herein we explore in detail through high-resolution pulsed electron paramagnetic resonance (EPR) and magnetic circular dichroism (MCD) spectroscopy in conjunction with density functional theory (DFT) the geometric and electronic structures of the mono- and dinuclear Cu(II) complexes of these cyclic pseudo hexapeptides. Orientation-selective hyperfine sublevel correlation, electron nuclear double resonance, and three-pulse electron spin echo envelope modulation spectroscopy of [Cu(II)(H2L(1))(MeOH)2](+) reveal delocalization of the unpaired electron spin onto the ligating and distal nitrogens of the coordinated heterocyclic rings and that they are magnetically inequivalent. DFT calculations confirm this and show similar spin densities on the distal heteroatoms in the heterocyclic rings coordinated to the Cu(II) ion in the other cyclic pseudo hexapeptide [Cu(II)(H2L(2,3,wa))(MeOH)2](+) complexes. The magnetic inequivalencies in [Cu(II)(H2L(1))(MeOH)2](+) arise from different orientations of the heterocyclic rings coordinated to the Cu(II) ion, and the delocalization of the unpaired electron onto the distal heteroatoms within these N-methylimidazole rings depends upon their location with respect to the Cu(II) d(x(2)-y(2)) orbital. A systematic study of DFT functionals and basis sets was undertaken to examine the ability to reproduce the experimentally determined spin Hamiltonian parameters. Inclusion of spin-orbit coupling (SOC) using MAG-ReSpect or ORCA with a BHLYP/IGLO-II Wachters setup with SOC corrections and ∼38% Hartree-Fock exchange gave the best predictions of the g and A((63)Cu) matrices. DFT calculations of the (14)N hyperfine and quadrupole parameters for the distal nitrogens of the coordinated heterocyclic

  20. Effect of gambierol and its tetracyclic and heptacyclic analogues in cultured cerebellar neurons: a structure-activity relationships study.

    PubMed

    Pérez, Sheila; Vale, Carmen; Alonso, Eva; Fuwa, Haruhiko; Sasaki, Makoto; Konno, Yu; Goto, Tomomi; Suga, Yuto; Vieytes, Mercedes R; Botana, Luis M

    2012-09-17

    The polycyclic ether class of marine natural products has attracted the attention of researchers due to their complex and large chemical structures and diverse biological activities. Gambierol is a marine polycyclic ether toxin, first isolated along with ciguatoxin congeners from the dinoflagellate Gambierdiscus toxicus. The parent compound gambierol and the analogues evaluated in this work share the main crucial elements for biological activity, previously described to be the C28=C29 double bond within the H ring and the unsaturated side chain [Fuwa, H., Kainuma, N., Tachibana, K., Tsukano, C., Satake, M., and Sasaki, M. (2004) Diverted total synthesis and biological evaluation of gambierol analogues: Elucidation of crucial structural elements for potent toxicity. Chem. Eur. J. 10, 4894-4909]. With the aim to gain a deeper understanding of the cellular mechanisms involved in the biological activity of these compounds, we compared its activity in primary cultured neurons. The three compounds inhibited voltage-gated potassium channels (Kv) in a concentration-dependent manner and with similar potency, caused a small inhibition of voltage-gated sodium channels (Nav), and evoked cytosolic calcium oscillations. Moreover, the three compounds elicited a "loss of function" effect on Kv channels at concentrations of 0.1 nM. Additionally, both the tetracyclic and the heptacyclic derivatives of gambierol elicited synchronous calcium oscillations similar to those previously described for gambierol in cultured cerebellar neurons. Neither gambierol nor its tetracyclic derivative elicited cell toxicity, while the heptacyclic analogue caused a time-dependent decrease in cell viability. Neither the tetracyclic nor the heptacyclic analogues of gambierol exhibited lethality in mice after ip injection of 50 or 80 μg/kg of each compound. Altogether, the results presented in this work support an identical mechanism of action for gambierol and its tetracyclic and heptacyclic analogues

  1. Parrots as key multilinkers in ecosystem structure and functioning.

    PubMed

    Blanco, Guillermo; Hiraldo, Fernando; Rojas, Abraham; Dénes, Francisco V; Tella, José L

    2015-09-01

    Mutually enhancing organisms can become reciprocal determinants of their distribution, abundance, and demography and thus influence ecosystem structure and dynamics. In addition to the prevailing view of parrots (Psittaciformes) as plant antagonists, we assessed whether they can act as plant mutualists in the dry tropical forest of the Bolivian inter-Andean valleys, an ecosystem particularly poor in vertebrate frugivores other than parrots (nine species). We hypothesised that if interactions between parrots and their food plants evolved as primarily or facultatively mutualistic, selection should have acted to maximize the strength of their interactions by increasing the amount and variety of resources and services involved in particular pairwise and community-wide interaction contexts. Food plants showed different growth habits across a wide phylogenetic spectrum, implying that parrots behave as super-generalists exploiting resources differing in phenology, type, biomass, and rewards from a high diversity of plants (113 species from 38 families). Through their feeding activities, parrots provided multiple services acting as genetic linkers, seed facilitators for secondary dispersers, and plant protectors, and therefore can be considered key mutualists with a pervasive impact on plant assemblages. The number of complementary and redundant mutualistic functions provided by parrots to each plant species was positively related to the number of different kinds of food extracted from them. These mutually enhancing interactions were reflected in species-level properties (e.g., biomass or dominance) of both partners, as a likely consequence of the temporal convergence of eco-(co)evolutionary dynamics shaping the ongoing structure and organization of the ecosystem. A full assessment of the, thus far largely overlooked, parrot-plant mutualisms and other ecological linkages could change the current perception of the role of parrots in the structure, organization, and

  2. Information Theoretic Secret Key Generation: Structured Codes and Tree Packing

    ERIC Educational Resources Information Center

    Nitinawarat, Sirin

    2010-01-01

    This dissertation deals with a multiterminal source model for secret key generation by multiple network terminals with prior and privileged access to a set of correlated signals complemented by public discussion among themselves. Emphasis is placed on a characterization of secret key capacity, i.e., the largest rate of an achievable secret key,…

  3. Exploring Microstructural Changes in Structural Analogues of Ibuprofen-Hosted In Situ Gelling System and Its Influence on Pharmaceutical Performance.

    PubMed

    Patil, Sharvil S; Venugopal, Edakkal; Bhat, Suresh; Mahadik, Kakasaheb R; Paradkar, Anant R

    2015-10-01

    The present work explores inner structuration of in situ gelling system consisting of glyceryl monooleate (GMO) and oleic acid (OA). The system under study involves investigation of microstructural changes which are believed to govern the pharmaceutical performance of final formulation. The changes which are often termed mesophasic transformation were analysed by small angle X-ray scattering (SAXS), differential scanning calorimetry (DSC), rheology and plane polarised light (PPL) microscopy. The current work revealed transformation of blank system from W/O emulsion to reverse hexagonal structure upon addition of structural analogues of ibuprofen. Such transformations are believed to occur due to increased hydrophobic volume within system as probed by SAXS analysis. The findings of SAXS studies were well supported by DSC, rheology and PPL microscopy. The study established inverse relationship between log P value of structural analogues of ibuprofen and the degree of binding of water molecules to surfactant chains. Such relationship had pronounced effect on sol-gel transformation process. The prepared in situ gelling system showed sustained drug release which followed Higuchi model. PMID:25716330

  4. Structural differences in diarylheptanoids analogues from Alnus viridis and Alnus glutinosa influence their activity and selectivity towards cancer cells.

    PubMed

    Dinić, Jelena; Novaković, Miroslav; Podolski-Renić, Ana; Vajs, Vlatka; Tešević, Vele; Isaković, Aleksandra; Pešić, Milica

    2016-04-01

    Diarylheptanoids represent a group of plant secondary metabolites that possess multiple biological properties and are increasingly recognized for their therapeutic potential. A comparative study was performed on structurally analogous diarylheptanoids isolated from the bark of green (Alnus viridis) and black alder (Alnus glutinosa) to address their biological effects and determine structure-activity relationship. The structures and configurations of all compounds were elucidated by NMR, HR-ESI-MS, UV and IR. Diarylheptanoids actions were studied in human non-small cell lung carcinoma cells (NCI-H460) and normal keratinocytes (HaCaT). A. viridis compounds 3v, 5v, 8v and 9v that possess a carbonyl group at C-3 were considerably more potent than compounds without this group. A. viridis/A. glutinosa analogue pairs, 5v/5g and 9v/9g, which differ in the presence of 3' and 3″-OH groups, were evaluated for anticancer activity and selectivity. 5v and 9v that do not possess 3' and 3″-OH groups showed significantly higher cytotoxicity compared to analogues 5g and 9g. In addition, these two A. viridis compounds induced a more prominent apoptosis in both cell lines and an increase in subG0 cell cycle phase, compared to their A. glutinosa analogues. 5v and 9v treatment triggered intracellular superoxide anion accumulation and notably decreased mitochondrial transmembrane potential. In HaCaT cells, 9v and 9g with a 4,5 double bond caused a more prominent loss of mitochondrial transmembrane potential compared to 5v and 5g which possess a 5-methoxy group instead. Although green alder diarylheptanoids 5v and 9v displayed higher cytotoxicity, their analogues from black alder 5g and 9g could be more favorable for therapeutic use since they were more active in cancer cells than in normal keratinocytes. These results indicate that minor differences in the chemical structure can greatly influence the effect of diarylheptanoids on apoptosis and redox status and determine their

  5. Constrained nucleoside analogues - Crystal and molecular structure of 6,5‧-O-anhydrouridines fixed in the anti conformation

    NASA Astrophysics Data System (ADS)

    Gajda, Roman; Bagiński, Maciej; Tomczyk, Ewelina; Mieczkowski, Adam; Woźniak, Krzysztof

    2015-10-01

    A series of analogues of anhydrouridine have been synthesized and their crystal structures established using X-ray diffraction. For all cases, the ribose ring has O(4‧)-exo, C(4‧)-endo pucker and the pyrimidine base is in the anti conformation. Investigated compounds crystallize in different crystal systems (monoclinic, orthorhombic), have different space group symmetry (P21, P212121) and exhibit different intermolecular interactions (halogen and hydrogen bonds) among molecules in their crystal lattices. Moreover, in the case of the 5-benzyl-6,5‧-O-anhydrouridine a significant positional disorder is present with the phenyl rings existing in two orientations.

  6. Comparison of the structural stability and dynamic properties of recombinant anthrax protective antigen and its 2-fluorohistidine-labeled analogue.

    PubMed

    Hu, Lei; Joshi, Sangeeta B; Andra, Kiran K; Thakkar, Santosh V; Volkin, David B; Bann, James G; Middaugh, C Russell

    2012-11-01

    Protective antigen (PA) is the primary protein antigenic component of both the currently used anthrax vaccine and related recombinant vaccines under development. An analogue of recombinant PA (2-FHis rPA) has been recently shown to block the key steps of pore formation in the process of inducing cytotoxicity in cells, and thus can potentially be used as an antitoxin or a vaccine. This rPA analogue was produced by fermentation to incorporate the unnatural amino acid 2-fluorohistidine (2-FHis). In this study, the effects of 2-FHis labeling on rPA antigen's conformational stability and dynamic properties were investigated by various biophysical techniques. Temperature/pH stability profiles of rPA and 2-FHis rPA were analyzed by the empirical phase diagram (EPD) approach, and physical stability differences between them were identified. Results showed that rPA and 2-FHis rPA had similar stability at pH 7-8. With decreasing solution pH, however, 2-FHis rPA was found to be more stable. Dynamic sensitive measurements of the two proteins at pH 5 found that 2-FHis rPA was more dynamic and/or differentially hydrated under acidic pH conditions. The biophysical characterization and stability data provide information useful for the potential development of 2-FHis rPA as a more stable rPA vaccine candidate. PMID:22911632

  7. The Crystal Structure of the Leishmania major Deoxyuridine Triphosphate Nucleotidohydrolase in Complex with Nucleotide Analogues, dUMP, and Deoxyuridine*

    PubMed Central

    Hemsworth, Glyn R.; Moroz, Olga V.; Fogg, Mark J.; Scott, Benjamin; Bosch-Navarrete, Cristina; González-Pacanowska, Dolores; Wilson, Keith S.

    2011-01-01

    Members of the Leishmania genus are the causative agents of the life-threatening disease leishmaniasis. New drugs are being sought due to increasing resistance and adverse side effects with current treatments. The knowledge that dUTPase is an essential enzyme and that the all α-helical dimeric kinetoplastid dUTPases have completely different structures compared with the trimeric β-sheet type dUTPase possessed by most organisms, including humans, make the dimeric enzymes attractive drug targets. Here, we present crystal structures of the Leishmania major dUTPase in complex with substrate analogues, the product dUMP and a substrate fragment, and of the homologous Campylobacter jejuni dUTPase in complex with a triphosphate substrate analogue. The metal-binding properties of both enzymes are shown to be dependent upon the ligand identity, a previously unseen characteristic of this family. Furthermore, structures of the Leishmania enzyme in the presence of dUMP and deoxyuridine coupled with tryptophan fluorescence quenching indicate that occupation of the phosphate binding region is essential for induction of the closed conformation and hence for substrate binding. These findings will aid in the development of dUTPase inhibitors as potential new lead anti-trypanosomal compounds. PMID:21454646

  8. Effects of adenosine, adenosine triphosphate and structural analogues on glucagon secretion from the perfused pancreas of rat in vitro.

    PubMed Central

    Chapal, J.; Loubatières-Mariani, M. M.; Roye, M.; Zerbib, A.

    1984-01-01

    The effects of adenosine, adenosine triphosphate (ATP) and structural analogues have been studied on glucagon secretion from the isolated perfused pancreas of the rat in the presence of glucose (2.8 mM). Adenosine induced a transient increase of glucagon secretion. This effect was concentration-dependent in the range of 0.165 to 165 microM. ATP also induced an increase, but the effect was no greater at 165 microM than at 16.5 microM. 2-Chloroadenosine, an analogue more resistant to metabolism or uptake systems than adenosine, was more effective. Among the three structural analogues of ATP or ADP studied, beta, gamma-methylene ATP which can be hydrolyzed into AMP and adenosine had an effect similar to adenosine or ATP at the same concentrations (1.65 and 16.5 microM); in contrast alpha, beta-methylene ATP and alpha, beta-methylene ADP (resistant to hydrolysis into AMP and adenosine) were ineffective. Theophylline (50 microM) a specific blocker of the adenosine receptor, suppressed the glucagon peak induced by adenosine, 2-chloroadenosine, ATP and beta, gamma-methylene ATP (1.65 microM). An inhibitor of 5' nucleotidase, alpha, beta-methylene ADP (16.5 microM), reduced the glucagon increase induced by ATP and did not affect the response to adenosine (1.65 microM). These results support the hypothesis of adenosine receptors (P1-purinoceptors) on the pancreatic glucagon secretory cells and indicate that ATP acts after hydrolysis to adenosine. PMID:6097328

  9. Three-dimensional quantitative structure-activity relationship study on antioxidant capacity of curcumin analogues

    NASA Astrophysics Data System (ADS)

    Chen, Bohong; Zhu, Zhibo; Chen, Min; Dong, Wenqi; Li, Zhen

    2014-03-01

    A comparative molecular similarity indices analysis (CoMSIA) was performed on a set of 27 curcumin-like diarylpentanoid analogues with the radical scavenging activities. A significant cross-validated correlation coefficient Q2 (0.784), SEP (0.042) for CoMSIA were obtained, indicating the statistical significance of the correlation. Further we adopt a rational approach toward the selection of substituents at various positions in our scaffold,and finally find the favored and disfavoured regions for the enhanced antioxidative activity. The results have been used as a guide to design compounds that, potentially, have better activity against oxidative damage.

  10. Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.

    PubMed

    Mir, Aamir; Golden, Barbara L

    2016-02-01

    The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid. PMID:26551631

  11. 3CAPS – a structural AP–site analogue as a tool to investigate DNA base excision repair

    PubMed Central

    Schuermann, David; Scheidegger, Simon P.; Weber, Alain R.; Bjørås, Magnar; Leumann, Christian J.; Schär, Primo

    2016-01-01

    Abasic sites (AP-sites) are frequent DNA lesions, arising by spontaneous base hydrolysis or as intermediates of base excision repair (BER). The hemiacetal at the anomeric centre renders them chemically reactive, which presents a challenge to biochemical and structural investigation. Chemically more stable AP-site analogues have been used to avoid spontaneous decay, but these do not fully recapitulate the features of natural AP–sites. With its 3′–phosphate replaced by methylene, the abasic site analogue 3CAPS was suggested to circumvent some of these limitations. Here, we evaluated the properties of 3CAPS in biochemical BER assays with mammalian proteins. 3CAPS-containing DNA substrates were processed by APE1, albeit with comparably poor efficiency. APE1-cleaved 3CAPS can be extended by DNA polymerase β but repaired only by strand displacement as the 5′–deoxyribophosphate (dRP) cannot be removed. DNA glycosylases physically and functionally interact with 3CAPS substrates, underlining its structural integrity and biochemical reactivity. The AP lyase activity of bifunctional DNA glycosylases (NTH1, NEIL1, FPG), however, was fully inhibited. Notably, 3CAPS-containing DNA also effectively inhibited the activity of bifunctional glycosylases on authentic substrates. Hence, the chemically stable 3CAPS with its preserved hemiacetal functionality is a potent tool for BER research and a potential inhibitor of bifunctional DNA glycosylases. PMID:26733580

  12. Quantitative structure-activity analysis of acetylcholinesterase inhibition by oxono and thiono analogues of organophosphorus compounds. (Reannouncement with new availability information)

    SciTech Connect

    Maxwell, D.M.; Brecht, K.M.

    1992-02-01

    A comparison of the bimolecular rate constants (ki) for inhibition of electric eel acetylcholinesterase (AChE) by the oxono (i.e., P=O) and thiono (i.e., P=S) analogues of parathion, methylparathion, leptophos, fonofos, sarin, and soman revealed that the oxono/thiono ratios of ki values varied from 14 for soman to 1240 for parathion. Analysis of the relative importance of the dissociation equilibrium constant and the phosphorylation rate constant in producing this variation in ki values indicated that the oxono analogues had phosphorylation rate constant values that varied in a narrow range from 8- to 14-fold greater than their thiono counterparts, while the oxono/thiono ratios for dissociation constants varied widely from 1 for soman to 82 for fonofos. The lower affinities of thiono analogues for AChE probably resulted from differences in the hydrophobic binding of oxono and thiono analogues to the active site of AChE, inasmuch as the hydrophobicities (i.e., octanol/water partition coefficients) of thiono organophosphorus compounds were much greater than the hydrophobicities of their oxono analogues. Quantitative structure-activity analysis indicated that the hydrophobic effects of oxono and thiono moieties correlated with log ki for AChE inhibition to a greater extent (r2 = 0.79) than their electronic effects (r2 equal to or less than 0.48). These observations suggest that the differences in hydrophobicity of oxono and thiono analogues of organophosphorus compounds may be as important as their electronic differences in determining their effectiveness as AChE inhibitors. Acetylcholinesterase, soman (GD), structure-activity analysis inhibition, oxono analogues, thiono analogues.

  13. A 4D Analogue Modeling Study Assessing the Effects of Transtension and Inherited Structures on Rift Interaction

    NASA Astrophysics Data System (ADS)

    Zwaan, F.; Schreurs, G.; Naliboff, J.; Buiter, S. J.

    2015-12-01

    The interaction of individual rift segments determines the evolution of a rift system and subsequent continental break-up. Inherited heterogeneities control where initial rifts will form and since these are often not properly aligned, rift segments form separately and need to interact. Another important factor affecting rift-segment interaction is the obliquity of plate divergence (transtension), which also promotes eventual continent break-up (Brune et al., 2012). Both analogue and numerical techniques have been used to model rift interaction (e.g. Acocella et al., 1999; Allken et al., 2012) but transtension has never been applied. Here we present a first-order analogue study that elaborates upon earlier studies by assessing the effects of (1) transtension, (2) rift offset and (3) presence and geometry of inherited weak zones that link rift segments. An improved analogue set-up allows more freedom in inherited structure geometry and model analysis with X-Ray Computer Tomography (CT) techniques reveals internal structures with time (Fig. 2 and 3). Our experiments yield the following conclusions: Increasing the degree of transtension (decreasing angle α in Fig. 1) controls general rift structures: from wide rifts in orthogonal divergence settings to narrower rifts with oblique internal structures under transtensional conditions to narrow strike-slip dominated systems towards the strike-slip domain; Rift linkage through transfer zones (hard linkage) is generally promoted by 1) decreasing rift offset and 2) increasing the degree of transtension. However, initial rift linkage might involve relay ramps (soft linkage) due to the interplay of divergence direction and rift offset; Inherited rift-linking weak zones have little effect on rift interaction unless they are oriented ca. perpendicular to the divergence direction; Since the orthogonal divergence models resemble natural examples (Fig. 3), our transtension models might predict what structures can be expected in

  14. Crystal Structure of Baeyer-Villiger Monooxygenase MtmOIV, the Key Enzyme of the Mithramycin Biosynthetic Pathway†

    PubMed Central

    Beam, Miranda P.; Bosserman, Mary A.; Noinaj, Nicholas; Wehenkel, Marie; Rohr, Jürgen

    2009-01-01

    Baeyer-Villiger monooxygenases (BVMOs), mostly flavoproteins, were shown to be powerful biocatalysts for synthetic organic chemistry applications and were also suggested to play key roles for the biosyntheses of various natural products. Here we present the three-dimensional structure of MtmOIV, a 56 kD homo-dimeric FAD- and NADPH-dependent monooxygenase, which catalyzes the key frame-modifying step of the mithramycin biosynthetic pathway and currently the only BVMO proven to react with its natural substrate via a Baeyer-Villiger reaction. MtmOIV’s structure was determined by X-ray crystallography using molecular replacement to a resolution of 2.9Å. MtmOIV cleaves a C-C bond, essential for the conversion of the biologically inactive precursor, premithramycin B, into the active drug mithramycin. The MtmOIV structure combined with substrate docking calculations and site-directed mutagenesis experiments implicate several residues to participate in co-factor and substrate binding. Future experimentation aimed at broadening the substrate specificity of the enzyme could facilitate the generation of chemically diverse mithramycin analogues through combinatorial biosynthesis. PMID:19364090

  15. Crystal structure of Baeyer-Villiger monooxygenase MtmOIV, the key enzyme of the mithramycin biosynthetic pathway .

    PubMed

    Beam, Miranda P; Bosserman, Mary A; Noinaj, Nicholas; Wehenkel, Marie; Rohr, Jürgen

    2009-06-01

    Baeyer-Villiger monooxygenases (BVMOs), mostly flavoproteins, were shown to be powerful biocatalysts for synthetic organic chemistry applications and were also suggested to play key roles for the biosyntheses of various natural products. Here we present the three-dimensional structure of MtmOIV, a 56 kDa homodimeric FAD- and NADPH-dependent monooxygenase, which catalyzes the key frame-modifying step of the mithramycin biosynthetic pathway and currently the only BVMO proven to react with its natural substrate via a Baeyer-Villiger reaction. MtmOIV's structure was determined by X-ray crystallography using molecular replacement to a resolution of 2.9 A. MtmOIV cleaves a C-C bond, essential for the conversion of the biologically inactive precursor, premithramycin B, into the active drug mithramycin. The MtmOIV structure combined with substrate docking calculations and site-directed mutagenesis experiments identifies several residues that participate in cofactor and substrate binding. Future experimentation aimed at broadening the substrate specificity of the enzyme could facilitate the generation of chemically diverse mithramycin analogues through combinatorial biosynthesis. PMID:19364090

  16. Crystal Structure of Baeyer−Villiger Monooxygenase MtmOIV, the Key Enzyme of the Mithramycin Biosynthetic Pathway

    SciTech Connect

    Beam, Miranda P.; Bosserman, Mary A.; Noinaj, Nicholas; Wehenkel, Marie; Rohr, Jurgen; Kentucky

    2009-06-01

    Baeyer-Villiger monooxygenases (BVMOs), mostly flavoproteins, were shown to be powerful biocatalysts for synthetic organic chemistry applications and were also suggested to play key roles for the biosyntheses of various natural products. Here we present the three-dimensional structure of MtmOIV, a 56 kDa homodimeric FAD- and NADPH-dependent monooxygenase, which catalyzes the key frame-modifying step of the mithramycin biosynthetic pathway and currently the only BVMO proven to react with its natural substrate via a Baeyer-Villiger reaction. MtmOIV's structure was determined by X-ray crystallography using molecular replacement to a resolution of 2.9 A. MtmOIV cleaves a C-C bond, essential for the conversion of the biologically inactive precursor, premithramycin B, into the active drug mithramycin. The MtmOIV structure combined with substrate docking calculations and site-directed mutagenesis experiments identifies several residues that participate in cofactor and substrate binding. Future experimentation aimed at broadening the substrate specificity of the enzyme could facilitate the generation of chemically diverse mithramycin analogues through combinatorial biosynthesis.

  17. Structure-based design, synthesis and preliminary anti-inflammatory activity of bolinaquinone analogues.

    PubMed

    Petronzi, Carmen; Filosa, Rosanna; Peduto, Antonella; Monti, Maria Chiara; Margarucci, Luigi; Massa, Antonio; Ercolino, Simona Francesca; Bizzarro, Valentina; Parente, Luca; Riccio, Raffaele; de Caprariis, Paolo

    2011-02-01

    As a part of our drug discovery efforts we developed a series of simplified derivatives of bolinaquinone (BLQ), a hydroxyquinone marine metabolite, showing potent anti-inflammatory activity. Thirteen new hydroxyquinone derivatives closely related to BLQ were synthesized and tested on mouse macrophage-like RAW 264.7 cell line in order to investigate their ability to modulate the production of Prostaglandin E2 (PGE2). This optimization process led to the identification of three strictly correlated compounds with comparable and higher inhibitory potency than BLQ on PGE2 production. To evaluate the affinity of BLQ and its analogues for hsPLA2, surface plasmon resonance (SPR) experiments were performed. PMID:21163556

  18. Valles Marineris as a Cryokarstic Structure Formed by a Giant Dyke System: Support From New Analogue Experiments

    NASA Astrophysics Data System (ADS)

    Ozeren, M. S.; Sengor, A. M. C.; Acar, D.; Ülgen, S. C.; Onsel, I. E.

    2014-12-01

    Valles Marineris is the most significant near-linear depression on Mars. It is some 4000 km long, up to about 200 km wide and some 7 km deep. Although its margins look parallel at first sight, the entire structure has a long spindle shape with significant enlargement in its middle (Melas Chasma) caused by cuspate slope retreat mechanisms. Farther to its north is Hebes Chasma which is an entirely closed depression with a more pronounced spindle shape. Tithonium Chasma is a parallel, but much narrower depression to its northeast. All these chasmae have axes parallel with one another and such structures occur nowhere else on Mars. A scabland surface exists to the east of the Valles Marineris and the causative water mass seems to have issued from it. The great resemblance of these chasmae on mars to poljes in the karstic regions on earth have led us to assume that they owed their existence to dissolution of rock layers underlying them. We assumed that the dissolving layer consisted of water ice forming substantial layers, in fact entirely frozen seas of several km depth. We have simulated this geometry by using bentonite and flour layers (in different experiments) overlying layers of ice in which a resistant coil was used to simulate a dyke. We used different thicknesses of bentonite and flour overlying ice layers again of various thicknesses. The flour seems to simulate the Martian crust better because on Mars, g is only about 3/8ths of its value on Earth, so (for equal crustal density) the depth to which the cohesion term C remains important in the Mohr-Coulomb shear failure criterion is about 8/3 times greater. As examples we show two of those experiments in which both the rock analogue and ice layers were of 1.5 cm. thick. Perfect analogues of the Valles Marineris formed above the dyke analogue thermal source complete with the near-linear structure, overall flat spindle shape, cuspate margins, a central ridge, parallel side faults, parallel depressions resembling

  19. Modified Method of rRNA Structure Analysis Reveals Novel Characteristics of Box C/D RNA Analogues.

    PubMed

    Filippova, J A; Stepanov, G A; Semenov, D V; Koval, O A; Kuligina, E V; Rabinov, I V; Richter, V A

    2015-01-01

    Ribosomal RNA (rRNA) maturation is a complex process that involves chemical modifications of the bases or sugar residues of specific nucleotides. One of the most abundant types of rRNA modifications, ribose 2'-O-methylation, is guided by ribonucleoprotein complexes containing small nucleolar box C/D RNAs. Since the majority of 2'-O-methylated nucleotides are located in the most conserved regions of rRNA that comprise functionally important centers of the ribosome, an alteration in a 2'-O-methylation profile can affect ribosome assembly and function. One of the key approaches for localization of 2'-O-methylated nucleotides in long RNAs is a method based on the termination of reverse transcription. The current study presents an adaptation of this method for the use of fluorescently labeled primers and analysis of termination products by capillary gel electrophoresis on an automated genetic analyzer. The developed approach allowed us to analyze the influence of the synthetic analogues of box C/D RNAs on post-transcriptional modifications of human 28S rRNA in MCF-7 cells. It has been established that the transfection of MCF-7 cells with a box C/D RNA analogue leads to an enhanced modification level of certain native sites of 2'-O-methylation in the target rRNA. The observed effect of synthetic RNAs on the 2'-O-methylation of rRNA in human cells demonstrates a path towards targeted regulation of rRNA post-transcriptional maturation. The described approach can be applied in the development of novel diagnostic methods for detecting diseases in humans. PMID:26085946

  20. An analogue-sensitive approach identifies basal body rotation and flagellum attachment zone elongation as key functions of PLK in Trypanosoma brucei

    PubMed Central

    Lozano-Núñez, Ana; Ikeda, Kyojiro N.; Sauer, Thomas; de Graffenried, Christopher L.

    2013-01-01

    Polo-like kinases are important regulators of cell division, playing diverse roles in mitosis and cytoskeletal inheritance. In the parasite Trypanosoma brucei, the single PLK homologue TbPLK is necessary for the assembly of a series of essential organelles that position and adhere the flagellum to the cell surface. Previous work relied on RNA interference or inhibitors of undefined specificity to inhibit TbPLK, both of which have significant experimental limitations. Here we use an analogue-sensitive approach to selectively and acutely inhibit TbPLK. T. brucei cells expressing only analogue-sensitive TbPLK (TbPLKas) grow normally, but upon treatment with inhibitor develop defects in flagellar attachment and cytokinesis. TbPLK cannot migrate effectively when inhibited and remains trapped in the posterior of the cell throughout the cell cycle. Using synchronized cells, we show that active TbPLK is a direct requirement for the assembly and extension of the flagellum attachment zone, which adheres the flagellum to the cell surface, and for the rotation of the duplicated basal bodies, which positions the new flagellum so that it can extend without impinging on the old flagellum. This approach should be applicable to the many kinases found in the T. brucei genome that lack an ascribed function. PMID:23447704

  1. Titan's organic aerosols: Molecular composition and structure of laboratory analogues inferred from pyrolysis gas chromatography mass spectrometry analysis

    NASA Astrophysics Data System (ADS)

    Morisson, Marietta; Szopa, Cyril; Carrasco, Nathalie; Buch, Arnaud; Gautier, Thomas

    2016-10-01

    Analogues of Titan's aerosols are of primary interest in the understanding of Titan's atmospheric chemistry and climate, and in the development of in situ instrumentation for future space missions. Numerous studies have been carried out to characterize laboratory analogues of Titan aerosols (tholins), but their molecular composition and structure are still poorly known. If pyrolysis gas chromatography mass spectrometry (pyr-GCMS) has been used for years to give clues about their chemical composition, highly disparate results were obtained with this technique. They can be attributed to the variety of analytical conditions used for pyr-GCMS analyses, and/or to differences in the nature of the analogues analyzed, that were produced with different laboratory set-ups under various operating conditions. In order to have a better description of Titan's tholin's molecular composition by pyr-GCMS, we carried out a systematic study with two major objectives: (i) exploring the pyr-GCMS analytical parameters to find the optimal ones for the detection of a wide range of chemical products allowing a characterization of the tholins composition as comprehensive as possible, and (ii) highlighting the role of the CH4 ratio in the gaseous reactive medium on the tholin's molecular structure. We used a radio-frequency plasma discharge to synthetize tholins with different concentrations of CH4 diluted in N2. The samples were pyrolyzed at temperatures covering the 200-700°C range. The extracted gases were then analyzed by GCMS for their molecular identification. The optimal pyrolysis temperature for characterizing the molecular composition of our tholins by GCMS analysis is found to be 600°C. This temperature choice results from the best compromise between the number of compounds released, the quality of the signal and the appearance of pyrolysis artifacts. About a hundred molecules are identified as pyrolysates. A common major chromatographic pattern appears clearly for all the

  2. Heterogeneous Diastereoselective Catalysis--A Powerful Strategy Toward C(15) Stereoselectivity from PGF2α Analogues Structure.

    PubMed

    Coman, Simona M; Parvulescu, Vasile I

    2015-01-01

    A major trend in fine chemicals and pharmaceuticals is the synthesis of molecules with increased complexity. This trend translates the aim of organic syntheses to conditions in which high degrees of chemo-, regio- and stereoselectivity can be provided. In this context, the chemoselective hydrogenation of one functional group in the presence of other reactive groups is a frequently encountered problem in fine chemicals manufacture. This study provides a critical analysis including elegant examples of reactions in which high chemo- and diastereoselectivities were achieved in the hydrogenation of a C=O group in the presence of C=C double bond. A particular emphasis is addressed to the stereoselective C(15) synthesis from Cloprostenol--a PGF2α structural analogue. PMID:26553252

  3. Improved thrombin binding aptamer analogues containing inversion of polarity sites: structural effects of extra-residues at the ends.

    PubMed

    Virgilio, A; Amato, T; Petraccone, L; Filosa, R; Varra, M; Mayol, L; Esposito, V; Galeone, A

    2016-08-10

    In this paper, we report the investigations, based on NMR, molecular modelling, CD measurements and electrophoresis, of thrombin binding aptamer (TBA) analogues containing an extra-residue at the 3'-end or at both the ends of the original TBA sequence, linked through 3'-3' or 5'-5' phosphodiester bonds. The data indicate that most of the modified aptamers investigated adopt chair-like G-quadruplex structures very similar to that of the TBA and that stacking interactions occur between the 3'-3' or 5'-5' extra residues and the deoxyguanosines of the upper G-tetrad. A comparison of the thermodynamic data of TBA-A and TBA-T containing a 3'-3' extra residue and their canonical versions clearly indicates that the 3'-3' phosphodiester bond is fundamental in endowing the modified aptamers with remarkably higher thermal stabilities than the original TBA. PMID:27461474

  4. Kinetic, thermodynamic and X-ray structural insights into the interaction of melatonin and analogues with quinone reductase 2

    SciTech Connect

    Calamini, Barbara; Santarsiero, Bernard D.; Boutin, Jean A.; Mesecar, Andrew D.

    2008-09-12

    Melatonin exerts its biological effects through at least two transmembrane G-protein-coupled receptors, MT1 and MT2, and a lower-affinity cytosolic binding site, designated MT3. MT3 has recently been identified as QR2 (quinone reductase 2) (EC 1.10.99.2) which is of significance since it links the antioxidant effects of melatonin to a mechanism of action. Initially, QR2 was believed to function analogously to QR1 in protecting cells from highly reactive quinones. However, recent studies indicate that QR2 may actually transform certain quinone substrates into more highly reactive compounds capable of causing cellular damage. Therefore it is hypothesized that inhibition of QR2 in certain cases may lead to protection of cells against these highly reactive species. Since melatonin is known to inhibit QR2 activity, but its binding site and mode of inhibition are not known, we determined the mechanism of inhibition of QR2 by melatonin and a series of melatonin and 5-hydroxytryptamine (serotonin) analogues, and we determined the X-ray structures of melatonin and 2-iodomelatonin in complex with QR2 to between 1.5 and 1.8 {angstrom} (1 {angstrom} = 0.1 nm) resolution. Finally, the thermodynamic binding constants for melatonin and 2-iodomelatonin were determined by ITC (isothermal titration calorimetry). The kinetic results indicate that melatonin is a competitive inhibitor against N-methyldihydronicotinamide (K{sub i} = 7.2 {mu}M) and uncompetitive against menadione (K{sub i} = 92 {mu}M), and the X-ray structures shows that melatonin binds in multiple orientations within the active sites of the QR2 dimer as opposed to an allosteric site. These results provide new insights into the binding mechanisms of melatonin and analogues to QR2.

  5. Structures and synthesis of framework Rb and Cs uranyl arsenates and their relationships with their phosphate analogues

    NASA Astrophysics Data System (ADS)

    Locock, Andrew J.; Burns, Peter C.

    2003-11-01

    Two hydrated uranyl arsenates, Cs 2(UO 2)[(UO 2)(AsO 4)] 4(H 2O) 2 ( CsUAs) and Rb 2(UO 2)[(UO 2)(AsO 4)] 4(H 2O) 4.5 ( RbUAs), were synthesized by hydrothermal methods. Intensity data were collected at room temperature using Mo Kα radiation and a CCD-based area detector. The crystal structure of RbUAs was solved by direct methods, whereas the structure model of the phosphate Cs 2(UO 2)[(UO 2)(PO 4)] 4(H 2O) 2 was used for CsUAs; both were refined by full-matrix least-squares techniques on the basis of F2 to agreement indices ( CsUAs, RbUAs) w R2=0.061,0.041, for all data, and R1=0.032,0.021, calculated for 5098, 4991 unique observed reflections (| Fo|>4 σF), respectively. The compound CsUAs is orthorhombic, space group Cmc2 1, Z=4, a=15.157(2), b=14.079(2), c=13.439(2) Å, V=2867.9(1) Å 3. RbUAs is monoclinic, space group C2/ m, Z=4, a=13.4619(4), b=15.8463(5), c=14.0068(4) Å, β=92.311(1)°, V=2985.52(2) Å 3. The structures consist of sheets of arsenate tetrahedra and uranyl pentagonal bipyramids, with composition [(UO 2)(AsO 4)] -, that are topologically identical to the uranyl silicate sheets in uranophane-beta. These sheets are connected by a uranyl pentagonal bipyramid in the interlayer that shares corners with two arsenate tetrahedra on each of two adjacent sheets and whose fifth equatorial vertex is an H 2O group, resulting in an open framework with alkali metal cations in the larger cavities of the structures. CsUAs is isostructural with its phosphate analogue, and has two Cs atoms and a H 2O group in its structural cavities. RbUAs is not isostructural with its phosphate analogue, although it has a homeotypic framework. Its structural cavities are occupied by three Rb atoms and four H 2O groups; one Rb position and three of the interstitial H 2O groups are half-occupied. The partial occupancies of these positions probably result from the accommodation of the larger As atoms (relative to P) in the framework and resultant larger cavities.

  6. Synthesis, biological activities and structure-activity relationships for new avermectin analogues.

    PubMed

    Zhang, Jian; Nan, Xiang; Yu, Hai-Tao; Cheng, Pi-Le; Zhang, Yan; Liu, Ying-Qian; Zhang, Shao-Yong; Hu, Guan-Fang; Liu, Huanxiang; Chen, An-Liang

    2016-10-01

    In an effort to discover new molecules with good insecticidal activities, more than 40 new avermectin derivatives were synthesized and evaluated for their biological activities against three species of arachnids, insects and nematodes, namely, Tetranychus Cinnabarinus, Aphis craccivora and Bursaphelenchus xylophilus. All the tested compounds showed potent inhibitory activities against three insect species. Notably, the majority of compounds exhibited high selectivity against T. cinnabarinus, some of which were much better in comparison with avermectin. Especially compounds 9j (LC50: 0.005 μM) and 16d (LC50: 0.002 μM) were 2.5- and 4.7-fold more active than avermectin (LC50: 0.013 μM), respectively, against T. cinnabarinus. Moreover, compounds 9b, 9d-f, 9h, 9j, 9l, 9n, 9p, 9r, 9v and 17d showed superior activities with LC50 values of 2.959-5.013 μM compared to that of 1 (LC50: 6.746 μM) against B. xylophilus. Meanwhile, the insecticidal activities of compounds 9f, 9g, 9h, and 9m against A. craccivora were 7-8 times better than that of avermectin, with LC50 values of 7.744, 5.634, 6.809, 7.939 and 52.234 μM, respectively. Furthermore, QSAR analysis showed that the molecular shape, size, connectivity degree and electronic distribution of avermectin analogues had substantial effects on insecticidal potency. These preliminary results provided useful insight in guiding further modifications of avermectin in the development of potential new insecticides. PMID:27318119

  7. The shell model approach: Key to hadron structure

    SciTech Connect

    Lipkin, H.J. . Dept. of Nuclear Physics)

    1989-08-14

    A shell model approach leads to a simple constituent quark model for hadron structure in which mesons and baryons consist only of constituent quarks. Hadron masses are the sums of the constituent quark effective masses and a hyperfine interaction inversely proportional to the product of these same masses. Hadron masses and magnetic moments are related by the assumption that the same effective mass parameter appears in the additive mass term, the hyperfine interaction, and the quark magnetic moment, both in mesons and baryons. The analysis pinpoints the physical assumptions needed for each relation and gives two new mass relations. Application to weak decays and recent polarized EMC data confirms conclusions previously obtained that the current quark contribution to the spin structure of the proton vanishes, but without need for the questionable assumption of SU(3) symmetry relating hyperon decays and proton structure. SU(3) symmetry breaking is clarified. 24 refs.

  8. COMPARATIVE ANALYSIS OF THE ELECTROSTATIC POTENTIALS OF SOME STRUCTURAL ANALOGUES OF 2,3,7,8-TETRACHLORODIBENZO-P-DIOXIN AND OF RELATED AROMATIC SYSTEMS

    EPA Science Inventory

    We have carried out an ab initio STO-5G computational analysis of the electrostatic potential of four structural analogues of the highly toxic 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and four related aromatic systems: benzo[a]pyrene, benz[a]anthracene and two isomeric benzofla...

  9. Modulation of Activity by Arg407: Structure of a Fungal [alpha]-1,2-Mannosidase in Complex with a Substrate Analogue

    SciTech Connect

    Lobsanov,Y.; Yoshida, T.; Desmet, T.; Nerinckx, W.; Yip, P.; Claeyssens, M.; Herscovics, A.; Howell, P.

    2008-01-01

    Class I {alpha}-mannosidases (glycoside hydrolase family GH47) play key roles in the maturation of N-glycans and the ER-associated degradation of unfolded glycoproteins. The 1.95 Angstroms resolution structure of a fungal {alpha}-1,2-mannosidase in complex with the substrate analogue methyl-{alpha}-D-lyxopyranosyl-(1',2)-{alpha}-D-mannopyranoside (LM) shows the intact disaccharide spanning the -1/+1 subsites, with the D-lyxoside ring in the -1 subsite in the 1C4 chair conformation, and provides insight into the mechanism of catalysis. The absence of the C5' hydroxymethyl group on the D-lyxoside moiety results in the side chain of Arg407 adopting two alternative conformations: the minor one interacting with Asp375 and the major one interacting with both the D-lyxoside and the catalytic base Glu409, thus disrupting its function. Chemical modification of Asp375 has previously been shown to inactivate the enzyme. Taken together, the data suggest that Arg407, which belongs to the conserved sequence motif RPExxE, may act to modulate the activity of the enzyme. The proposed mechanism for modulating the activity is potentially a general mechanism for this superfamily.

  10. The structures of thymidine kinase from herpes simplex virus type 1 in complex with substrates and a substrate analogue.

    PubMed Central

    Wild, K.; Bohner, T.; Folkers, G.; Schulz, G. E.

    1997-01-01

    Thymidine kinase from Herpes simplex virus type 1 (TK) was crystallized in an N-terminally truncated but fully active form. The structures of TK complexed with ADP at the ATP-site and deoxythymidine-5'-monophosphate (dTMP), deoxythymidine (dT), or idoxuridine-5'-phosphate (5-iodo-dUMP) at the substrate-site were refined to 2.75 A, 2.8 A, and 3.0 A resolution, respectively. TK catalyzes the phosphorylation of dT resulting in an ester, and the phosphorylation of dTMP giving rise to an anhydride. The presented TK structures indicate that there are only small differences between these two modes of action. Glu83 serves as a general base in the ester reaction. Arg163 parks at an internal aspartate during ester formation and binds the alpha-phosphate of dTMP during anhydride formation. The bound deoxythymidine leaves a 35 A3 cavity at position 5 of the base and two sequestered water molecules at position 2. Cavity and water molecules reduce the substrate specificity to such an extent that TK can phosphorylate various substrate analogues useful in pharmaceutical applications. TK is structurally homologous to the well-known nucleoside monophosphate kinases but contains large additional peptide segments. PMID:9336833

  11. CONSIDERATION OF REACTION INTERMEDIATES IN STRUCTURE-ACTIVITY RELATIONSHIPS: A KEY TO UNDERSTANDING AND PREDICTION

    EPA Science Inventory

    Consideration of Reaction Intermediates in Structure- Activity Relationships: A Key to Understanding and Prediction

    A structure-activity relationship (SAR) represents an empirical means for generalizing chemical information relative to biological activity, and is frequent...

  12. DATA NORMALIZATION : A KEY FOR STRUCTURAL HEALTH MONITORING

    SciTech Connect

    Farrar, C. R.; Sohn, H.; Worden, K.

    2001-01-01

    Structural health monitoring (SHM) is the implementation of a damage detection strategy for aerospace, civil and mechanical engineering infrastructure. Typical damage experienced by this infrastructure might be the development of fatigue cracks, degradation of structural connections, or bearing wear in rotating machinery. For SHM strategies that rely on vibration response measurements, the ability to normalize the measured data with respect to varying operational and environmental conditions is essential if one is to avoid false-positive indications of damage. Examples of common normalization procedure include normalizing the response measurements by the measured inputs as is commonly done when extracting modal parameters. When environmental cycles influence the measured data, a temporal normalization scheme may be employed. This paper will summarize various strategies for performing this data normalization task. These strategies fall into two general classes: (1) Those employed when measures of the varying environmental and operational parameters are available; (2) Those employed when such measures are not available. Whenever data normalization is performed, one runs the risk that the damage sensitive features to be extracted from the data will be obscured by the data normalization procedure. This paper will summarize several normalization procedures that have been employed by the authors and issues that have arose when trying to implement them on experimental and numerical data.

  13. Analysis of Wave Propagation in Stratified Structures Using Circuit Analogues, with Application to Electromagnetic Absorbers

    ERIC Educational Resources Information Center

    Sjoberg, Daniel

    2008-01-01

    This paper presents an overview of how circuit models can be used for analysing wave propagation in stratified structures. Relatively complex structures can be analysed using models which are accessible to undergraduate students. Homogeneous slabs are modelled as transmission lines, and thin sheets between the slabs are modelled as lumped…

  14. Multilevel polarization shift keying: Optimum receiver structure and performance evaluation

    SciTech Connect

    Benedetto, S.; Poggiolini, P.T.

    1994-02-01

    Multilevel digital coherent optical modulation schemes based on the state of polarization of a fully polarized lightwave are proposed and analyzed. Based on the complete statistical characterization of the Stokes parameters, extracted though appropriate signal processing in the presence of shot and additive gaussian noise, the optimum maximum likelihood receiver operating symbol by symbol is derived. The exact performance in terms of the average symbol error probability is found. Optimum constellations for the case of equipower 4, 8, 16 and 32 signals are found on the basis of the minimization of the error probability for a given average power. Their performance turns out to be promising as compared to other standard modulation techniques. The spectral analysis of polarization modulated signals is presented. A new receiver structure, which solves the problem of the excess penalties incurred in the presence of channel dichroism, is proposed and analyzed. 22 refs.

  15. Detecting Key Structural Features within Highly Recombined Genes

    PubMed Central

    Wertz, John E; McGregor, Karen F; Bessen, Debra E

    2007-01-01

    Many microorganisms exhibit high levels of intragenic recombination following horizontal gene transfer events. Furthermore, many microbial genes are subject to strong diversifying selection as part of the pathogenic process. A multiple sequence alignment is an essential starting point for many of the tools that provide fundamental insights on gene structure and evolution, such as phylogenetics; however, an accurate alignment is not always possible to attain. In this study, a new analytic approach was developed in order to better quantify the genetic organization of highly diversified genes whose alleles do not align. This BLAST-based method, denoted BLAST Miner, employs an iterative process that places short segments of highly similar sequence into discrete datasets that are designated “modules.” The relative positions of modules along the length of the genes, and their frequency of occurrence, are used to identify sequence duplications, insertions, and rearrangements. Partial alleles of sof from Streptococcus pyogenes, encoding a surface protein under host immune selection, were analyzed for module content. High-frequency Modules 6 and 13 were identified and examined in depth. Nucleotide sequences corresponding to both modules contain numerous duplications and inverted repeats, whereby many codons form palindromic pairs. Combined with evidence for a strong codon usage bias, data suggest that Module 6 and 13 sequences are under selection to preserve their nucleic acid secondary structure. The concentration of overlapping tandem and inverted repeats within a small region of DNA is highly suggestive of a mechanistic role for Module 6 and 13 sequences in promoting aberrant recombination. Analysis of pbp2X alleles from Streptococcus pneumoniae, encoding cell wall enzymes that confer antibiotic resistance, supports the broad applicability of this tool in deciphering the genetic organization of highly recombined genes. BLAST Miner shares with phylogenetics the

  16. Functional and structural analysis of a key region of the cell wall inhibitor moenomycin.

    PubMed

    Fuse, Shinichiro; Tsukamoto, Hirokazu; Yuan, Yanqiu; Wang, Tsung-Shing Andrew; Zhang, Yi; Bolla, Megan; Walker, Suzanne; Sliz, Piotr; Kahne, Daniel

    2010-07-16

    Moenomycin A (MmA) belongs to a family of natural products that inhibit peptidoglycan biosynthesis by binding to the peptidoglycan glycosyltransferases, the enzymes that make the glycan chains of peptidoglycan. MmA is remarkably potent, but its clinical utility has been hampered by poor physicochemical properties. Moenomycin contains three structurally distinct regions: a pentasaccharide, a phosphoglycerate, and a C25 isoprenyl (moenocinyl) lipid tail that gives the molecule its name. The phosphoglycerate moiety links the pentasaccharide to the moenocinyl chain. This moiety contains two negatively charged groups, a phosphoryl group and a carboxylate. Both the phosphoryl group and the carboxylate have previously been implicated in target binding but the role of the carboxylate has not been explored in detail. Here we report the synthesis of six MmA analogues designed to probe the importance of the phosphoglycerate. These analogues were evaluated for antibacterial and enzyme inhibitory activity; the specific contacts between the phosphoglycerate and the protein target were assessed by X-ray crystallography in conjunction with molecular modeling. Both the phosphoryl group and the carboxylate of the phosphoglycerate chain play roles in target binding. The negative charge of the carboxylate, and not its specific structure, appears to be the critical feature in binding since replacing it with a negatively charged acylsulfonamide group produces a more active compound than replacing it with the isosteric amide. Analysis of the ligand-protein contacts suggests that the carboxylate makes a critical contact with an invariant lysine in the active site. The reported work provides information and validated computational methods critical for the design of analogues based on moenomycin scaffolds. PMID:20496948

  17. Bisphenol A and Its Analogues Activate Human Pregnane X Receptor

    PubMed Central

    Sui, Yipeng; Ai, Ni; Park, Se-Hyung; Rios-Pilier, Jennifer; Perkins, Jordan T.; Welsh, William J.

    2012-01-01

    Background: Bisphenol A (BPA) is a base chemical used extensively in many consumer products. BPA and its analogues are present in environmental and human samples. Many endocrine-disrupting chemicals, including BPA, have been shown to activate the pregnane X receptor (PXR), a nuclear receptor that functions as a master regulator of xenobiotic metabolism. However, the detailed mechanism by which these chemicals activate PXR remains unknown. Objective: We investigated the mechanism by which BPA interacts with and activates PXR and examined selected BPA analogues to determine whether they bind to and activate PXR. Methods: Cell-based reporter assays, in silico ligand–PXR docking studies, and site-directed mutagenesis were combined to study the interaction between BPA and PXR. We also investigated the influence of BPA and its analogues on the regulation of PXR target genes in human LS180 cells. Results: We found that BPA and several of its analogues are potent agonists for human PXR (hPXR) but do not affect mouse PXR activity. We identified key residues within hPXR’s ligand-binding pocket that constitute points of interaction with BPA. We also deduced the structural requirements of BPA analogues that activate hPXR. BPA and its analogues can also induce PXR target gene expression in human LS180 cells. Conclusions: The present study advances our understanding of the mechanism by which BPA interacts with and activates human PXR. Activation of PXR by BPA may explain some of the adverse effects of BPA in humans. PMID:22214767

  18. Total synthesis and biological evaluation of tubulysin U, tubulysin V, and their analogues.

    PubMed

    Balasubramanian, Ranganathan; Raghavan, Bhooma; Begaye, Adrian; Sackett, Dan L; Fecik, Robert A

    2009-01-22

    A stereoselective total synthesis of the cytotoxic natural products tubulysin U, tubulysin V, and its unnatural epimer epi-tubulysin V, is reported. Simplified analogues containing N,N-dimethyl-D-alanine as a replacement for the N-terminal N-Me-pipecolinic acid residue of the tubulysins are also disclosed. Biological evaluation of these natural products and analogues provided key information with regard to structural and stereochemical requirements for antiproliferative activity and tubulin polymerization inhibition. PMID:19102699

  19. Non-natural acetogenin analogues as potent Trypanosoma brucei inhibitors

    PubMed Central

    Florence, Gordon J.; Fraser, Andrew L.; Gould, Eoin R.; King, Elizabeth F.; Menzies, Stefanie K.; Morris, Joanne C.; Tulloch, Lindsay B.; Smith, Terry K.

    2015-01-01

    A series of novel bis-tetrahydropyran 1,4-triazole analogues based on the acetogenin framework display low micromolar trypanocidal activities towards both bloodstream and insect forms of Trypanosoma brucei, the causative agent of African sleeping sickness. A divergent synthetic strategy was adopted for the synthesis of the key tetrahydropyran intermediates to enable rapid access to diastereochemical variation either side of the 1,4-triazole core. The resulting diastereomeric analogues displayed varying degrees of trypanocidal activity and selectivity in structure activity relationship studies. PMID:25145275

  20. Functional and structural analysis of mice TRPC6 with human analogue through homology modelling.

    PubMed

    Chigurupati, Soumya; Bhasin, Arnima; Inampudi, Krishna Kishore; Asuthkar, Swapna; Madarampalli, Bhanupriya; Kammili, Ramana Kumar; Velpula, Kiran Kumar

    2014-01-01

    Homology models are increasingly used to determine structural and functional relationships of genes and proteins in biomedical research. In the current study, for the first time, we compared the TRPC6 gene in mouse and human. The protein encoded by this gene forms a receptor activated calcium channel in cell membrane. Defects in this gene have been implicated in a wide range of diseases including glioblastomas. To determine the structural similarities in mouse and human TRPC6, we used standard bioinformatics tools such as fold prediction to identify the protein 3D structure, sequence-structure comparison, and prediction of template and protein structure. We also used glioblastoma cell line U373MG and human glioblastoma tumour tissues to study the expression of TRPC6 in disease conditions to implicate this gene in pathological ailment. Based on the results we conclude that human TRPC6 contains 90% identity and 93% similarity with mouse TRPC6, suggesting that this protein is well conserved in these two species. These isoforms likely demonstrate similar mechanisms in regulating gene expression; thus TRPC6 studies in mice may be extrapolated to humans. PMID:24589838

  1. Aspartame and Its Analogues

    NASA Astrophysics Data System (ADS)

    Pavlova, L. A.; Komarova, T. V.; Davidovich, Yurii A.; Rogozhin, S. V.

    1981-04-01

    The results of studies on the biochemistry of the sweet taste are briefly reviewed. The methods of synthesis of "aspartame" — a sweet dipeptide — are considered, its structural analogues are described, and quantitative estimates are made of the degree of sweetness relative to sucrose. Attention is concentrated mainly on problems of the relation between the structure of the substance and its taste in the series of aspartyl derivatives. The bibliography includes 118 references.

  2. Interactions of taurine and structurally related analogues with the GABAergic system and taurine binding sites of rabbit brain

    PubMed Central

    Frosini, Maria; Sesti, Casilde; Dragoni, Stefania; Valoti, Massimo; Palmi, Mitri; Dixon, Henry B F; Machetti, Fabrizio; Sgaragli, Giampietro

    2003-01-01

    The aim of this study was to find taurinergic compounds that do not interact with brain GABA ergic systems. Washed synaptic membranes (SM) from whole rabbit brain were able to bind [3H]muscimol. Saturation experiments of the binding of [3H]GABA to GABAB receptors showed that SM possess two binding components; twice Triton X-100-treated SM contained 0.048 mmol endogenous taurine/kg protein and bound [3H]taurine in a saturable manner (Kd=249.0±6.3 nM and Bmax=3.4±1.0 pmol mg−1 prot). Among the 19 structural analogues of taurine, 6-aminomethyl-3-methyl-4H-1,2,4-benzothiadiazine 1,1-dioxide (TAG), 2-aminoethylarsonic (AEA), 2-hydroxyethanesulfonic (ISE) and (±)cis-2-aminocyclohexane sulfonic acids (CAHS) displaced [3H]taurine binding (Ki=0.13, 0.13, 13.5 and 4.0 μM, respectively). These analogues did not interact with GABAA and GABAB receptors and did not affect taurine- and GABA-uptake systems and GABA-transaminase activity. 3-Aminopropanesulfonic acid (OMO), β-alanine, pyridine-3-sulfonic acid, N,N,N-trimethyltaurine (TMT), 2-(guanidino)ethanesulfonic acid (GES), ethanolamine-O-sulphate, N,N-dimethyltaurine (DMT), taurine and (±)piperidine-3-sulfonic acid (PSA) inhibited [3H]muscimol binding to GABAA receptors with different affinities (Ki=0.013, 7.9, 24.6, 47.5, 52.0, 91.0, 47.5, 118.1 and 166.3 μM, respectively). Taurine, 2-aminoethylphosphonic acid, DMT, TMT and OMO inhibited the binding of [3H]GABA to GABAB receptors with Ki's in the μM range (0.8, 3.5, 4.4, 11.3 and 5.0, respectively). GES inhibited taurine uptake (IC50=3.72 μM) and PSA GABA transaminase activity (IC50=103.0 μM). In conclusion, AEA, TAG, ISE and CAHS fulfill the criteria for taurinergic agents. PMID:12684273

  3. Structural perturbation of a dipalmitoylphosphatidylcholine (DPPC) bilayer by warfarin and its bolaamphiphilic analogue: A molecular dynamics study.

    PubMed

    Ayee, Manuela Aseye Ayele; Roth, Charles William; Akpa, Belinda Sena

    2016-04-15

    Compounds with nominally similar biological activity may exhibit differential toxicity due to differences in their interactions with cell membranes. Many pharmaceutical compounds are amphiphilic and can be taken up by phospholipid bilayers, interacting strongly with the lipid-aqueous interface whether or not subsequent permeation through the bilayer is possible. Bolaamphiphilic compounds, which possess two hydrophilic ends and a hydrophobic linker, can likewise undergo spontaneous uptake by bilayers. While membrane-spanning bolaamphiphiles can stabilize membranes, small molecules with this characteristic have the potential to create membrane defects via disruption of bilayer structure and dynamics. When compared to the amphiphilic therapeutic anticoagulant, warfarin, the bolaamphiphilic analogue, brodifacoum, exhibits heightened toxicity that goes beyond superior inhibition of the pharmacological target enzyme. We explore, herein, the consequences of anticoagulant accumulation in a dipalmitoylphosphatidylcholine (DPPC) bilayer. Coarse-grained molecular dynamics simulations reveal that permeation of phospholipid bilayers by brodifacoum causes a disruption of membrane barrier function that is driven by the bolaamphiphilic nature and size of this molecule. We find that brodifacoum partitioning into bilayers causes membrane thinning and permeabilization and promotes lipid flip-flop - phenomena that are suspected to play a role in triggering cell death. These phenomena are either absent or less pronounced in the case of the less toxic, amphiphilic compound, warfarin. PMID:26852346

  4. Thermodynamic functions and intraparticle mass transfer kinetics of structural analogues of a template on molecularly imprinted polymers in liquid chromatography

    SciTech Connect

    Kim, Hyunjung; Guiochon, Georges A

    2005-08-01

    The parameters of the thermodynamics and mass transfer kinetics of the structural analogues (L-enantiomers) of the template were measured on an Fmoc-L-tryptophan (Fmoc-L-Trp) imprinted polymer, at different temperatures. The equilibrium isotherm data and the overloaded band profiles of these compounds were measured at temperatures of 298, 313, 323, and 333 K. The isotherm data were modeled. The thermodynamic functions of the different adsorption sites were derived from the isotherm parameters, using van't Hoff plots. The mass transfer parameters were derived by comparing the experimental peak profiles and profiles calculated using the lumped pore diffusion (POR) model for chromatography. These data show that (1) the strength between the substrate molecules and the MIP increases with increasing number of functional groups on the substrates; (2) enthalpy is the driving force for the affinity of the substrates for the MIP; (3) surface diffusion is the dominant mass transfer mechanism of the substrates through the porous MIP. For those substrate molecules that have the same stereochemistry as the template, the energetic surface heterogeneity needs to be incorporated into the surface diffusion coefficients. Heterogeneous surface diffusivities decrease with increasing affinity of the substrates for the MIP.

  5. Structure Activity Relationship and Mechanism of Action Studies of Manzamine Analogues for the Control of Neuroinflammation and Cerebral Infections

    PubMed Central

    Peng, Jiangnan; Kudrimoti, Sucheta; Prasanna, Sivaprakasam; Odde, Srinivas; Doerksen, Robert J.; Pennaka, Hari K; Choo, Yeun-Mun; Rao, Karumanchi V.; Tekwani, Babu L.; Madgula, Vamsi; Khan, Shabana I.; Wang, Bin; Mayer, Alejandro M. S.; Jacob, Melissa R.; Tu, Lan Chun; Gertsch, Jürg; Hamann, Mark T.

    2010-01-01

    Structure-activity relationship studies were carried out by chemical modification of manzamine A (1), 8-hydroxymanzamine A (2), manzamine F (14), and ircinol isolated from the sponge Acanthostrongylophora. The derived analogues were evaluated for antimalarial, antimicrobial, and antineuroinflammatory activities. Several modified products exhibited potent and improved in vitro antineuroinflammatory, antimicrobial, and antimalarial activity. 1 showed improved activity against malaria compared to chloroquine in both multi- and single-dose in vivo experiments. The significant antimalarial potential was revealed by a 100% cure rate of malaria in mice with one administration of 100 mg/kg of 1. The potent antineuroinflammatory activity of the manzamines will provide great benefit for the prevention and treatment of cerebral infections (e.g. Cryptococcus and Plasmodium). In addition, 1 was shown to permeate across the blood-brain barrier (BBB) in an in vitro model using a MDR-MDCK monolayer. Docking studies support that 2 binds to the ATP-noncompetitive pocket of glycogen synthesis kinase-3β (GSK-3β), which is a putative target of manzamines. Based on the results presented here it will be possible to initiate rational drug design efforts around this natural product scaffold for the treatment of several different diseases. PMID:20017491

  6. Crystal structure of Pb 3O 2(OH)Br, a Br-analogue of damaraite

    NASA Astrophysics Data System (ADS)

    Krivovichev, Sergey V.; Burns, Peter C.

    2001-05-01

    The crystal structure of Pb 3O 2(OH)Br (orthorhombic, Pmc2 1, a=5.8447(8), b=7.0715(10), c=15.309(2) Å, V=632.75(15) Å 3) has been solved by direct methods and refined to R1=0.046 ( wR=0.077). The structure is based on [O 2Pb 3] chains of edge-sharing OPb 4 oxocentered tetrahedra that extend parallel to the a axis and occur in two orientations inclined to each other by ˜50°. The [O 2Pb 3] chains are linked through OH(3) groups to form an [Pb 3O 2](OH) sheet that is parallel to (010). Additional OH(4) groups are attached to the [O 2Pb 3] chains. The OH groups form two short (OH)Pb bonds that results in (OH)Pb 2 dimers.

  7. Synthesis, biological activities, and quantitative structure-activity relationship (QSAR) study of novel camptothecin analogues.

    PubMed

    Wu, Dan; Zhang, Shao-Yong; Liu, Ying-Qian; Wu, Xiao-Bing; Zhu, Gao-Xiang; Zhang, Yan; Wei, Wei; Liu, Huan-Xiang; Chen, An-Liang

    2015-01-01

    In continuation of our program aimed at the development of natural product-based pesticidal agents, three series of novel camptothecin derivatives were designed, synthesized, and evaluated for their biological activities against T. Cinnabarinus, B. brassicae, and B. xylophilus. All of the derivatives showed good-to-excellent activity against three insect species tested, with LC50 values ranging from 0.00761 to 0.35496 mmol/L. Remarkably, all of the compounds were more potent than CPT against T. Cinnabarinus, and compounds 4d and 4c displayed superior activity (LC50 0.00761 mmol/L and 0.00942 mmol/L, respectively) compared with CPT (LC50 0.19719 mmol/L) against T. Cinnabarinus. Based on the observed bioactivities, preliminary structure-activity relationship (SAR) correlations were also discussed. Furthermore, a three-dimensional quantitative structure-activity relationship (3D-QSAR) model using comparative molecular field analysis (CoMFA) was built. The model gave statistically significant results with the cross-validated q2 values of 0.580 and correlation coefficient r2 of 0.991 and  of 0.993. The QSAR analysis indicated that the size of the substituents play an important in the activity of 7-modified camptothecin derivatives. These findings will pave the way for further design, structural optimization, and development of camptothecin-derived compounds as pesticidal agents. PMID:25985362

  8. Inhibition and Structure of Trichomonas vaginalis Purine Nucleoside Phosphorylase with Picomolar Transition State Analogues

    SciTech Connect

    Rinaldo-Matthis,A.; Wing, C.; Ghanem, M.; Deng, H.; Wu, P.; Gupta, A.; Tyler, P.; Evans, G.; Furneaux, R.; et al.

    2007-01-01

    Trichomonas vaginalis is a parasitic protozoan purine auxotroph possessing a unique purine salvage pathway consisting of a bacterial type purine nucleoside phosphorylase (PNP) and a purine nucleoside kinase. Thus, T. vaginalis PNP (TvPNP) functions in the reverse direction relative to the PNPs in other organisms. Immucillin-A (ImmA) and DADMe-Immucillin-A (DADMe-ImmA) are transition stte mimics of adenosine with geometric and electrostatic features that resemble early and late transition states of adenosine at the transition state stabilized by TvPNP. ImmA demonstrates slow-onset tight-binding inhibition with TvPNP, to give an equilibrium dissociation constant of 87 pM, an inhibitor release half-time of 17.2 min, and a K{sub m}/K{sub d} ratio of 70,100. DADMe-ImmA resembles a late ribooxacarbenium ion transition state for TvPNP to give a dissociation constant of 30 pM, an inhibitor release half-time of 64 min, and a K{sub m}/K{sub d} ratio of 203,300. The tight binding of DADMe-ImmA supports a late S{sub N}1 transition state. Despite their tight binding to TvPNP, ImmA and DADMe-ImmA are weak inhibitors of human and P. falciparum PNPs. The crystal structures of the TvPNP-ImmA{center_dot}PO{sub 4} and TvPNP{center_dot}DADMe-ImmA{center_dot}PO{sub 4} ternary complexes differ from previous structures with substrate anologues. The tight binding with DADMe-ImmA is in part due to a 2.7 {angstrom} ionic interaction between a PO{sub 4} oxygen and the N1 cation of the hydroxypyrrolidine and is weaker in the TvPNP{center_dot}ImmA{center_dot}PO{sub 4} structure at 3.5 {angstrom}. However, the TvPNP{center_dot}ImmA{center_dot}PO{sub 4} structure includes hydrogen bonds between the 2'-hydroxyl and the protein that are not present in TvPNP{center_dot}DADMe-ImmA{center_dot}PO{sub 4}. These structures explain why DADMe-ImmA binds tighter than ImmA. Immucillin-H is a 12 nM inhibitor of TvPNP but a 56 pM inhibitor of human PNP. And this difference is explained by isotope

  9. Structure Determination of Cisplatin-Amino Acid Analogues by Infrared Multiple Photon Dissociation Action Spectroscopy

    NASA Astrophysics Data System (ADS)

    He, Chenchen; Bao, Xun; Zhu, Yanlong; Strobehn, Stephen; Kimutai, Bett; Nei, Y.-W.; Chow, C. S.; Rodgers, M. T.; Gao, Juehan; Oomens, J.

    2015-06-01

    To gain a better understanding of the binding mechanism and assist in the optimization of relevant drug and chemical probe design, both experimental and theoretical studies were performed on a series of amino acid-linked cisplatin derivatives, including glycine-, lysine-, and ornithine-linked cisplatin, Gplatin, Kplatin, and Oplatin, respectively. Cisplatin, the first FDA-approved platinum-based anticancer drug, has been widely used in cancer chemotherapy. Its pharmacological mechanism has been identified as its ability to coordinate to genomic DNA, and guanine is its major target. In previous reports, cisplatin was successfully utilized as a chemical probe to detect solvent accessible sites in ribosomal RNA (rRNA). Among the amino-acid-linked cisplatin derivatives, Oplatin exhibits preference for adenine over guanine. The mechanism behind its different selectivity compared to cisplatin may relate to its potential of forming a hydrogen bond between the carboxylate group in Pt (II) complex and the 6-amino moiety of adenosine stabilizes A-Oplatin products. Tandem mass spectrometry analysis also indicates that different coordination sites of Oplatin on adenosine affect glycosidic bond stability. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments were performed on all three amino acid-linked cisplatin to characterize their structures. An extensive theoretical study has been performed on Gplatin to guide the selection of the most effective theory and basis set based on its geometric information. The results for Gplatin provide the foundation for characterization of the more complex amino acid-linked cisplatin derivatives, Oplatin and Kplatin. Structural and energetic information elucidated for these compounds, particularly Oplatin reveal the reason for its alternative selectivity compared to cisplatin.

  10. Synthesis, Nitric Oxide Release, and Anti-Leukemic Activity of Glutathione-Activated Nitric Oxide Prodrugs: Structural Analogues of PABA/NO, an Anti-Cancer Lead Compound

    PubMed Central

    Chakrapani, Harinath; Wilde, Thomas C.; Citro, Michael L.; Goodblatt, Michael M.; Keefer, Larry K.; Saavedra, Joseph E.

    2008-01-01

    Diazeniumdiolate anions and their prodrug forms are reliable sources of nitric oxide (NO) that have generated interest as promising therapeutic agents. A number of structural analogues of O2-(2,4-dinitro-5-(4-(N-methylamino)benzoyloxy)phenyl) 1-(N,N-dimethylamino)diazen-1-ium-1,2-diolate (PABA/NO), an anti-cancer lead compound that is designed to release NO upon activation by glutathione, were prepared. The nitric oxide release patterns of these O2-(2,4-dinitrophenyl) diazeniumdiolates in the presence of glutathione were tested and it was found that in the absence of competing pathways, these compounds release nearly quantitative amounts of NO. The ability of PABA/NO and its structural analogues to inhibit human leukemia cell proliferation was determined and it was found that compounds releasing elevated amounts of NO displayed superior cytotoxic effects. PMID:18060792

  11. Structure-Activity Relationships in Human Toll-like Receptor 7-Active Imidazoquinoline Analogues

    PubMed Central

    Shukla, Nikunj M.; Malladi, Subbalakshmi S.; Mutz, Cole A.; Balakrishna, Rajalakshmi; David, Sunil A.

    2010-01-01

    Engagement of toll-like receptors serve to link innate immune responses with adaptive immunity and can be exploited as powerful vaccine adjuvants for eliciting both primary and anamnestic immune responses. TLR7 agonists are highly immunostimulatory without inducing dominant proinflammatory cytokine responses. A structure-activity study was conducted on the TLR7-agonistic imidazoquinolines, starting with 1-(4-amino-2-((ethylamino)methyl)-1H-imidazo[4,5-c]quinolin-1-yl)-2-methylpropan-2-ol as a lead. Modifications of the secondary amine of the C2 ethylaminomethylene sidechain are poorly tolerated. The 4-amino group must be retained for activity. Replacement of the imidazole ring of the scaffold with triazole or cyclic urea led to complete loss of activity. A systematic exploration of N1-benzyl-C2-alkyl substituents showed a very distinct relationship between alkyl length and TLR7-agonistic potency with the optimal compound bearing a C2-n-butyl group. Transposition of the N1 and C2 substituents led to the identification of an extremely active TLR7-agonistic compound with an EC50 value of 8.6 nM. The relative potencies in human TLR7-based primary reporter gene assays were paralleled by interferon-α induction activities in whole human blood models. PMID:20481492

  12. The structure-AChE inhibitory activity relationships study in a series of pyridazine analogues.

    PubMed

    Saracoglu, M; Kandemirli, F

    2009-07-01

    The structure-activity relationships (SAR) are investigated by means of the Electronic-Topological Method (ETM) followed by the Neural Networks application (ETM-NN) for a class of anti-cholinesterase inhibitors (AChE, 53 molecules) being pyridazine derivatives. AChE activities of the series were measured in IC(50) units, and relative to the activity levels, the series was partitioned into classes of active and inactive compounds. Based on pharmacophores and antipharmacophores calculated by the ETM-software as sub-matrices containing important spatial and electronic characteristics, a system for the activity prognostication is developed. Input data for the ETM were taken as the results of conformational and quantum-mechanics calculations. To predict the activity, we used one of the most well known neural networks, namely, the feed-forward neural networks (FFNNs) trained with the back propagation algorithm. The supervised learning was performed using a variant of FFNN known as the Associative Neural Networks (ASNN). The result of the testing revealed that the high ETM's ability of predicting both activity and inactivity of potential AChE inhibitors. Analysis of HOMOs for the compounds containing Ph1 and APh1 has shown that atoms with the highest values of the atomic orbital coefficients are mainly those atoms that enter into the pharmacophores. Thus, the set of pharmacophores and antipharmacophores found as the result of this study forms a basis for a system of the anti-cholinesterase activity prediction. PMID:19689389

  13. The influence of cooling on the advance of lava flows: insights from analogue experiments on the feedbacks between flow dynamics and thermal structure

    NASA Astrophysics Data System (ADS)

    Garel, F.; Kaminski, E.; Tait, S.; Limare, A.

    2012-12-01

    During an effusive volcanic eruption, the crisis management is mainly based on the prediction of lava flows advance and its velocity. The spreading of a lava flow, seen as a gravity current, depends on its "effective rheology" and the eruptive mass flux. These two parameters are not known a priori during an eruption and a key question is how to evaluate them in near real-time (rather than afterwards.) There is no generic macroscopic model for the rheology of an advancing lava flow, and analogue modelling is a precious tool to empirically estimate the rheology of a complex flow. We investigate through laboratory experiments the simultaneous spreading and cooling of horizontal currents fed at constant rate from a point source. The materials used are silicone oil (isoviscous), and poly-ethylene glycol (PEG) wax injected in liquid state and solidiying during its advance. In the isoviscous case, the temperature field is a passive tracer of the flow dynamics, whereas in the PEG experiments there is a feedback between the cooling of the flow and its effective rheology. We focus on the evolution of the current area and of the surface thermal structure, imaged with an infrared camera, to assess how the thermal structure can be related to the flow rate. The flow advance is continuous in the viscous case, and follows the predictions of Huppert (1982); in that case the surface temperature become steady after a transient time and the radiated heat flux is shown to be proportional to the input rate. For the PEG experiments, the spreading occurs through an alternation of stagnation and overflow phases, with a mean spreading rate decreasing as the experiment goes on. As in the case of lava flows, these experiments can exhibit a compound flow field, solid levees, thermal erosion, liquid overflows and channelization. A key observation is that the effective rheology of the solifying PEG material depends on the input flow rate, with high input rates yielding a rheology closer to the

  14. Synthesis and cytotoxic activities of semisynthetic zearalenone analogues.

    PubMed

    Tadpetch, Kwanruthai; Kaewmee, Benyapa; Chantakaew, Kittisak; Kantee, Kawalee; Rukachaisirikul, Vatcharin; Phongpaichit, Souwalak

    2016-08-01

    Zearalenone is a β-resorcylic acid macrolide with various biological activities. Herein we report the synthesis and cytotoxic activities of 34 zearalenone analogues against human oral epidermoid carcinoma (KB) and human breast adenocarcinoma (MCF-7) cells as well as noncancerous Vero cells. Some zearalenone analogues showed moderately enhanced cytotoxic activities against the two cancer cell lines. We have discovered the potential lead compounds with diminished or no cytotoxicity to Vero cells. Preliminary structure-activity relationship studies revealed that the double bond at the 1' and 2' positions of zearalenone core was crucial for cytotoxic activities on both cell lines. In addition, for zearalenol analogues, the unprotected hydroxyl group at C-2 and an alkoxy substituent at C-4 played key roles on cytotoxic effects of both cell lines. PMID:27311894

  15. Bispidin-9,9-diol Analogues of Cisplatin, Carboplatin, and Oxaliplatin: Synthesis, Structures, and Cytotoxicity.

    PubMed

    Cui, Huiling; Goddard, Richard; Pörschke, Klaus-Richard; Hamacher, Alexandra; Kassack, Matthias U

    2016-03-21

    3,7-Diallyl-bispidin-9-one (6) (bispidin-9-one = 3,7-diazabicyclo[3.3.1]nonan-9-one) is converted to N-unsubstituted spiro[bispidin-9,2'-[1,3]dioxolane] (12; 35%). The ketal crystallizes in the forms of anhydrous 12a and the dihydrate 12b. The molecules in anhydrous 12a are linked to each other, forming N1-H1···N2-H2···N1* hydrogen-bond chiral helices of alternating chirality. In the dihydrate 12b, the ketal molecules are connected to a central string of water molecules by O3-H···O1 and O4-H···N1 hydrogen bonds, but not to themselves. Reaction of 12 with (1,5-hexadiene)PtCl2 affords almost quantitatively spiro[bispidin-9,2'-[1,3]dioxolane]PtCl2 (13). Cleavage of the ketal to retrieve the ketone produces the geminal diol (bispidin-9,9-diol)PtCl2 (14; 85%). Compound 14 reacts with Ag2cbdca (cbdca = 1,1-cyclobutanedicarboxylate) to give the dihydrate (bispidin-9,9-diol)Pt(cbdca)·2H2O (15b), which can be dehydrated to obtain anhydrous (bispidin-9,9-diol)Pt(cbdca) (15a). Similarly, anhydrous (bispidin-9,9-diol)Pt(oxalate) (16) is obtained. Crystal structures of 14 and 15b reveal association by various forms of O-H···O, O-H···Cl, N-H···Cl, and N-H···O hydrogen bonds. Biological studies showed a moderate cytotoxic activity of the bispidin-9,9-diol complexes 14-16, compared to the 9,9-unsubstituted bispidine complexes. No unspecific cytotoxicity of 14-16 up to 316 μM was found against the noncancer cell line HEK293. PMID:26918619

  16. The role of pre-existing tectonic structures and magma chamber shape on the geometry of resurgent blocks: Analogue models

    NASA Astrophysics Data System (ADS)

    Marotta, Enrica; de Vita, Sandro

    2014-02-01

    A set of analogue models has been carried out to understand the role of an asymmetric magma chamber on the resurgence-related deformation of a previously deformed crustal sector. The results are then compared with those of similar experiments, previously performed using a symmetric magma chamber. Two lines of experiments were performed to simulate resurgence in an area with a simple graben-like structure and resurgence in a caldera that collapsed within the previously generated graben-like structure. On the basis of commonly accepted scaling laws, we used dry-quartz sand to simulate the brittle behaviour of the crust and Newtonian silicone to simulate the ductile behaviour of the intruding magma. An asymmetric shape of the magma chamber was simulated by moulding the upper surface of the silicone. The resulting empty space was then filled with sand. The results of the asymmetric-resurgence experiments are similar to those obtained with symmetrically shaped silicone. In the sample with a simple graben-like structure, resurgence occurs through the formation of a discrete number of differentially displaced blocks. The most uplifted portion of the deformed depression floor is affected by newly formed, high-angle, inward-dipping reverse ring-faults. The least uplifted portion of the caldera is affected by normal faults with similar orientation, either newly formed or resulting from reactivation of the pre-existing graben faults. This asymmetric block resurgence is also observed in experiments performed with a previous caldera collapse. In this case, the caldera-collapse-related reverse ring-fault is completely erased along the shortened side, and enhances the effect of the extensional faults on the opposite side, so facilitating the intrusion of the silicone. The most uplifted sector, due to an asymmetrically shaped intrusion, is always in correspondence of the thickest overburden. These results suggest that the stress field induced by resurgence is likely dictated by

  17. Structure of beta-crystallite assemblies formed by Alzheimer beta-amyloid protein analogues: analysis by x-ray diffraction.

    PubMed Central

    Inouye, H.; Fraser, P. E.; Kirschner, D. A.

    1993-01-01

    To elucidate the relation between amyloid fibril formation in Alzheimer disease and the primary structure of the beta/A4 protein, which is the major component of the amyloid, we have been investigating the ability of peptides sharing sequences with beta/A4 to form fibrils in vitro. In previous studies we focused on the macroscopic morphology of the assemblies formed by synthetic peptides corresponding in sequence to different regions of this protein. In the present study we analyze the x-ray diffraction patterns obtained from these assemblies. All specimens showed wide angle reflections that could be indexed by an orthogonal lattice of beta-crystallites having unit cell dimensions a = 9.4 A, b = 7 A, and c = 10 A, where a refers to hydrogen bonding direction, b to polypeptide chain direction, and c to intersheet direction. Given the amino acid sequence of beta/A4 as NH2-DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIAT-COOH, we found that, based on their orientation and assembly, the analogues could be classified into three groups: Group A, residues 19-28, 13-28, 12-28, 11-28, 9-28, 1-28, 1-38, 1-40, 6-25, 11-25 and 34-42; Group B, residues 18-28, 17-28, and 15-28; and Group C, residues 22-35 and 26-33. For Groups A and C, the sharpest reflections were (h00), indicating that the assemblies were fibrillar, i.e., elongated in a single direction. Lateral alignment of the crystallites in Group A account for its cross-beta pattern, in which the hydrogen bonding (H-bonding) direction is the fiber (rotation) axis. By comparison, the beta-crystallites of Group C had no preferential orientation, thus giving circular scattering. For Group B, the sharpest reflections were (h0l) on the meridian, indicating that the assemblies were plate-like, i.e., extended in two directions. A series of equatorial Bragg reflections having a 40 A period indicated regular stacking of the plates, and the rotation axis was normal to the surface of the plates. Of the Group A peptides, the analogues 11

  18. Titan's Organic Aerosols : Molecular Composition And Structure Inferred From Systematic Pyrolysis Gas Chromatography Mass Spectrometry Analysis of Analogues

    NASA Astrophysics Data System (ADS)

    Morisson, Marietta; Szopa, Cyril; Buch, Arnaud; Carrasco, Nathalie; Gautier, Thomas

    2015-04-01

    In spite of numerous studies carried out to characterize the chemical composition of laboratory analogues of Titan aerosols (tholins), their molecular composition as well as their structuration are still little known. If Pyrolysis gas chromatography mass spectrometry (Pyr-GCMS) has been used for years to give clues about this composition, the highly disparate results obtained show that they can be attributed to the analytical conditions used, to differences in the nature of the analogues studied, or both. In order to have a better description of Titan's tholins molecular composition, we led a systematic analysis of these materials by pyr-GCMS, exploring the analytical parameters to estimate the biases this technique can induce. With this aim, we used the PAMPRE experiment, a capacitively coupled RF cold plasma reactor (Szopa et al. 2006), to synthetize tholins with 2%, 5% and 10% of CH4 in N2. The three samples were systematically pyrolyzed in the temperature range 200-600°C with a 100°C step. The evolved gases were then injected into a GC-MS device for molecular identification. This systematic pyr-GC-MS analysis had two major objectives: (i) optimizing all the analytical parameters for the detection of a wide range of compounds and thus a characterization of the tholins composition as comprehensive as possible, and (ii) highlighting the role of the CH4 ratio on the tholins molecular structure. About a hundred of molecules have been identified in the pyrolysis products. Although an identical major pattern of nitriles and ethylene appears clearly for the three samples, some discriminant signatures were highlighted. The samples mainly differ by the number of released compounds. The results show especially an increase in the hydrocarbonaceous chains when the CH4 ratio increases. At the opposite, the formation of poly-nitrogenous compounds seems to be easier for lower CH4 ratios. We also performed a semi-quantitative study on the best represented chemical family in

  19. A dinaphtho[8,1,2-cde:2',1',8'-uva]pentacene derivative and analogues: synthesis, structures, photophysical and electrochemical properties.

    PubMed

    Li, Xiao-Jun; Li, Meng; Lu, Hai-Yan; Chen, Chuan-Feng

    2015-07-28

    Dinaphtho[8,1,2-cde:2',1',8'-uva]pentacene and analogues as a new type of acene derivatives with scorpion-shaped structures were conveniently synthesized. Their structures, photophysical and electrochemical properties were experimentally and theoretically investigated. It was found that the pentacene derivative has a twisted configuration, but shows marked intermolecular π-π interactions, strong electronic delocalization, and a small HOMO-LUMO bandgap, which are different from those of pentacene and pentatwistacene derivatives with similar structures. PMID:26104736

  20. Combined Quantum Chemistry and Photoelectron Spectroscopy Study of the Electronic Structure and Reduction Potentials of Rubredoxin Redox Site Analogues

    SciTech Connect

    Niu, Shuqiang; Wang, Xue B.; Nichols, J. A.; Wang, Lai S.; Ichiye, Toshiko

    2003-04-24

    Iron-sulfur proteins are an important class of electron carriers in a wide variety of biological reactions. Determining the intrinsic contribution of the metal site to the redox potential is crucial in understanding how the protein environment influences the overall redox properties of the Fe-S proteins. Here we combine density functional theory and coupled cluster methods with photodetachment spectroscopy to study the electronic structures and gas-phase redox potentials of the [Fe(SCH3)(4)](2-/-/0) and [Fe(SCH3)(3)](-/0) analogues of the rubredoxin redox site. The calculations show that oxidations of [Fe(SCH3)(4)](2-) and [Fe(SCH3)(4)](-) involve mainly the Fe 3d and S 3p orbitals, respectively. The calculated adiabatic and vertical detachment energies are in good agreement with the experiment for [Fe(SCH3)(3)](-) and [Fe(SCH3)(4)](-). The current results further confirm the "inverted level scheme" for the high-spin [1Fe] systems. The redox couple, [Fe(SCH3)(4)](- /2), which is the one found in rubredoxin, but cannot be accessed experimentally in the gas phase, was investigated using a thermodynamic cycle that relates it to the [Fe(SCH3)(3)](-/0) couple and the ligand association reaction, [Fe(SCH3)(3)](0/-) + SCH3- --> [Fe(SCH3)(4)](-/2-). The calculated reduction energy of [Fe(SCH3)(4)](-) (1.7 eV) compares well with the value (1.6 eV) estimated from the calculated bond energies and the experimental detachment energy of [Fe(SCH3)(3)](-). Thus, this thermodynamic cycle method can be used to estimate metal-ligand bonding energies and determine intrinsic reduction potentials from photodetachment experiments when the reduced forms are not stable in the gas phase.

  1. Isatin Derived Spirocyclic Analogues with α-Methylene-γ-butyrolactone as Anticancer Agents: A Structure-Activity Relationship Study.

    PubMed

    Rana, Sandeep; Blowers, Elizabeth C; Tebbe, Calvin; Contreras, Jacob I; Radhakrishnan, Prakash; Kizhake, Smitha; Zhou, Tian; Rajule, Rajkumar N; Arnst, Jamie L; Munkarah, Adnan R; Rattan, Ramandeep; Natarajan, Amarnath

    2016-05-26

    Design, synthesis, and evaluation of α-methylene-γ-butyrolactone analogues and their evaluation as anticancer agents is described. SAR identified a spirocyclic analogue 19 that inhibited TNFα-induced NF-κB activity, cancer cell growth and tumor growth in an ovarian cancer model. A second iteration of synthesis and screening identified 29 which inhibited cancer cell growth with low-μM potency. Our data suggest that an isatin-derived spirocyclic α-methylene-γ-butyrolactone is a suitable core for optimization to identify novel anticancer agents. PMID:27077228

  2. Antimicrobial Peptide from the Wild Bee Hylaeus signatus Venom and Its Analogues: Structure-Activity Study and Synergistic Effect with Antibiotics.

    PubMed

    Nešuta, Ondřej; Hexnerová, Rozálie; Buděšínský, Miloš; Slaninová, Jiřina; Bednárová, Lucie; Hadravová, Romana; Straka, Jakub; Veverka, Václav; Čeřovský, Václav

    2016-04-22

    Venoms of hymenopteran insects have attracted considerable interest as a source of cationic antimicrobial peptides (AMPs). In the venom of the solitary bee Hylaeus signatus (Hymenoptera: Colletidae), we identified a new hexadecapeptide of sequence Gly-Ile-Met-Ser-Ser-Leu-Met-Lys-Lys-Leu-Ala-Ala-His-Ile-Ala-Lys-NH2. Named HYL, it belongs to the category of α-helical amphipathic AMPs. HYL exhibited weak antimicrobial activity against several strains of pathogenic bacteria and moderate activity against Candida albicans, but its hemolytic activity against human red blood cells was low. We prepared a set of HYL analogues to evaluate the effects of structural modifications on its biological activity and to increase its potency against pathogenic bacteria. This produced several analogues exhibiting significantly greater activity compared to HYL against strains of both Staphylococcus aureus and Pseudomonas aeruginosa even as their hemolytic activity remained low. Studying synergism of HYL peptides and conventional antibiotics showed the peptides act synergistically and preferentially in combination with rifampicin. Fluorescent dye propidium iodide uptake showed the tested peptides were able to facilitate entrance of antibiotics into the cytoplasm by permeabilization of the outer and inner bacterial cell membrane of P. aeruginosa. Transmission electron microscopy revealed that treatment of P. aeruginosa with one of the HYL analogues caused total disintegration of bacterial cells. NMR spectroscopy was used to elucidate the structure-activity relationship for the effect of amino acid residue substitution in HYL. PMID:26998557

  3. 3D modelling of a dolomitized syn-sedimentary structure: an exhumed potential analogue of hydrocarbon reservoir.

    NASA Astrophysics Data System (ADS)

    Martinelli, Mattia; Franceschi, Marco; Massironi, Matteo; Bistacchi, Andrea; Di Cuia, Raffaele; Rizzi, Alessandro

    2016-04-01

    The decrease in discoveries of new hydrocarbon reservoirs has twofold implications: i) the need to improve our knowledge of classic reservoirs, such as traps within extensional syn-sedimentary structures, and ii) enhanced efforts aimed at better understanding complex type of reservoirs. In particular, in the last few years, fault related dolomitized bodies, often associated to extensional faults, received worldwide attention thanks to the capability of dolomitizing fluids to improve the pore network. However, the shape and geometries of the dolomitized bodies within complex fault network as well as the related porosity distribution and evolution is difficult to predict. The study of outcrop analogues can help to solve these issues. In this work, we focused our attention on the Early Jurassic carbonate sediments of the Calcari Grigi Group deposited on the Trento Platform (Italian Southern Alps). The stratigraphic succession encompasses (from bottom to top): the peritidal limestones of the Monte Zugna Formation, the initially highly porous Loppio Oolitic Limestone and the nearly tight marls and marly limestones of the lower Rotzo Formation. During Early Jurassic, after the deposition of the Loppio Oolitic Limestone, the Trento Platform underwent syn-sedimentary extensional tectonics, which caused the formation of numerous tilted blocks. Differential subsidence of these blocks is testified by abrupt thickness changes in Rotzo Formation. This created a structural framework favourable to the formation of syn-sedimentary extensional traps (with the Loppio Oolitic Limestone as reservoir and Rotzo Formation as seal). In the Tertiary, Alpine compressional tectonics caused the reactivation of the Jurassic faults with a strike slip kinematics and was associated with the circulation of dolomitizing fluids. The combination of these events led to the formation of secondary fault-related dolomitized bodies. The enhanced pore network in correspondence of the dolomitized dykes

  4. Structural insights into the interactions of xpt riboswitch with novel guanine analogues: a molecular dynamics simulation study.

    PubMed

    Jain, Swapan S; Sonavane, Uddhavesh B; Uppuladinne, Mallikarjunachari V N; McLaughlin, Emily C; Wang, Weiqing; Black, Sheneil; Joshi, Rajendra R

    2015-01-01

    Ligand recognition in purine riboswitches is a complex process requiring different levels of conformational changes. Recent efforts in the area of purine riboswitch research have focused on ligand analogue binding studies. In the case of the guanine xanthine phosphoribosyl transferase (xpt) riboswitch, synthetic analogues that resemble guanine have the potential to tightly bind and subsequently influence the genetic expression of xpt mRNA in prokaryotes. We have carried out 25 ns Molecular Dynamics (MD) simulation studies of the aptamer domain of the xpt G-riboswitch in four different states: guanine riboswitch in free form, riboswitch bound with its cognate ligand guanine, and with two guanine analogues SJ1 and SJ2. Our work reveals novel interactions of SJ1 and SJ2 ligands with the binding core residues of the riboswitch. The ligands proposed in this work bind to the riboswitch with greater overall stability and lower root mean square deviations and fluctuations compared to guanine ligand. Reporter gene assay data demonstrate that the ligand analogues, upon binding to the RNA, lower the genetic expression of the guanine riboswitch. Our work has important implications for future ligand design and binding studies in the exciting field of riboswitches. PMID:24404773

  5. Synthesis and high-throughput characterization of structural analogues of molecular glassformers: 1,3,5-trisarylbenzenes.

    PubMed

    Liu, Tianyi; Cheng, Kevin; Salami-Ranjbaran, Elmira; Gao, Feng; Glor, Ethan C; Li, Mu; Walsh, Patrick J; Fakhraai, Zahra

    2015-10-14

    We report the synthesis and characterization of an analogous series of small organic molecules derived from a well-known glass former, 1,3-bis(1-naphthyl)-5-(2-naphthyl)benzene (α,α,β-TNB). Synthesized molecules include α,α,β-TNB, 3,5-di(naphthalen-1-yl)-1-phenylbenzene (α,α-P), 9-(3,5-di(naphthalen-1-yl)phenyl)anthracene (α,α-A), 9,9'-(5-(naphthalen-2-yl)-1,3-phenylene)dianthracene (β-AA) and 3,3',5,5'-tetra(naphthalen-1-yl)-1,1'-biphenyl (α,α,α,α-TNBP). The design of molecules was based on increasing molecular weight with varied π-π interactions in one or more substituents. The synthesis is based on Suzuki cross-coupling of 1-bromo-3-chloro-5-iodobenzene with arylboronic acids, which allows attachment of various substituents to tailor the chemical structure. The bulk compounds were characterized using NMR spectroscopy and differential scanning calorimetry (DSC). Thin films of these compounds were produced using physical vapor deposition and were subsequently annealed above the glass transition temperatures (Tg). For each molecular glass, cooling rate-dependent glass transition temperature measurements (CR-Tg) were performed using ellipsometry as a high-throughput method to characterize thin film properties. CR-Tg allows rapid characterization of glassy properties, such as Tg, apparent thermal expansion coefficients, apparent activation energy at Tg and fragility. DSC measurements confirmed the general trend that increasing molecular weight leads to increasing melting point (Tm) and Tg. Furthermore, CR-Tg provided evidence that the introduction of stronger π-interacting substituents in the chosen set of structural analogues increases fragility and decreases the ability to form glasses, such that β-AA has the largest fragility and highest tendency to crystallize among all the compounds. These strong interactions also significantly elevate Tg and promote more harmonic intermolecular potentials, as observed by decreasing value of the apparent

  6. Design, Synthesis and Structure-Activity Relationship Studies of Novel 4 (1-adamantyl) Phenyl Analogues as HIF-1α Inhibitors.

    PubMed

    Xia, Yan; Duan, Qiong; Zhao, Bao-Hua; Li, Dong-Feng; Hou, Rui-Bin

    2016-01-01

    Hypoxia inducible factor-1 (HIF-1) is a key mediator during cancer cells to adapt tumor hypoxic condition. In this study, a series of adamantane-based compounds were synthesized and evaluated as potential inhibitors of HIF-1α. Examination of their structure-activity relationship (SAR) identified the adamantane-containing indole derivative 20a as a potent inhibitor of HIF-1α in Hep3B cell lines under tumor hypoxia (IC50 = 0.02 µM). The study herein may provide valuable information for the development of novel therapeutics against cancer and tumor angiogenesis. PMID:26548744

  7. Maximum key-profile correlation (MKC) as a measure of tonal structure in music.

    PubMed

    Takeuchi, A H

    1994-09-01

    Tonal structure is musical organization on the basis of pitch, in which pitches vary in importance and rate of occurrence according to their relationship to a tonal center. Experiment 1 evaluated the maximum key-profile correlation (MKC), a product of Krumhansl and Schmuckler's key-finding algorithm (Krumhansl, 1990), as a measure of tonal structure. The MKC is the maximum correlation coefficient between the pitch class distribution in a musical sample and key profiles, which indicate the stability of pitches with respect to particular tonal centers. The MKC values of melodies correlated strongly with listeners' ratings of tonal structure. To measure the influence of the temporal order of pitches on perceived tonal structure, three measures (fifth span, semitone span, and pitch contour) taken from previous studies of melody perception were also correlated with tonal structure ratings. None of the temporal measures correlated as strongly or as consistently with tonal structure ratings as did the MKC, and nor did combining them with the MKC improve prediction of tonal structure ratings. In Experiment 2, the MKC did not correlate with recognition memory of melodies. However, melodies with very low MKC values were recognized less accurately than melodies with very high MKC values. Although it does not incorporate temporal, rhythmic, or harmonic factors that may influence perceived tonal structure, the MKC can be interpreted as a measure of tonal structure, at least for brief melodies. PMID:7971133

  8. Structure-Activity Studies of Brassinosteroids and the Search for Novel Analogues and Mimetics with Improved Bioactivity.

    PubMed

    Back, Thomas G.; Pharis, Richard P.

    2003-12-01

    A number of novel brassinosteroid analogues were synthesized and subjected to the rice leaf lamina inclination bioassay. Modified B-ring analogues included lactam, thiolactone, cyclic ether, ketone, hydroxyl, and exocyclic methylene derivatives of brassinolide. Those derivatives containing polar functional groups retained considerable bioactivity, whereas the exocyclic methylene compounds were devoid of activity. Analogues containing normal alkyl and cycloalkyl substituents at C-24 (in place of the isopropyl group of brassinolide) showed an inverse relationship between activity and chain length or ring size, respectively. The corresponding cyclopropyl and cyclobutyl derivatives were significantly more active than brassinolide and appear to be the most potent brassinosteroids reported to date. When synergized with the auxin indole-3-acetic acid (IAA), their bioactivity can be further enhanced by 1-2 orders of magnitude. The cyclopropyl derivative, when coapplied with the auxin naphthaleneacetic acid, gave a significant increase in yield of wheat in a field trial. Certain 25- and 26-hydroxy derivatives are known metabolites of brassinosteroids. All of the C-25 stereoisomers of 25-hydroxy, 26-hydroxy, and 25,26-dihydroxy derivatives of brassinolide were prepared and shown to be much less active than brassinolide. This indicates that they are likely metabolic deactivation products of the parent phytohormone. A series of methyl ethers of brassinolide was synthesized to block deactivation by glucosylation of the free hydroxyl groups. The most significant finding was that the compound where three of the four hydroxyl groups (at C-3, C-22, and C-23) had been converted to methyl ethers retained substantial bioactivity. This type of modification could, in theory, allow brassinolide or 24-epibrassinolide to resist deactivation and thus offer greater persistence in field applications. A series of nonsteroidal mimetics of brassinolide was designed and synthesized. Two of the

  9. Erythrocyte membrane modifying agents and the inhibition of Plasmodium falciparum growth: structure-activity relationships for betulinic acid analogues.

    PubMed

    Ziegler, Hanne L; Franzyk, Henrik; Sairafianpour, Majid; Tabatabai, Mehrnoush; Tehrani, Mahboubeh D; Bagherzadeh, Karim; Hägerstrand, Henry; Staerk, Dan; Jaroszewski, Jerzy W

    2004-01-01

    The natural triterpene betulinic acid and its analogues (betulinic aldehyde, lupeol, betulin, methyl betulinate and betulinic acid amide) caused concentration-dependent alterations of erythrocyte membrane shape towards stomatocytes or echinocytes according to their hydrogen bonding properties. Thus, the analogues with a functional group having a capacity of donating a hydrogen bond (COOH, CH(2)OH, CONH(2)) caused formation of echinocytes, whereas those lacking this ability (CH(3), CHO, COOCH(3)) induced formation of stomatocytes. Both kinds of erythrocyte alterations were prohibitive with respect to Plasmodium falciparum invasion and growth; all compounds were inhibitory with IC(50) values in the range 7-28 microM, and the growth inhibition correlated well with the extent of membrane curvature changes assessed by transmission electron microscopy. Erythrocytes pre-loaded with betulinic acid or its analogues and extensively washed in order to remove excess of the chemicals could not serve as hosts for P. falciparum parasites. Betulinic acid and congeners can be responsible for in vitro antiplasmodial activity of plant extracts, as shown for Zataria multiflora Boiss. (Labiatae) and Zizyphus vulgaris Lam. (Rhamnaceae). The activity is evidently due to the incorporation of the compounds into the lipid bilayer of erythrocytes, and may be caused by modifications of cholesterol-rich membrane rafts, recently shown to play an important role in parasite vacuolization. The established link between erythrocyte membrane modifications and antiplasmodial activity may provide a novel target for potential antimalarial drugs. PMID:14697777

  10. Raman spectroscopic characterisations and analytical discrimination between caffeine and demethylated analogues of pharmaceutical relevance

    NASA Astrophysics Data System (ADS)

    Edwards, H. G. M.; Munshi, T.; Anstis, M.

    2005-05-01

    The FT Raman spectrum of caffeine was analysed along with that of its demethylated analogues, theobromine and theophylline. The similar but not identical structures of these three compounds allowed a more detailed assignment of the Raman bands. Noticeable differences in the Raman spectra of these compounds were apparent and key marker bands have been identified for the spectroscopic identification of these three compounds.

  11. One-step separation of nine structural analogues from Poria cocos (Schw.) Wolf. via tandem high-speed counter-current chromatography.

    PubMed

    Zeng, Hualiang; Liu, Qi; Yu, Jingang; Jiang, Xinyu; Wu, Zhiliang; Wang, Meiling; Chen, Miao; Chen, Xiaoqing

    2015-11-01

    A novel one-step separation strategy-tandem high-speed counter-current chromatography (HSCCC) was developed with a six-port valve serving as the switch interface. Nine structural analogues including three isomers were successfully isolated from Poria cocos (Schw.) Wolf. by one step. Compared with conventional HSCCC, peak resolution of target compounds was effectively improved in tandem one. Purities of isolated compounds were all over 90% as determined by HPLC. Their structures were then identified via UV, MS and (1)H NMR, and eventually assigned as poricoic acid B (1), poricoic acid A (2), 3β,16α-dihydroxylanosta-7, 9(11), 24-trien-21-oic acid (3), dehydrotumulosic acid (4), polyporenic acid C (5), 3-epi-dehydrotumulosic acid (6), 3-o-acetyl-16α-hydroxydehydrotrametenolic acid (7), dehydropachymic acid (8) and dehydrotrametenolic acid (9) respectively. The results indicated that tandem HSCCC can effectively improve peak resolution of target compounds, and can be a good candidate for HSCCC separation of structural analogues. PMID:26435185

  12. Recent advances in topoisomerase I-targeting agents, camptothecin analogues.

    PubMed

    Kim, Dae-Kee; Lee, Namkyu

    2002-12-01

    The present review concentrates on camptothecin (CPT) analogues, the most extensively studied topoisomerase I (topo I) inhibitors, and provides concise information on the structural features of human topo I enzyme, mechanisms of interaction of CPT with topo I, structure-activity relationship study of CPT analogues including the influence of lactone stability on antitumor activity, and recent updates of valuable CPT analogues. PMID:12370044

  13. Structure-activity relationships of new analogues of arecaidine propargyl ester at muscarinic M1 and M2 receptor subtypes.

    PubMed Central

    Moser, U.; Lambrecht, G.; Wagner, M.; Wess, J.; Mutschler, E.

    1989-01-01

    1. The potency of arecaidine propargyl ester (APE) and of several analogues containing a modified ester side chain has been assessed at M1 and M2 muscarinic receptor subtypes. APE was shown to act as a potent agonist at ganglionic M1 receptors in the pithed rat, at M2 receptors in guinea-pig isolated atria (-log EC50 = 8.22) and ileum (-log EC50 = 7.77). 2. The arecaidine 2-butynyl and 2-pentynyl esters were approximately equipotent with APE at M1 and M2 receptors, whereas the 2-hexynyl derivative was found to be less potent than APE in atria (-log EC50 = 6.80) and ileum (-log EC50 = 6.70) by about one order of magnitude. The 2-heptynyl and 3-phenyl propargyl esters exhibited no agonist actions in atria and ileum. 3. Shifting the triple bond from the 2 to the 3 position and introducing a bulky group at position 1 of the ester side chain of APE and analogues resulted in competitive antagonists (pA2 ranging from 4.9 to 7.3). 4. APE and its 2-butynyl analogue showed some agonistic selectivity for cardiac M2 receptors (potency ratio, ileum/atria = 2.8 and 4.6 respectively). All antagonists in this series of compounds were not selective in terms of affinity since their pA2 values at cardiac and ileal M2 receptors were similar (potency ratios, ileum/atria = 0.4 to 1.2). PMID:2924082

  14. Synthesis of cyclic N 1-pentylinosine phosphate, a new structurally reduced cADPR analogue with calcium-mobilizing activity on PC12 cells

    PubMed Central

    Borbone, Nicola; Pinto, Brunella; Secondo, Agnese; Costantino, Valeria; Tedeschi, Valentina; Piccialli, Vincenzo; Piccialli, Gennaro

    2015-01-01

    Summary Cyclic N 1-pentylinosine monophosphate (cpIMP), a novel simplified inosine derivative of cyclic ADP-ribose (cADPR) in which the N 1-pentyl chain and the monophosphate group replace the northern ribose and the pyrophosphate moieties, respectively, was synthesized. The role played by the position of the phosphate group in the key cyclization step, which consists in the formation of a phosphodiester bond, was thoroughly investigated. We have also examined the influence of the phosphate bridge on the ability of cpIMP to mobilize Ca2+ in PC12 neuronal cells in comparison with the pyrophosphate bridge present in the cyclic N 1-pentylinosine diphosphate analogue (cpIDP) previously synthesized in our laboratories. The preliminary biological tests indicated that cpIMP and cpIDP induce a rapid increase of intracellular Ca2+ concentration in PC12 neuronal cells. PMID:26877790

  15. Crystal Structures of the Iron-Sulfur Cluster-Dependent Quinolinate Synthase in Complex with Dihydroxyacetone Phosphate, Iminoaspartate Analogues, and Quinolinate.

    PubMed

    Fenwick, Michael K; Ealick, Steven E

    2016-08-01

    The quinolinate synthase of prokaryotes and photosynthetic eukaryotes, NadA, contains a [4Fe-4S] cluster with unknown function. We report crystal structures of Pyrococcus horikoshii NadA in complex with dihydroxyacetone phosphate (DHAP), iminoaspartate analogues, and quinolinate. DHAP adopts a nearly planar conformation and chelates the [4Fe-4S] cluster via its keto and hydroxyl groups. The active site architecture suggests that the cluster acts as a Lewis acid in enediolate formation, like zinc in class II aldolases. The DHAP and putative iminoaspartate structures suggest a model for a condensed intermediate. The ensemble of structures suggests a two-state system, which may be exploited in early steps. PMID:27404889

  16. Structural characterization of the full-length response regulator spr1814 in complex with a phosphate analogue reveals a novel conformational plasticity of the linker region.

    PubMed

    Park, Ae Kyung; Lee, Jeong Hye; Chi, Young Min; Park, Hyun

    2016-04-29

    Spr1814 of Streptococcus pneumoniae is a response regulator (RR) that belongs to the NarL/FixJ subfamily and has a four-helix helix-turn-helix DNA-binding domain. Here, the X-ray crystal structure of the full-length spr1814 in complex with a phosphate analogue beryllium fluoride (BeF3(-)) was determined at 2.0 Å. This allows for a structural comparison with the previously reported full-length unphosphorylated spr1814. The phosphorylation of conserved aspartic acid residue of N-terminal receiver domain triggers a structural perturbation at the α4-β5-α5 interface, leading to the domain reorganization of spr1814, and this is achieved by a rotational change in the C-terminal DNA-binding domain. PMID:27038544

  17. The crystal structure of an isopenicillin N synthase complex with an ethereal substrate analogue reveals water in the oxygen binding site.

    PubMed

    Clifton, Ian J; Ge, Wei; Adlington, Robert M; Baldwin, Jack E; Rutledge, Peter J

    2013-08-19

    Isopenicillin N synthase (IPNS) is a non-heme iron oxidase central to the biosynthesis of β-lactam antibiotics. IPNS converts the tripeptide δ-(L-α-aminoadipoyl)-L-cysteinyl-D-valine (ACV) to isopenicillin N while reducing molecular oxygen to water. The substrate analogue δ-(L-α-aminoadipoyl)-L-cysteinyl-O-methyl-D-threonine (ACmT) is not turned over by IPNS. Epimeric δ-(L-α-aminoadipoyl)-L-cysteinyl-O-methyl-D-allo-threonine (ACmaT) is converted to a bioactive penam product. ACmT and ACmaT differ from each other only in the stereochemistry at the β-carbon atom of their third residue. These substrates both contain a methyl ether in place of the isopropyl group of ACV. We report an X-ray crystal structure for the anaerobic IPNS:Fe(II):ACmT complex. This structure reveals an additional water molecule bound to the active site metal, held by hydrogen-bonding to the ether oxygen atom of the substrate analogue. PMID:23860486

  18. Synthesis and structure--activity relationships of substituted cinnamic acids and amide analogues: a new class of herbicides.

    PubMed

    Vishnoi, Shipra; Agrawal, Vikash; Kasana, Virendra K

    2009-04-22

    In the present investigation, substituted cinnamic acids (3-hydroxy, 4-hydroxy, 2-nitro, 3-nitro, 4-nitro, 3-chloro, and 4-methoxy) and their amide analogues with four different types of substituted anilines have been synthesized. The synthesized compounds have been screened for their germination inhibition activity on radish (Raphanus sativus L. var. Japanese White) seeds at 50, 100, and 200 ppm concentrations, and the activity was compared with standard herbicide, metribuzin formulation (sencor). Significant activity was exhibited by all of the compounds. It was observed that with the increase in concentration of the test solution, the activity also increased. All of the compounds showed more than 70% inhibition at 100 ppm concentration except 4-hydroxy cinnamanilide. The compound, 2-chloro (4'-hydroxy) cinnamanilide was the best among the tested compounds, and it was found to be at par with the standard, metribuzin at all concentrations. Thus, it can be concluded that substituted cinnamic acids and their amide analogues may be developed as potential herbicides. PMID:19368353

  19. One pot synthesis, structural and spectral analysis of some symmetrical curcumin analogues catalyzed by calcium oxide under microwave irradiation

    NASA Astrophysics Data System (ADS)

    Elavarasan, S.; Bhakiaraj, D.; Chellakili, B.; Elavarasan, T.; Gopalakrishnan, M.

    2012-11-01

    A series of sixteen number of curcumin analogues have been synthesized under microwave irradiation using calcium oxide as a catalyst. The synthesized compounds have been characterized using FT-IR, MS, elemental analysis, 1H and 13C NMR spectroscopic techniques. The UV-Vis absorption studies for these compounds have been studied in order to provide the electronic transitions taking place in the molecule. When compared to the curcumin ((1E,4Z,6E)-5-hydroxy-1,7-bis(4-hydroxy-3-methoxyphenyl)hepta-1,4,6-trien-3-one), the absorption maxima, λmax for all the synthesized curcumin analogues with a variety of substituents gets blue shifted i.e., hypsochromic shift was observed. This shift may be assigned to the change of dipole moment within the solvated molecule. Theoretical calculations regarding the optimization of the synthesized molecules, electronic properties like highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and mapped electron density surface diagrams were done. The geometrical energy, dipole moments and heat of formation values have also been calculated using the ArgusLab package by AM1 semi-empirical method.

  20. Effect of inherited structures on strike-slip plate boundaries: insight from analogue modelling of the central Levant Fracture System, Lebanon

    NASA Astrophysics Data System (ADS)

    Ghalayini, Ramadan; Daniel, Jean-Marc; Homberg, Catherine; Nader, Fadi

    2015-04-01

    Analogue sandbox modeling is a tool to simulate deformation style and structural evolution of sedimentary basins. The initial goal is to test what is the effect of inherited and crustal structures on the propagation, evolution, and final geometry of major strike-slip faults at the boundary between two tectonic plates. For this purpose, we have undertaken a series of analogue models to validate and reproduce the structures of the Levant Fracture System, a major NNE-SSW sinistral strike-slip fault forming the boundary between the Arabian and African plates. Onshore observations and recent high quality 3D seismic data in the Levant Basin offshore Lebanon demonstrated that Mesozoic ENE striking normal faults were reactivated into dextral strike-slip faults during the Late Miocene till present day activity of the plate boundary which shows a major restraining bend in Lebanon with a ~ 30°clockwise rotation in its trend. Experimental parameters consisted of a silicone layer at the base simulating the ductile crust, overlain by intercalated quartz sand and glass sand layers. Pre-existing structures were simulated by creating a graben in the silicone below the sand at an oblique (>60°) angle to the main throughgoing strike-slip fault. The latter contains a small stepover at depth to create transpression during sinistral strike-slip movement and consequently result in mountain building similarly to modern day Lebanon. Strike-slip movement and compression were regulated by steady-speed computer-controlled engines and the model was scanned using a CT-scanner continuously while deforming to have a final 4D model of the system. Results showed that existing normal faults were reactivated into dextral strike-slip faults as the sinistral movement between the two plates accumulated. Notably, the resulting restraining bend is asymmetric and segmented into two different compartments with differing geometries. One compartment shows a box fold anticline, while the second shows an

  1. Phytoplankton community structure defined by key environmental variables in Tagus estuary, Portugal.

    PubMed

    Brogueira, Maria José; Oliveira, Maria do Rosário; Cabeçadas, Graça

    2007-12-01

    In this work, we analyze environmental (physical and chemical) and biological (phytoplankton) data obtained along Tagus estuary during three surveys, carried out in productive period (May/June/July) at ebb tide. The main objective of this study was to identify the key environmental factors affecting phytoplankton structure in the estuary. BIOENV analysis revealed that, in study period, temperature, salinity, silicate and total phosphorus were the variables that best explained the phytoplankton spatial pattern in the estuary (Spearman correlation, rho=0.803). A generalized linear model (GLM) also identified salinity, silicate and phosphate as having a high explanatory power (63%) of phytoplankton abundance. These selected nutrients appear to be consistent with the requirements of the dominant phytoplankton group, Baccilariophyceae. Apparently, phytoplankton community is adapted to fluctuations in light intensity, as suspended particulate matter did not come out as a key factor in shaping phytoplankton structure along Tagus estuary. PMID:17884159

  2. Structure-Odor Activity Studies on Monoterpenoid Mercaptans Synthesized by Changing the Structural Motifs of the Key Food Odorant 1-p-Menthene-8-thiol.

    PubMed

    Schoenauer, Sebastian; Schieberle, Peter

    2016-05-18

    1-p-Menthene-8-thiol (1) has been discovered as the key odorant in grapefruit juice several decades ago and contributes to the overall odor of the fruit with an extremely low odor threshold of 0.000034 ng/L in air. This value is among the lowest odor thresholds ever reported for a food odorant. To check whether modifications in the structure of 1 would lead to changes in odor threshold and odor quality, 34 mercapto-containing p-menthane and 1-p-menthene derivatives as well as several aromatic and open-chain mercapto monoterpenoids were synthesized. Eighteen of them are reported for the first time in the literature, and their odor thresholds and odor qualities as well as analytical data are supplied. A comparison of the sensory data with those of 1 showed that hydrogenation of the double bond led to a clear increase in the odor threshold. Furthermore, moving the mercapto group into the ring always resulted in higher odor thresholds compared to thiols with a mercapto group in the side chains. Although all tertiary thiols always exhibited low odor thresholds, none of the 31 compounds reached the extremely low threshold of 1. Also, none of the synthesized mercapto monoterpenoids showed a similar odor quality resembling grapefruit. Although the saturated and aromatic analogues exhibited similar scents as 1, the aromas of the majority of the other compounds were described as sulfury, rubber-like, burned, soapy, or even mushroom-like. NMR and MS data as well as retention indices of the 23 newly reported sulfur-containing compounds might aid in future research to identify terpene-derived mercaptans possibly present in trace levels in foods. PMID:27121638

  3. Issues of geologically-focused situational awareness in robotic planetary missions: Lessons from an analogue mission at Mistastin Lake impact structure, Labrador, Canada

    NASA Astrophysics Data System (ADS)

    Antonenko, I.; Osinski, G. R.; Battler, M.; Beauchamp, M.; Cupelli, L.; Chanou, A.; Francis, R.; Mader, M. M.; Marion, C.; McCullough, E.; Pickersgill, A. E.; Preston, L. J.; Shankar, B.; Unrau, T.; Veillette, D.

    2013-07-01

    Remote robotic data provides different information than that obtained from immersion in the field. This significantly affects the geological situational awareness experienced by members of a mission control science team. In order to optimize science return from planetary robotic missions, these limitations must be understood and their effects mitigated to fully leverage the field experience of scientists at mission control.Results from a 13-day analogue deployment at the Mistastin Lake impact structure in Labrador, Canada suggest that scale, relief, geological detail, and time are intertwined issues that impact the mission control science team's effectiveness in interpreting the geology of an area. These issues are evaluated and several mitigation options are suggested. Scale was found to be difficult to interpret without the reference of known objects, even when numerical scale data were available. For this reason, embedding intuitive scale-indicating features into image data is recommended. Since relief is not conveyed in 2D images, both 3D data and observations from multiple angles are required. Furthermore, the 3D data must be observed in animation or as anaglyphs, since without such assistance much of the relief information in 3D data is not communicated. Geological detail may also be missed due to the time required to collect, analyze, and request data.We also suggest that these issues can be addressed, in part, by an improved understanding of the operational time costs and benefits of scientific data collection. Robotic activities operate on inherently slow time-scales. This fact needs to be embraced and accommodated. Instead of focusing too quickly on the details of a target of interest, thereby potentially minimizing science return, time should be allocated at first to more broad data collection at that target, including preliminary surveys, multiple observations from various vantage points, and progressively smaller scale of focus. This operational model

  4. Non-scaled analogue modelling of AMS development during viscous flow: A simulation on diapir-like structures

    NASA Astrophysics Data System (ADS)

    Kratinová, Zuzana; Závada, Prokop; Hrouda, František; Schulmann, Karel

    2006-05-01

    Development of magnetic fabric within a diapirically ascending columnar body was investigated using non-scaled analogue model made of plaster of Paris containing small amount of fine-grained homogeneously mixed magnetite. The apparatus for the modelling consists of a manual squeezer with calibrated spring and a Perspex container. Set of weak coloured layers at the bottom of the container was forced to intrude overlying fine-grained sand through a hole in a board attached to the squeezer. The development of AMS fabric is correlated with complex flow pattern indicated by coloured and originally horizontal plaster layers. Strongly constrictional and vertical fabric in the base and in the lower domain of the diapir resulting from convergent and upwards flows is overprinted by subhorizontal oblate fabrics due to vertical flattening and initial divergent flow in the apical parts. The measured AMS fabrics are compared with natural examples of magmatic stocks and dykes.

  5. Scale-integrated observations of morphological biosignatures and associated relict structures: Addressing the practicalities of in situ astrobiology using martian analogue "field" specimens and space instrumentation

    NASA Astrophysics Data System (ADS)

    Pullan, D.; Cockell, C. S.; Pafs-Net

    We investigate how morphological biosignatures 1 could be identified with an array of viable instruments of choice in the framework of robotic planetary surface operations For purposes of the study a modest number of geological hand specimens from our archive of planetary analogues were selected on the basis of feature morphology scale and analogy Three morphological criteria were considered preserved microbial filaments 2 crypto-chasmoendoliths 3 and relict sedimentatry structures 4 The materials originate from a variety of topical martian analogue localities on Earth including impact craters high latitude deserts ancient epochs i e Early Archaean and hydrothermal deposits Instrumentation and techniques available to us included flight spare assets from the Beagle2 deployable package aka the PAW panoramic camera microscope M o ssbauer spectrometer X-ray spectrometer soil sampling Mole aka Planetary Underground Tool PLUTO and rock corer In addition selected commercial equipment served as emulators of potential future instruments including a multi-spectral imager Nuance system a micro-Raman spectrometer Bruker NIR non-confocal and Renishaw VNIR VIS Raman microscopes and a bespoke in situ X-Ray diffractometer Basic requirements for identifying morphological biosignatures are scale-integrated imaging spatial and spectral characterization of host material by analytical means and accessibility to features sample preparation We introduce a scaling philosophy that defines practical working distances for

  6. Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation

    PubMed Central

    Lawrence, Sara L.; Feil, Susanne C.; Morton, Craig J.; Farrand, Allison J.; Mulhern, Terrence D.; Gorman, Michael A.; Wade, Kristin R.; Tweten, Rodney K.; Parker, Michael W.

    2015-01-01

    Pore-forming proteins are weapons often used by bacterial pathogens to breach the membrane barrier of target cells. Despite their critical role in infection important structural aspects of the mechanism of how these proteins assemble into pores remain unknown. Streptococcus pneumoniae is the world’s leading cause of pneumonia, meningitis, bacteremia and otitis media. Pneumolysin (PLY) is a major virulence factor of S. pneumoniae and a target for both small molecule drug development and vaccines. PLY is a member of the cholesterol-dependent cytolysins (CDCs), a family of pore-forming toxins that form gigantic pores in cell membranes. Here we present the structure of PLY determined by X-ray crystallography and, in solution, by small-angle X-ray scattering. The crystal structure reveals PLY assembles as a linear oligomer that provides key structural insights into the poorly understood early monomer-monomer interactions of CDCs at the membrane surface. PMID:26403197

  7. Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation.

    PubMed

    Lawrence, Sara L; Feil, Susanne C; Morton, Craig J; Farrand, Allison J; Mulhern, Terrence D; Gorman, Michael A; Wade, Kristin R; Tweten, Rodney K; Parker, Michael W

    2015-01-01

    Pore-forming proteins are weapons often used by bacterial pathogens to breach the membrane barrier of target cells. Despite their critical role in infection important structural aspects of the mechanism of how these proteins assemble into pores remain unknown. Streptococcus pneumoniae is the world's leading cause of pneumonia, meningitis, bacteremia and otitis media. Pneumolysin (PLY) is a major virulence factor of S. pneumoniae and a target for both small molecule drug development and vaccines. PLY is a member of the cholesterol-dependent cytolysins (CDCs), a family of pore-forming toxins that form gigantic pores in cell membranes. Here we present the structure of PLY determined by X-ray crystallography and, in solution, by small-angle X-ray scattering. The crystal structure reveals PLY assembles as a linear oligomer that provides key structural insights into the poorly understood early monomer-monomer interactions of CDCs at the membrane surface. PMID:26403197

  8. Synthesis and SAR of vinca alkaloid analogues.

    PubMed

    Voss, Matthew E; Ralph, Jeffery M; Xie, Dejian; Manning, David D; Chen, Xinchao; Frank, Anthony J; Leyhane, Andrew J; Liu, Lei; Stevens, Jason M; Budde, Cheryl; Surman, Matthew D; Friedrich, Thomas; Peace, Denise; Scott, Ian L; Wolf, Mark; Johnson, Randall

    2009-02-15

    Versatile intermediates 12'-iodovinblastine, 12'-iodovincristine and 11'-iodovinorelbine were utilized as substrates for transition metal based chemistry which led to the preparation of novel analogues of the vinca alkaloids. The synthesis of key iodo intermediates, their transformation into final products, and the SAR based upon HeLa and MCF-7 cell toxicity assays is presented. Selected analogues 27 and 36 show promising anticancer activity in the P388 murine leukemia model. PMID:19147348

  9. VIRION MORPHOLOGY AND STRUCTURAL ORGANIZATION OF POLYVALENT BACTERIOPHAGES TT10-27 AND KEY.

    PubMed

    Faidiuk, I V; Boyko, A A; Muchnyk, F V; Tovkach, F I

    2015-01-01

    Fine ultrastructure of polyvalent bacteriophages TT10-27 and KEY isolated from affected with fire blight disease plant tissues, was studied using electron microscopy. Phages have isometric heads connected to short complex tail (TT10-27, C1-morphotype) or long non-contractile tail (KEY B-1 morphotype). Maximum diameter of TT10-27 head, measured as the distance between opposite vertices, is 71.3 nm; tail tube of 22 nm in diameter and 9.0 nm in width is framed with 12 appendages that form flabellate structure of 47.0-58.6 nm in diameter. KEY features capsid of 78.6 nm in diameter and flexible non-contractile tail of 172.5 nm long, which ends with a conical tip. Due to a number of features phage TT10-27 was assigned to a group of N4-like phages of Podoviridae family. KEY is a representative of family Siphoviridae, the least freaquent group of Erwinia amylovora phages. PMID:26214897

  10. Key Players in I-DmoI Endonuclease Catalysis Revealed from Structure and Dynamics.

    PubMed

    Molina, Rafael; Besker, Neva; Marcaida, Maria Jose; Montoya, Guillermo; Prieto, Jesús; D'Abramo, Marco

    2016-05-20

    Homing endonucleases, such as I-DmoI, specifically recognize and cleave long DNA target sequences (∼20 bp) and are potentially powerful tools for genome manipulation. However, inefficient and off-target DNA cleavage seriously limits specific editing in complex genomes. One approach to overcome these limitations is to unambiguously identify the key structural players involved in catalysis. Here, we report the E117A I-DmoI mutant crystal structure at 2.2 Å resolution that, together with the wt and Q42A/K120M constructs, is combined with computational approaches to shed light on protein cleavage activity. The cleavage mechanism was related both to key structural effects, such as the position of water molecules and ions participating in the cleavage reaction, and to dynamical effects related to protein behavior. In particular, we found that the protein perturbation pattern significantly changes between cleaved and noncleaved DNA strands when the ions and water molecules are correctly positioned for the nucleophilic attack that initiates the cleavage reaction, in line with experimental enzymatic activity. The proposed approach paves the way for an effective, general, and reliable procedure to analyze the enzymatic activity of endonucleases from a very limited data set, i.e., structure and dynamics. PMID:26909878

  11. Pseudocyanides of sanguinarine and chelerythrine and their series of structurally simple analogues as new anticancer lead compounds: Cytotoxic activity, structure-activity relationship and apoptosis induction.

    PubMed

    Cao, Fang-Jun; Yang, Rui; Lv, Chao; Ma, Qun; Lei, Ming; Geng, Hui-Ling; Zhou, Le

    2015-01-25

    6-Cyano dihydrosanguinarine (CNS) and 6-cyano dihydrochelerythrine (CNC) are respectively artificial derivatives of sanguinarine and chelerythrine, two anticancer quaternary benzo[c]phenanthridine alkaloids (QBAs) while 1-cyano-2-aryl-1,2,3,4-tetrahydroisoquinolines (CATHIQs) are a class of structurally simple analogues of CNS or CNC. This study investigated the inhibition activity of CNS, CNC and CATHIQs on cancer cells, apoptosis induction as well as their preliminary SAR. The results showed that CNS and 18 out of CATHIQs showed IC50 values of 0.53 and 0.62-2.24μM against NB4 and 1.53 and 2.99-11.17μM against MKN-45 cells, respectively, superior to a standard anticancer drug cis-platinum with IC50 of 2.39 and 11.36μM. CNC showed a higher activity against NB4 cells (IC50=1.85μM) and a moderate activity against MKN-45 cells (IC50=12.72μM). Among all CATHIQs, 2 and 17 gave the highest activity against NB4 cells and MKN-45 cells (IC50=0.62 and 2.99μM), respectively. DAPI staining, AO/EB staining and ultrastructure analysis of cells demonstrated that CATHIQs were able to induce apoptosis of the cells in a concentration-dependent manner. SAR showed that substitution patterns on the N-aromatic ring significantly influenced the activity of CATHIQs. The general trend was that the introduction of electron-withdrawing substituents like halogen atom, nitro, trifluoromethyl led to a significant improvement of the activity, while the presence of electron-donating groups like methyl, methoxyl caused a reduction of the activity. In most cases, the 2' site was the most favorable substitution position for the improvement of the activity. Thus, the present results strongly suggested that QBA-type pseudocyanides may serve as potential alternatives of anticancer QBAs while CATHIQs should be a class of promising lead compounds for the development of new QBA-like-type anticancer drugs. CNS exhibited the highest cytotoxicities with IC50 values of 0.53μM on NB4 cells and 1.53

  12. B38: an all-boron fullerene analogue

    NASA Astrophysics Data System (ADS)

    Lv, Jian; Wang, Yanchao; Zhu, Li; Ma, Yanming

    2014-09-01

    Fullerene-like structures formed by elements other than carbon have long been sought. Finding all-boron (B) fullerene-like structures is challenging due to the geometrical frustration arising from competitions among various structural motifs. We report here the prediction of a B38 fullerene analogue found through first-principles swarm structure searching calculations. The structure is highly symmetric and consists of 56 triangles and four hexagons, which provide an optimal void in the center of the cage. Energetically, it is more favorable than the planar and tubular structures, and possesses an unusually high chemical stability: a large energy gap (~2.25 eV) and a high double aromaticity, superior to those of most aromatic quasi-planar B12 and double-ring B20 clusters. Our findings represent a key step forward towards to the understanding of structures of medium-sized B clusters and map out the experimental direction of the synthesis of an all-B fullerene analogue.Fullerene-like structures formed by elements other than carbon have long been sought. Finding all-boron (B) fullerene-like structures is challenging due to the geometrical frustration arising from competitions among various structural motifs. We report here the prediction of a B38 fullerene analogue found through first-principles swarm structure searching calculations. The structure is highly symmetric and consists of 56 triangles and four hexagons, which provide an optimal void in the center of the cage. Energetically, it is more favorable than the planar and tubular structures, and possesses an unusually high chemical stability: a large energy gap (~2.25 eV) and a high double aromaticity, superior to those of most aromatic quasi-planar B12 and double-ring B20 clusters. Our findings represent a key step forward towards to the understanding of structures of medium-sized B clusters and map out the experimental direction of the synthesis of an all-B fullerene analogue. Electronic supplementary information

  13. An optimized structure on FPGA of key point description in SIFT algorithm

    NASA Astrophysics Data System (ADS)

    Xu, Chenyu; Peng, Jinlong; Zhu, En; Zou, Yuxin

    2015-12-01

    SIFT algorithm is one of the most significant and effective algorithms to describe the features of image in the field of image matching. To implement SIFT algorithm to hardware environment is apparently considerable and difficult. In this paper, we mainly discuss the realization of Key Point Description in SIFT algorithm, along with Matching process. In Key Point Description, we have proposed a new method of generating histograms, to avoid the rotation of adjacent regions and insure the rotational invariance. In Matching, we replace conventional Euclidean distance with Hamming distance. The results of the experiments fully prove that the structure we propose is real-time, accurate, and efficient. Future work is still needed to improve its performance in harsher conditions.

  14. Antizyme induction by polyamine analogues as a factor of cell growth inhibition.

    PubMed Central

    Mitchell, John L A; Leyser, Aviva; Holtorff, Michelle S; Bates, Jill S; Frydman, Benjamin; Valasinas, Aldonia L; Reddy, Venodhar K; Marton, Laurence J

    2002-01-01

    The polyamines spermidine and spermine and their diamine precursor putrescine are essential for mammalian cell growth and viability, and strategies are sought for reducing polyamine levels in order to inhibit cancer growth. Several structural analogues of the polyamines have been found to decrease natural polyamine levels and inhibit cell growth, probably by stimulating normal feedback mechanisms. In the present study, a large selection of spermine analogues has been tested for their effectiveness in inducing the production of antizyme, a key protein in feedback inhibition of putrescine synthesis and cellular polyamine uptake. Bisethylnorspermine, bisethylhomospermine, 1,19-bis-(ethylamino)-5,10,15-triazanonadecane, longer oligoamine constructs and many conformationally constrained analogues of these compounds were found to stimulate antizyme synthesis to different levels in rat liver HTC cells, with some producing far more antizyme than the natural polyamine spermine. Uptake of the tested compounds was found to be dependent on, and limited by, the polyamine transport system, for which all these have approximately equal affinity. These analogues differed in their ability to inhibit HTC cell growth during 3 days of exposure, and this ability correlated with their antizyme-inducing potential. This is the first direct evidence that antizyme is induced by several polyamine analogues. Selection of analogues with this potential may be an effective strategy for maximizing polyamine deprivation and growth inhibition. PMID:11972449

  15. Structural comparison of complexes of methotrexate analogues with Lactobacillus casei dihydrofolate reductase by two-dimensional /sup 1/H NMR at 500 MHz

    SciTech Connect

    Hammond, S.J.; Birdsall, B.; Feeney, J.; Searle, M.S.; Roberts, G.C.K.; Cheung, H.T.A.

    1987-12-29

    The authors have used two-dimensional (2D) NMR methods to examine complexes of Lactobacillus casei dihydrofolate reductase and methotrexate (MTX) analogues having structural modifications of the benzoyl ring and also the glutamic acid moiety. Assignments of the /sup 1/H signals in the spectra of the various complexes were made by comparison of their 2D spectra with those complexes containing methotrexate where we have previously assigned resonances from 32 of the 162 amino acid residues. In the complexes formed with the dihalomethotrexate analogues, the glutamic acid and pteridine ring moieties were shown to bind to the enzyme in a manner similar to that found in the methotrexate-enzyme complex. Perturbations in /sup 1/H chemical shifts of protons in Phe-49, Leu-54, and Leu-27 and the methotrexate H7 and NMe protons were observed in the different complexes and were accounted for by changes in orientation of the benzoyl ring in the various complexes. Binding of oxidized or reduced coenzyme to the binary complexes did not result in different shifts for Leu-27, Leu-54, or Leu-19 protons, and thus, the orientation of the benzoyl ring of the methotrexate analogues is not perturbed greatly by the presence of either oxidized or reduced coenzyme. In the complex with the ..gamma..-monoamide analog, the /sup 1/H signals of assigned residues in the protein had almost identical shifts with the corresponding protons in the methotrexate-enzyme complex for all residues except His-28 and, to a lesser extent, Leu-27. This indicates that while the His-28 interaction with the MTX ..gamma..-CO/sub 2//sup -/ is no longer present in this complex with the ..gamma..-amide, there has not been a major change in the overall structure of the two complexes. This behavior contrasts to that of the ..cap alpha..-amide complex where /sup 1/H signals from protons in several amino acid residues are different compared with their values in the complex formed with methotrexate.

  16. Loratadine and analogues: discovery and preliminary structure-activity relationship of inhibitors of the amino acid transporter B(0)AT2.

    PubMed

    Cuboni, Serena; Devigny, Christian; Hoogeland, Bastiaan; Strasser, Andrea; Pomplun, Sebastian; Hauger, Barbara; Höfner, Georg; Wanner, Klaus T; Eder, Matthias; Buschauer, Armin; Holsboer, Florian; Hausch, Felix

    2014-11-26

    B(0)AT2, encoded by the SLC6A15 gene, is a transporter for neutral amino acids that has recently been implicated in mood and metabolic disorders. It is predominantly expressed in the brain, but little is otherwise known about its function. To identify inhibitors for this transporter, we screened a library of 3133 different bioactive compounds. Loratadine, a clinically used histamine H1 receptor antagonist, was identified as a selective inhibitor of B(0)AT2 with an IC50 of 4 μM while being less active or inactive against several other members of the SLC6 family. Reversible inhibition of B(0)AT2 was confirmed by electrophysiology. A series of loratadine analogues were synthesized to gain insight into the structure-activity relationships. Our studies provide the first chemical tool for B(0)AT2. PMID:25318072

  17. Larvicidal activity and structure activity relationship of cinnamoyl amides from Zanthoxylum armatum and their synthetic analogues against diamondback moth, Plutella xylostella

    PubMed Central

    Kumar, Vishal; Reddy, S. G. Eswara; Bhardwaj, Anuja; Dolma, Shudh Kirti; Kumar, Neeraj

    2016-01-01

    Cinnamoyl amides isolated from Zanthoxylum armatum (Rutaceae) and their synthetic analogues were tested for their insecticidal activity against the second instar larvae of diamondback moth, Plutella xylostella (L.) (Lepidoptera: Yponomeutidae) to determine the promising structures with insecticidal activity. Most of the test compounds showed promising activity against larvae of P. xylostella. However, the activities of different compounds varied depending on the presence of different substituents at various positions of both the aromatic rings A and B. Among the tested compounds, 8, N-(3-bromo-4-methoxyphenethyl)cinnamamide showed best larvicidal activity with an LC50 = 62.13 mg/L followed by 6, N-(3׳-bromophenethyl)cinnamamide (LC50=128.49 mg/L) and 2 N-(4׳-methoxyphenylethyl)cinnamamide (LC50 = 225.65 mg/L). PMID:27231477

  18. Drug design by machine learning: the use of inductive logic programming to model the structure-activity relationships of trimethoprim analogues binding to dihydrofolate reductase.

    PubMed

    King, R D; Muggleton, S; Lewis, R A; Sternberg, M J

    1992-12-01

    The machine learning program GOLEM from the field of inductive logic programming was applied to the drug design problem of modeling structure-activity relationships. The training data for the program were 44 trimethoprim analogues and their observed inhibition of Escherichia coli dihydrofolate reductase. A further 11 compounds were used as unseen test data. GOLEM obtained rules that were statistically more accurate on the training data and also better on the test data than a Hansch linear regression model. Importantly machine learning yields understandable rules that characterized the chemistry of favored inhibitors in terms of polarity, flexibility, and hydrogen-bonding character. These rules agree with the stereochemistry of the interaction observed crystallographically. PMID:1454814

  19. Simultaneous evaluation of multiple key material properties of complex stratified structures with large spatial extent

    NASA Astrophysics Data System (ADS)

    Fallahpour, M.; Kajbaf, H.; Ghasr, M. T.; Case, J. T.; Zoughi, R.

    2012-05-01

    Measured complex reflection coefficient of a spatially-extended stratified composite structure, using an open-ended waveguide, can be effectively used to extract key material and geometrical characteristics of any given layer. This is accomplished using a combination of an electromagnetic model and corresponding measurement data. Previously, it was shown that one parameter can be extracted if all others are known. However, practically it is desirable to extract as many pieces of information as possible. To this end the model must be "inverted". However, there is no closed-form solution for the inverse problem, given the mathematical complexity of the forward model. Consequently, we introduce a forward-iterative optimization method to simultaneously extract several pieces of information about the structure. This method defines key unknowns and uses an analytical approach to estimate the reflection coefficient by minimizing a cost-function using conjugate gradient descent (CGD) as optimizer. This paper presents this method along with an experimental result. Information such as thickness and dielectric properties of a layer in a stratified structure is shown to be extracted concurrently.

  20. Insights into the substrate specificity of the MutT pyrophosphohydrolase using structural analogues of 8-oxo-2'-deoxyguanosine nucleotide.

    PubMed

    Hamm, Michelle L; McFadden, Emily J; Ghio, Michael; Lindell, Maria A M; Gerien, Kenneth S; O'Handley, Suzanne F

    2016-04-15

    The bacterial repair enzyme MutT hydrolyzes the damaged nucleotide OdGTP (the 5'-triphosphate derivative of 8-oxo-2'-deoxyguanosine; OdG), which is a known mutagen and has been linked to antibacterial action. Previous work has indicated important roles for the C8-oxygen, N7-hydrogen, and C2-exocyclic amine during OdGTP recognition by MutT. In order to gain a more nuanced understanding of the contribution of these three sites to the overall activity of MutT, we determined the reaction parameters for dGTP, OdGTP, and nine of their analogues using steady state kinetics. Our results indicate that overall high reaction efficiencies can be achieved despite altering any one of these sites. However, altering two or more sites leads to a significant decrease in efficiency. The data also suggest that, similar to another bacterial OdG repair enzyme, MutM, a specific carbonyl in the enzyme can not only promote activity by forming an active site hydrogen bond with the N7-hydrogen of OdGTP, but can also hinder activity through electrostatic repulsion with the N7-lone pair of dGTP. PMID:26965860

  1. An all sulfur analogue of the smallest subunit of F420-non-reducing hydrogenase from Methanococcus voltae--metal binding and structure.

    PubMed

    Pfeiffer, M; Klein, A; Steinert, P; Schomburg, D

    The 25 amino acid long subunit VhuU of the F420-non-reducing hydrogenase from Methanococcus voltae contains selenocysteine within the consensus sequence of known [NiFe] hydrogenases DP(C or U)CxxCxxH (U = selenocysteine). The sulfur-analogue VhuUc was chemically synthesized, purified and its metal binding capability, the catalytic properties, and structural features were investigated. The polypeptide was able to bind nickel, but did not catalyse the heterolytic activation of H2. 2D-NMR spectroscopy revealed an alpha-helical secondary structure for the 15 N-terminal amino acids in 50% TFE. Nickel only binds to the C-terminus, which contains the conserved amino acid motif. Structures derived from the NMR data are compatible with the participation of both sulfur atoms from the conserved cysteine residues in a metal ion binding. Structures obtained from the data sets for Ni.VhuUc as well as Zn.VhuUc showed no further ligands. The informational value for Ni.VhuUc was low due to paramagnetism. PMID:9084873

  2. Heterocyclic chalcone analogues as potential anticancer agents.

    PubMed

    Sharma, Vikas; Kumar, Vipin; Kumar, Pradeep

    2013-03-01

    Chalcones, aromatic ketones and enones acting as the precursor for flavonoids such as Quercetin, are known for their anticancer effects. Although, parent chalcones consist of two aromatic rings joined by a three-carbon α,β-unsaturated carbonyl system, various synthetic compounds possessing heterocyclic rings like pyrazole, indole etc. are well known and proved to be effective anticancer agents. In addition to their use as anticancer agents in cancer cell lines, heterocyclic analogues are reported to be effective even against resistant cell lines. In this connection, we hereby highlight the potential of various heterocyclic chalcone analogues as anticancer agents with a brief summary about therapeutic potential of chalcones, mechanism of anticancer action of various chalcone analogues, and current and future prospects related to the chalcones-derived anticancer research. Furthermore, some key points regarding chalcone analogues have been reviewed by analyzing their medicinal properties. PMID:22721390

  3. Geometry and field dependence of the formation of magnetic antivortices in pound-key-like structures

    NASA Astrophysics Data System (ADS)

    Asmat-Uceda, Martin; Li, Lin; Haldar, Arabinda; Shaw, Brian; Buchanan, Kristen S.

    2015-05-01

    In this work, we assess the effects of field history and structure shape on the formation of magnetic antivortices. The magnetic reversal process was investigated for a series of patterned micron-sized permalloy pound-key structures with varying degrees of asymmetry using magneto-optical Kerr effect hysteresis measurements combined with magnetic force microscopy. The largest number of antivortices was observed in the structures with the highest level of structure asymmetry, which also show an intermediate state in the hysteresis loop. A significant enhancement of the antivortex formation rate—from 5% to almost 80%—was achieved by adjusting the structure dimensions. Images of the magnetic states obtained at various points in the hysteresis loop show that the highest rate of antivortex formation occurs near the coercive field, also the nucleation field, and that the antivortex formation is also sensitive to the angle of the applied field, where the highest antivortex formation rate is observed when the field is aligned along the structure diagonal. A comparison of the experimental results with micromagnetic simulations shows that the areas with lower shape anisotropy lead the reversal in the formation step and the upper field limit for the antivortex stability is related to the reversal of the regions with higher shape anisotropy, although the simulations suggest that the annihilation mechanism will change to one that involves domain wall propagation when the smallest structure dimensions are below ˜60 nm. These results demonstrate how shape anisotropy can be used to promote the formation of isolated magnetic antivortices, which will facilitate future investigations of this topological magnetic state.

  4. X-ray crystal structures of rabbit N-acetylglucosaminyltransferase I (GnT I) in complex with donor substrate analogues.

    PubMed

    Gordon, Roni D; Sivarajah, Prashanth; Satkunarajah, Malathy; Ma, Dengbo; Tarling, Chris A; Vizitiu, Dragos; Withers, Stephen G; Rini, James M

    2006-06-30

    The Golgi-resident glycosyltransferase, UDP-N-acetyl-d-glucosamine:alpha-3-d-mannoside beta-1,2-N-acetylglucosaminyltransferase I (GnT I), initiates the conversion of high-mannose oligosaccharides to complex and hybrid structures in the biosynthesis of N-linked glycans. Reported here are the X-ray crystal structures of GnT I in complex with UDP-CH2-GlcNAc (a non-hydrolyzable C-glycosidic phosphonate), UDP-2-deoxy-2-fluoro-glucose, UDP-glucose and UDP. Collectively, these structures provide evidence for the importance of the GlcNAc moiety and its N-acetyl group in donor substrate binding, as well as insight into the role played by the flexible 318-330 loop in substrate binding and product release. In addition, the UDP-CH2-GlcNAc complex reveals a well-defined glycerol molecule poised for nucleophilic attack on the C1 atom of the donor substrate analogue. The position and orientation of this glycerol molecule have allowed us to model the binding of the Manalpha1,3Manbeta1 moiety of the acceptor substrate and, based on the model, to suggest a rationalization for the main determinants of GnT I acceptor specificity. PMID:16769084

  5. Structured Benefit-risk assessment: a review of key publications and initiatives on frameworks and methodologies.

    PubMed

    Mt-Isa, Shahrul; Ouwens, Mario; Robert, Veronique; Gebel, Martin; Schacht, Alexander; Hirsch, Ian

    2016-07-01

    Introduction The conduct of structured benefit-risk assessment (BRA) of pharmaceutical products is a key area of interest for regulatory agencies and the pharmaceutical industry. However, the acceptance of a standardized approach and implementation are slow. Statisticians play major roles in these organizations, and have a great opportunity to be involved and drive the shaping of future BRA. Method We performed a literature search of recent reviews and initiatives assessing BRA methodologies, and grouped them to assist those new to BRA in learning, understanding, and choosing methodologies. We summarized the key points and discussed the impact of this emerging field on various stakeholders, particularly statisticians in the pharmaceutical industry. Results We provide introductory, essential, special interest, and further information and initiatives materials that direct readers to the most relevant materials, which were published between 2000 and 2013.  Based on recommendations in these materials we supply a toolkit of advocated BRA methodologies. Discussion Despite initiatives promoting these methodologies, there are still barriers, one of which being the lack of a consensus on the most appropriate methodologies among stakeholders. However, this opens up opportunities, for statisticians in the pharmaceutical industry especially, to champion appropriate BRA methodology use throughout the pharmaceutical product lifecycle. Conclusions This article may serve as a starting point for discussions and to reach a mutual consensus for methodology selection in a particular situation. Regulators and pharmaceutical industry should continue to collaborate to develop and take forward BRA methodologies, and by clear communication develop a mutual understanding of the key issues. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25981683

  6. Natural analogues of nuclear waste glass corrosion.

    SciTech Connect

    Abrajano, T.A. Jr.; Ebert, W.L.; Luo, J.S.

    1999-01-06

    This report reviews and summarizes studies performed to characterize the products and processes involved in the corrosion of natural glasses. Studies are also reviewed and evaluated on how well the corrosion of natural glasses in natural environments serves as an analogue for the corrosion of high-level radioactive waste glasses in an engineered geologic disposal system. A wide range of natural and experimental corrosion studies has been performed on three major groups of natural glasses: tektite, obsidian, and basalt. Studies of the corrosion of natural glass attempt to characterize both the nature of alteration products and the reaction kinetics. Information available on natural glass was then compared to corresponding information on the corrosion of nuclear waste glasses, specifically to resolve two key questions: (1) whether one or more natural glasses behave similarly to nuclear waste glasses in laboratory tests, and (2) how these similarities can be used to support projections of the long-term corrosion of nuclear waste glasses. The corrosion behavior of basaltic glasses was most similar to that of nuclear waste glasses, but the corrosion of tektite and obsidian glasses involves certain processes that also occur during the corrosion of nuclear waste glasses. The reactions and processes that control basalt glass dissolution are similar to those that are important in nuclear waste glass dissolution. The key reaction of the overall corrosion mechanism is network hydrolysis, which eventually breaks down the glass network structure that remains after the initial ion-exchange and diffusion processes. This review also highlights some unresolved issues related to the application of an analogue approach to predicting long-term behavior of nuclear waste glass corrosion, such as discrepancies between experimental and field-based estimates of kinetic parameters for basaltic glasses.

  7. Structure of the key species in the enzymatic oxidation of methane to methanol

    PubMed Central

    Banerjee, Rahul; Proshlyakov, Yegor; Lipscomb, John D.; Proshlyakov, Denis A.

    2015-01-01

    Methane monooxygenase (MMO) catalyses the O2-dependent conversion of methane to methanol in methanotrophic bacteria, thereby preventing the atmospheric egress of approximately one billion tons of this potent greenhouse gas annually. The key reaction cycle intermediate of the soluble form of MMO (sMMO) is termed compound Q (Q). Q contains a unique dinuclear FeIV cluster that reacts with methane to break an exceptionally strong 105 kcal mol−1 C-H bond and insert one oxygen atom1,2. No other biological oxidant, except that found in the particulate form of MMO, is capable of such catalysis. The structure of Q remains controversial despite numerous spectroscopic, computational and synthetic model studies2–7. A definitive structural assignment can be made from resonance Raman vibrational spectroscopy but, despite efforts over the past two decades, no vibrational spectrum of Q has yet been obtained. Here we report the core structures of Q and the following product complex, compound T, using time-resolved resonance Raman spectroscopy (TR3). TR3 permits fingerprinting of intermediates by their unique vibrational signatures through extended signal averaging for short-lived species. We report unambiguous evidence that Q possesses a bis-μ-oxo diamond core structure and show that both bridging oxygens originate from O2. This observation strongly supports a homolytic mechanism for O-O bond cleavage. We also show that T retains a single oxygen atom from O2 as a bridging ligand, while the other oxygen atom is incorporated into the product8. Capture of the extreme oxidizing potential of Q is of great contemporary interest for bioremediation and the development of synthetic approaches to methane-based alternative fuels and chemical industry feedstocks. Insight into the formation and reactivity of Q from the structure reported here is an important step towards harnessing this potential. PMID:25607364

  8. eIF2B: recent structural and functional insights into a key regulator of translation.

    PubMed

    Wortham, Noel C; Proud, Christopher G

    2015-12-01

    The eukaryotic translation initiation factor (eIF) eIF2B is a key regulator of mRNA translation, being the guanine nt exchange factor (GEF) responsible for the recycling of the heterotrimeric G-protein, eIF2, which is required to allow translation initiation to occur. Unusually for a GEF, eIF2B is a multi-subunit protein, comprising five different subunits termed α through ε in order of increasing size. eIF2B is subject to tight regulation in the cell and may also serve additional functions. Here we review recent insights into the subunit organization of the mammalian eIF2B complex, gained both from structural studies of the complex and from studies of mutations of eIF2B that result in the neurological disorder leukoencephalopathy with vanishing white matter (VWM). We will also discuss recent data from yeast demonstrating a novel function of the eIF2B complex key for translational regulation. PMID:26614666

  9. A key factor to the spin parameter of uniformly rotating compact stars: crust structure

    NASA Astrophysics Data System (ADS)

    Qi, Bin; Zhang, Nai-Bo; Sun, Bao-Yuan; Wang, Shou-Yu; Gao, Jian-Hua

    2016-04-01

    We study the dimensionless spin parameter j ≡ cJ/(GM2) of different kinds of uniformly rotating compact stars, including traditional neutron stars, hyperonic neutron stars and hybrid stars, based on relativistic mean field theory and the MIT bag model. It is found that jmax ∼ 0.7, which had been suggested in traditional neutron stars, is sustained for hyperonic neutron stars and hybrid stars with M > 0.5 M⊙. Not the interior but rather the crust structure of the stars is a key factor to determine jmax for three kinds of selected compact stars. Furthermore, a universal formula j = 0.63(f/fK) ‑ 0.42(f/fK)2 + 0.48(f/fK)3 is suggested to determine the spin parameter at any rotational frequency f smaller than the Keplerian frequency fK.

  10. Potassium as a key modulator of tropical woody vegetation structure and function

    NASA Astrophysics Data System (ADS)

    Lloyd, Jonathan

    2015-04-01

    Sampling a range of tropical vegetation types across Africa, Australia and South America we find - other things being equal - lower soil and plant potassium concentrations in savanna as opposed to forest species. There is also a trend- similarly observed in cross-continental comparisons, for foliar [K] to increase with declining precipitation. Moreover, when considered in a multivariate context with mean annual precipitation and soil plant available water storage capacity as covariates, soil exchangeable K turns to be an excellent predictor of stand-level canopy areas across vegetation types, providing drastically improved predictions as compared to models considering just precipitation or soil water storage potential alone This underlying basis of an important role for potassium as a modulator of tropical vegetation structure and function will be considered in terms of its role in plant water relations as well as in relation to recent key findings implicating potassium to have an important role in many root-shoot signalling pathways.

  11. Structural Revisions of a Class of Natural Products: Scaffolds of Aglycon Analogues of Fusicoccins and Cotylenins Isolated from Fungi.

    PubMed

    Tang, Ying; Xue, Yongbo; Du, Guang; Wang, Jianping; Liu, Junjun; Sun, Bin; Li, Xiao-Nian; Yao, Guangmin; Luo, Zengwei; Zhang, Yonghui

    2016-03-14

    The reisolation and structural revision of brassicicene D is described, and inspired us to reassign the core skeletons of brassicicenes C-H, J and K, ranging from dicyclopenta[a,d]cyclooctane to tricyclo[9.2.1.0(3,7)]tetradecane using quantum-chemical predictions and experimental validation strategies. Three novel, highly modified fusicoccanes, brassicicenes L-N, were also isolated from the fungus Alternaria brassicicola, and their structures were unequivocally established by spectroscopic data, ECD calculations, and crystallography. The reassigned structures represent the first class of bridgehead double-bond-containing natural products with a bicyclo[6.2.1]undecane carbon skeleton. Furthermore, their stabilities were first predicted with olefin strain energy calculations. Collectively, these findings extend our view of the application of computational predictions and biosynthetic logic-based structure elucidation to address problems related to the structure and stability of natural products. PMID:26916098

  12. Synthesis, crystal structure, high-temperature behavior and magnetic properties of CoBiO(AsO4), a Co analogue of paganoite

    NASA Astrophysics Data System (ADS)

    Aliev, Almaz; Kozin, Michael S.; Colmont, Marie; Siidra, Oleg I.; Krivovichev, Sergey V.; Mentré, Olivier

    2015-09-01

    Single crystals and powder samples of Co analogue of paganoite CoBiO(AsO4) have been obtained by high-temperature solid-state reactions. Crystal structure [triclinic, , a = 5.2380(3), b = 6.8286(4), c = 7.6150(4) Å, α = 111.631(2), β = 108.376(2), γ = 108.388(2)°, V = 209.55(2) Å3] has been refined to R 1 = 0.018 on the basis of 1524 unique observed reflections. CoBiO(AsO4) is isotypic to paganoite, NiBiO(AsO4). The crystal structure can be described as based upon [OCoBi]3+ chains of edge-sharing (OBi2Co2) tetrahedra linked via (AsO4) groups. Differential thermal analysis reveals no phase decomposition till 850 °C, when the compound starts to melt. A small endothermic peak is observed near 330 °C. Thermal expansion has been studied by high-temperature powder X-ray diffraction. Thermal expansion coefficients ( α a = 10.1 × 10-6, α b = 12.6 × 10-6, α c = 10.5 × 10-6 K-1) indicate a relatively isotropic behavior with the less intense expansion direction parallel to the direction of the chains of oxocentered tetrahedra. Magnetic susceptibility of CoBiO(AsO4) reveals the presence of an antiferromagnetic ordering at T N = 15.4 K.

  13. Structural and magnetic properties of Prussian blue analogue molecular magnet Fe1.5[Cr(CN)6].mH2O

    NASA Astrophysics Data System (ADS)

    Bhatt, Pramod; Meena, S. S.; Mukadam, M. D.; Yusuf, S. M.

    2016-05-01

    Molecular magnets, based on Prussian blue analogues, Fe1.5[Cr(CN)6].mH2O have been synthesized in the bulk as well as nanoparticle forms using a co-precipitation method, and their structural and magnetic properties have been investigated using x-ray diffraction (XRD) Mössbauer spectroscopy and dc magnetization. The XRD study confirms the single phase crystalline and nanoparticle nature of the compounds with a face centered cubic (fcc) structure of space group Fm3m. The values of lattice constant are found to be ~10.18(5) Å and ~9.98(9)Å, for the bulk and nanoparticle samples, respectively. The dc magnetization shows a Curie temperature (TC) of ~17 K and ~5 K for the bulk and nanopartcile samples, respectively. The Mossouber spectroscopy reveal that the compound shows spin flipping from the high spin (HS) Fe (CrIII-C≡N-FeII) to low spin (LS) FeII ions (CrIII-N≡C-FeII). Moreover, the TC and the HS state of the Fe ions decreases (converts to its LS states) with time as well as in the nanoparticle form compared to bulk.

  14. Designer DNA-binding drugs: the crystal structure of a meta-hydroxy analogue of Hoechst 33258 bound to d(CGCGAATTCGCG)2.

    PubMed Central

    Clark, G R; Squire, C J; Gray, E J; Leupin, W; Neidle, S

    1996-01-01

    An analogue of the DNA binding compound Hoechst 33258, which has the para hydroxyl group altered to be at the meta position, together with the replacement of one benzimidazole group by pyridylimidazole, has been cocrystallized with the dodecanucleotide sequence d(CGCGAATTCGCG)2. The X-ray structure has been determined at 2.2 A resolution and refined to an R factor of 20.1%. The ligand binds in the minor groove at the sequence 5'-AATTC with the bulky piperazine group extending over the CxG base pair. This binding is stabilised by hydrogen bonding and numerous close van der Waals contacts to the surface of the groove walls. The meta-hydroxyl group was found in two distinct orientations, neither of which participates in direct hydrogen bonds to the exocyclic amino group of a guanine base. The conformation of the drug differs from that found previously in other X-ray structures of Hoechst 33258-DNA complexes. There is significant variation between the minor groove widths in the complexes of Hoechst 33258 and the meta-hydroxyl derivative as a result of these conformational differences. Reasons are discussed for the inability of this derivative to actively recognise guanine. PMID:9017011

  15. Demystifying fluorine chemical shifts: electronic structure calculations address origins of seemingly anomalous (19)F-NMR spectra of fluorohistidine isomers and analogues.

    PubMed

    Kasireddy, Chandana; Bann, James G; Mitchell-Koch, Katie R

    2015-11-11

    Fluorine NMR spectroscopy is a powerful tool for studying biomolecular structure, dynamics, and ligand binding, yet the origins of (19)F chemical shifts are not well understood. Herein, we use electronic structure calculations to describe the changes in (19)F chemical shifts of 2F- and 4F-histidine/(5-methyl)-imidazole upon acid titration. While the protonation of the 2F species results in a deshielded chemical shift, protonation of the 4F isomer results in an opposite, shielded chemical shift. The deshielding of 2F-histidine/(5-methyl)-imidazole upon protonation can be rationalized by concomitant decreases in charge density on fluorine and a reduced dipole moment. These correlations do not hold for 4F-histidine/(5-methyl)-imidazole, however. Molecular orbital calculations reveal that for the 4F species, there are no lone pair electrons on the fluorine until protonation. Analysis of a series of 4F-imidazole analogues, all with delocalized fluorine electron density, indicates that the deshielding of (19)F chemical shifts through substituent effects correlates with increased C-F bond polarity. In summary, the delocalization of fluorine electrons in the neutral 4F species, with gain of a lone pair upon protonation may help explain the difficulty in developing a predictive framework for fluorine chemical shifts. Ideas debated by chemists over 40 years ago, regarding fluorine's complex electronic effects, are shown to have relevance for understanding and predicting fluorine NMR spectra. PMID:26524669

  16. Paleoproterozoic structural evolution of the Man-Leo Shield (West Africa). Key structures for vertical to transcurrent tectonics

    NASA Astrophysics Data System (ADS)

    Lompo, Martin

    2010-08-01

    In the Man-Leo Shield, Paleoproterozoic (Birimian) belts crop out in nine countries of West Africa. Dominant domains include: (i) greenstone belts composed of plutono-volcanic, volcano-clastic and sedimentary rocks, deformed and weakly metamorphosed under regional greenschist facies conditions; (ii) widespread granitoid batholiths. The domains display a basin and dome-like architecture, and are overprinted by partitioned structures from successively shallower crustal depth. Analyses of key ductile and brittle structures has shown that the structural evolution of Man-Leo Shield is characterized by early vertical magmato-tectonics and subsequently, horizontal transcurrent tectonics with progression from ductile to brittle behavior. Basin and dome-like architectures, and the formation of an ubiquitous vertical foliation (MF) formed during emplacement of early amphibole-bearing (PAG) granite plutons at ca. 2.2 Ga by diapirism during NW-SE crustal shortening. Subsequent to a late stage of predominantly NW-SE shortening that created steeply-dipping mylonite zones (Mz1), transcurrent faults became predominant. The formation of transcurrent faults began transpressively, with development of N-S trending regional-scale mylonite zones (Mz1), and a steeply-plunging stretching lineation that probably formed during emplacement of PAG-type granitoids ca. 2.15 Ga. NNE-SSW transpressive sinistral horsetail faults and many NW-SE trending tension veins are interpreted to have formed at this stage. After cooling of the upper crust ca. 2.1 Ga, transcurrent faults became strike-slip in character with formation of dominantly NE-SW dextral faults (Mz2) and the passive emplacement of biotite (PBG) granitoids. Clockwise rotation of the extensional stress axis ( σ3) from NNE-SSW trending to ENE-SSW trending assisted the propagation of dextral NE-SW and sinistral NW-SE extensional en echelon horsetail faults. WNW-ESE trending extension jogs (Egz) are interpreted to have been initiated under

  17. STRUCTURE-ACTIVITY STUDY OF PARACETAMOL ANALOGUES: INHIBITION OF REPLICATIVE DNA SYNTHESIS IN V79 CHINESE HAMSTER CELLS

    EPA Science Inventory

    Experimental and theoretical evidence pertaining to cytotoxic and genotoxic activity of paracetamol in biological systems was used to formulate a simple mechanistic hypothesis to explain the relative inhibition of replicative DNA synthesis by a series of 19 structurally similar p...

  18. Structural style of a compressive wedge with salt and coal shale decollement levels: Analogue and seismic modelling of the Kuqa Thrust Belt (North Tarim, China)

    NASA Astrophysics Data System (ADS)

    Callot, Jean Paul; Guichong, Wang; Moretti, Isabelle; Yongxing, Gu; Letouzey, Jean; Wu, Shengyu

    2013-04-01

    The Kuqa foreland fold and thrust belt developed at the contact between the uplifted basement block of the Tien Shan and the Tarim basin in foreland setting, since early Oligocene. It is mainly controlled by two major decollement levels. Thin skin deformation and Mesozoic thrust sheet develop above the Triassic and Jurassic coal and shale layers. The Paleogene and Neogene salt ridges and synclines developed above the stacked thrust sheets through the Paleogene salt layer. 4D Analogue models imaged with X-ray tomography are used to analyse the relative importance several parameters such as (1) the kinematic boundary conditions, (2) the rheological behaviour of the main decollement levels, and (3) erosion and sedimentation, on the present structure evolution. The experiments demonstrate that the geometry of the belt is controlled by the regional distribution of both decollement levels. The lower decollement requires a weak frictional behaviour, pinching toward the south, whereas the viscous Paleogene salt layer, pinching regularly to the South and passing gradually to clastic deposits to the North close to the Tien Shan boundary. The geometry of salt ridges and diapirs dvlopped during the early tectonic phase associated with a low sedimentation rate controls the shape and localisation of the future foreland synclines and boundaries. The synclines grow during the late stage of evolution with a rapid increase in flexure and sedimentation rate. The backstop geometry is the second major element, controlling the dip of the Mesozoic stacked thrust sheet below the salt. Inverted basement block associated to a basement short cut emplaced during the late stage of evolution are both needed to generate the overall geometry of these units. Based on the analogue models, the geometry of the thrust sheet and foreland syncline is used to perform a synthetic seismic profile in order to test the ability to image the deep parts of the thrust sheets below complex structures. The

  19. Key factors limiting carbon nanotube yarn strength: exploring processing-structure-property relationships.

    PubMed

    Beese, Allison M; Wei, Xiaoding; Sarkar, Sourangsu; Ramachandramoorthy, Rajaprakash; Roenbeck, Michael R; Moravsky, Alexander; Ford, Matthew; Yavari, Fazel; Keane, Denis T; Loutfy, Raouf O; Nguyen, SonBinh T; Espinosa, Horacio D

    2014-11-25

    Studies of carbon nanotube (CNT) based composites have been unable to translate the extraordinary load-bearing capabilities of individual CNTs to macroscale composites such as yarns. A key challenge lies in the lack of understanding of how properties of filaments and interfaces across yarn hierarchical levels govern the properties of macroscale yarns. To provide insight required to enable the development of superior CNT yarns, we investigate the fabrication-structure-mechanical property relationships among CNT yarns prepared by different techniques and employ a Monte Carlo based model to predict upper bounds on their mechanical properties. We study the correlations between different levels of alignment and porosity and yarn strengths up to 2.4 GPa. The uniqueness of this experimentally informed modeling approach is the model's ability to predict when filament rupture or interface sliding dominates yarn failure based on constituent mechanical properties and structural organization observed experimentally. By capturing this transition and predicting the yarn strengths that could be obtained under ideal fabrication conditions, the model provides critical insights to guide future efforts to improve the mechanical performance of CNT yarn systems. This multifaceted study provides a new perspective on CNT yarn design that can serve as a foundation for the development of future composites that effectively exploit the superior mechanical performance of CNTs. PMID:25353651

  20. Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits.

    PubMed

    Hocky, Glen M; Baker, Joseph L; Bradley, Michael J; Sinitskiy, Anton V; De La Cruz, Enrique M; Voth, Gregory A

    2016-05-26

    Ions regulate the assembly and mechanical properties of actin filaments. Recent work using structural bioinformatics and site-specific mutagenesis favors the existence of two discrete and specific divalent cation binding sites on actin filaments, positioned in the long axis between actin subunits. Cation binding at one site drives polymerization, while the other modulates filament stiffness and plays a role in filament severing by the regulatory protein, cofilin. Existing structural methods have not been able to resolve filament-associated cations, and so in this work we turn to molecular dynamics simulations to suggest a candidate binding pocket geometry for each site and to elucidate the mechanism by which occupancy of the "stiffness site" affects filament mechanical properties. Incorporating a magnesium ion in the "polymerization site" does not seem to require any large-scale change to an actin subunit's conformation. Binding of a magnesium ion in the "stiffness site" adheres the actin DNase-binding loop (D-loop) to its long-axis neighbor, which increases the filament torsional stiffness and bending persistence length. Our analysis shows that bound D-loops occupy a smaller region of accessible conformational space. Cation occupancy buries key conserved residues of the D-loop, restricting accessibility to regulatory proteins and enzymes that target these amino acids. PMID:27146246

  1. OptZyme: Computational Enzyme Redesign Using Transition State Analogues

    PubMed Central

    Grisewood, Matthew J.; Gifford, Nathanael P.; Pantazes, Robert J.; Li, Ye; Cirino, Patrick C.; Janik, Michael J.; Maranas, Costas D.

    2013-01-01

    OptZyme is a new computational procedure for designing improved enzymatic activity (i.e., kcat or kcat/KM) with a novel substrate. The key concept is to use transition state analogue compounds, which are known for many reactions, as proxies for the typically unknown transition state structures. Mutations that minimize the interaction energy of the enzyme with its transition state analogue, rather than with its substrate, are identified that lower the transition state formation energy barrier. Using Escherichia coli β-glucuronidase as a benchmark system, we confirm that KM correlates (R2 = 0.960) with the computed interaction energy between the enzyme and the para-nitrophenyl- β, D-glucuronide substrate, kcat/KM correlates (R2 = 0.864) with the interaction energy of the transition state analogue, 1,5-glucarolactone, and kcat correlates (R2 = 0.854) with a weighted combination of interaction energies with the substrate and transition state analogue. OptZyme is subsequently used to identify mutants with improved KM, kcat, and kcat/KM for a new substrate, para-nitrophenyl- β, D-galactoside. Differences between the three libraries reveal structural differences that underpin improving KM, kcat, or kcat/KM. Mutants predicted to enhance the activity for para-nitrophenyl- β, D-galactoside directly or indirectly create hydrogen bonds with the altered sugar ring conformation or its substituents, namely H162S, L361G, W549R, and N550S. PMID:24116038

  2. The analysis of structure-anticancer and antiviral activity relationships for macrocyclic pyridinophanes and their analogues on the basis of 4D QSAR models (simplex representation of molecular structure).

    PubMed

    Kuz'min, Victor E; Artemenko, Anatoly G; Lozitsky, Victor P; Muratov, Eugene N; Fedtchouk, Alla S; Dyachenko, Natalia S; Nosach, Lidiya N; Gridina, Tatiyana L; Shitikova, Larisa I; Mudrik, Liubov M; Mescheriakov, Aleksey K; Chelombitko, Vladislav A; Zheltvay, Andrey I; Vanden Eynde, Jean-Jaques

    2002-01-01

    A new 4D-QSAR approach has been considered. For all investigated molecules the 3D structural models have been created and the set of conformers (fourth dimension) have been used. Each conformer is represented as a system of different simplexes (tetratomic fragments of fixed structure, chirality and symmetry). The investigation of influence of molecular structure of macrocyclic pyridinophanes, their analogues and certain other compounds on anticancer and antiviral (anti-influenza, antiherpes and antiadenovirus) activity has been carried out by means of the 4D-QSAR. Statistic characteristics for QSAR of PLS (partial least squares) models are satisfactory (R = 0.92-0.97; CVR = 0.63-0.83). Molecular fragments increasing and decreasing biological activity were defined. This information may be useful for design, and direct synthesis of novel anticancer and antiviral agents. PMID:12136936

  3. Chemical Synthesis, Crystal Structure and Enzymatic Evaluation of a Dinucleotide Spore Photoproduct Analogue Containing a Formacetal Linker

    PubMed Central

    Lin, Gengjie; Chen, Chun-Hsing; Pink, Maren; Pu, Jingzhi; Li, Lei

    2011-01-01

    Spore photoproduct (SP) is the exclusive DNA photodamage product found in bacterial endospores. Its photoformation and repair by a metal-loenzyme spore photoproduct lyase (SPL) composes the unique SP biochemistry. Despite the fact that the SP was discovered almost 50 years ago, its crystal structure is still unknown and the lack of structural information greatly hinders the study of SP biochemistry. Employing a formacetal linker and organic synthesis, we successfully prepared a dinucleotide SP isostere 5R-CH2SP, which contains a neutral CH2 moiety between the two thymine residues instead of a phosphate. The neutral linker dramatically facilitates the crystallization process, allowing us to obtain the crystal structure for this intriguing thymine dimer half a century after its discovery. Further ROESY spectroscopic, DFT computational, and enzymatic studies of this 5R-CH2SP compound prove that it possesses similar properties with the 5R-SP species, suggesting that the revealed structure truly reflects that of SP generated in Nature. PMID:21780208

  4. Augmenting the activity of antifungal agents against aspergilli using structural analogues of benzoic acid as chemosensitizing agents

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Several benzoic acid analogs showed antifungal activity against strains of Aspergillus flavus, A. fumigatus and A. terreus, causative agents of human aspergillosis. Structure-activity analysis revealed that antifungal activities of benzoic and gallic acids increased by addition of a methyl, methoxyl...

  5. Augmenting the activity of antifungal agents against aspergilli using structural analogues of benzoic acid as chemosensitizing agents

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Structure-activity analysis revealed that antifungal activities of benzoic and gallic acids were increased against strains of Aspergillus flavus, A. fumigatus and A. terreus, causative agents of human aspergillosis, by addition of a methyl, methoxyl or a chloro group at position 4 of the aromatic ri...

  6. Crystal structures and hydrogen bonding in the morpholinium salts of four phen­oxy­acetic acid analogues

    PubMed Central

    Smith, Graham; Lynch, Daniel E.

    2015-01-01

    The anhydrous salts morpholinium (tetra­hydro-2-H-1,4-oxazin-4-ium) phen­oxy­acetate, C4H10NO+·C8H7O3 −, (I), morpholinium (4-fluoro­phen­oxy)acetate, C4H10NO+·C8H6 FO3 −, (II), and isomeric morpholinium (3,5-di­chloro­phen­oxy)acetate (3,5-D), (III), and morpholinium (2,4-di­chloro­phen­oxy)acetic acid (2,4-D), C4H10NO+·C8H5Cl2O3 −, (IV), have been determined and their hydrogen-bonded structures are described. In the crystals of (I), (III) and (IV), one of the the aminium H atoms is involved in a three-centre asymmetric cation–anion N—H⋯O,O′ R 1 2(4) hydrogen-bonding inter­action with the two carboxyl O-atom acceptors of the anion. With the structure of (II), the primary N—H⋯O inter­action is linear. In the structures of (I), (II) and (III), the second N—H⋯Ocarbox­yl hydrogen bond generates one-dimensional chain structures extending in all cases along [100]. With (IV), the ion pairs are linked though inversion-related N—H⋯O hydrogen bonds [graph set R 4 2(8)], giving a cyclic hetero­tetra­meric structure. PMID:26594518

  7. Evaluating minimalist mimics by exploring key orientations on secondary structures (EKOS)☟

    PubMed Central

    Xin, Dongyue; Ko, Eunhwa; Perez, Lisa M.; Ioerger, Thomas R.; Burgess, Kevin

    2013-01-01

    Peptide mimics that display amino acid side-chains on semi-rigid scaffolds (not peptide polyamides) can be referred to as minimalist mimics. Accessible conformations of these scaffolds may overlay with secondary structures giving, for example, “minimalist helical mimics”. It is difficult for researchers who want to apply minimalist mimics to decide which one to use because there is no widely accepted protocol for calibrating how closely these compounds mimic secondary structures. Moreover, it is also difficult for potential practitioners to evaluate which ideal minimalist helical mimics are preferred for a particular set of side-chains. For instance, what mimic presents i, i+4, i+7 side-chains in orientations that best resemble an ideal α-helix, and is a different mimic required for a i, i+3, i+7 helical combination? This article describes a protocol for fitting each member of an array of accessible scaffold conformations on secondary structures. The protocol involves: (i) use quenched molecular dynamics (QMD) to generate an ensemble consisting of hundreds of accessible, low energy conformers of the mimics; (ii) representation of each of these as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds;(iii) similar representation of each combination of three side-chains in each ideal secondary structure as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds; and, (iv) overlay Cα and Cβ coordinates of all the conformers on all the sets of side-chain “triads” in the ideal secondary structures and express the goodness of fit in terms of root mean squared deviation (RMSD, Å) for each overlay. We refer to this process as Exploring Key Orientations on Secondary structures (EKOS). Application of this procedure reveals the relative bias of a scaffold to overlay on different secondary structures, the “side-chain correspondences” (eg i, i+4, i+7 or i, i+3

  8. Evaluation of Cancer Preventive Activity and Structure-Activity Relationships of 3-Demethylubiquinone Q2, Isolated from the Ascidian Aplidium glabrum, and its Synthetic Analogues

    PubMed Central

    Fedorov, Sergey N.; Radchenko, Oleg S.; Shubina, Larisa K.; Balaneva, Nadezhda N.; Bode, Ann M.; Stonik, Valentin A.; Dong, Zigang

    2006-01-01

    Purpose 3-Demethylubiquinone Q2 (1) was isolated from the ascidian Aplidium glabrum. The cancer preventive properties and the structure-activity relationship for 3-demethylubiquinone Q2 (1) and 12 of its synthetic analogues (3–14) are reported. Methods Compounds 3–14, having one or several di- or triprenyl substitutions and quinone moieties with methoxyls in different positions, were synthesized. The cancer preventive properties of compounds 1 and 3–14 were tested in JB6 Cl41 mouse skin cells, using a variety of assessments, including the MTS assay, flow cytometry, and soft agar assay. Statistical nonparametric methods were used to confirm statistical significance. Results All quinones tested were shown to inhibit JB6 Cl41 cell transformation, to induce apoptosis, AP-1 and NF-κB activity, and to inhibit p53 activity. The most promising effects were indicated for compounds containing two isoprene units in a side chain and a methoxyl group at the para-position to a polyprenyl substitution. Conclusions Quinones 1 and 3–14 demonstrated cancer preventive activity in JB6 Cl41 cells, which may be attributed to the induction of p53-independent apoptosis. These activities depended on the length of side chains and on the positions of the methoxyl groups in the quinone part of the molecule. PMID:16320003

  9. Fluorous Analogue of Chloramine-T: Preparation, X-ray Structure Determination, and Use as an Oxidant for Radioiodination and s-Tetrazine Synthesis.

    PubMed

    Dzandzi, James P K; Beckford Vera, Denis R; Genady, Afaf R; Albu, Silvia A; Eltringham-Smith, Louise J; Capretta, Alfredo; Sheffield, William P; Valliant, John F

    2015-07-17

    A fluorous oxidant that can be used to introduce radioiodine into small molecules and proteins and generate iodinated tetrazines for bioorthogonal chemistry has been developed. The oxidant was prepared in 87% overall yield by combining a fluorous amine with tosyl chloride, followed by chlorination using aqueous sodium hypochlorite. A crystal structure of the oxidant, which is a fluorous analogue of chloramine-T, was obtained. The compound was shown to be stable for 7 days in EtOH and for longer than three months as a solid. The oxidant was effective at promoting the labeling of arylstannanes using [(125)I]NaI, where products were isolated in high specific activity in yields ranging from 46% to 86%. Similarly, iodinated biologically active proteins (e.g., thrombin) were successfully produced, as well as a radioiodinated tetrazine, through a concomitant oxidation-halodemetalation reaction. Because of its fluorous nature, unreacted oxidant and associated reaction byproducts can be removed quantitatively from reaction mixtures by passing solutions through fluorous solid phase extraction cartridges. This feature enables rapid and facile purification, which is critical when working with radionuclides and is similarly beneficial for general synthetic applications. PMID:26030355

  10. Structure of Bacillus subtilis γ-glutamyltranspeptidase in complex with acivicin: diversity of the binding mode of a classical and electrophilic active-site-directed glutamate analogue

    SciTech Connect

    Ida, Tomoyo; Suzuki, Hideyuki; Fukuyama, Keiichi; Hiratake, Jun; Wada, Kei

    2014-02-01

    The binding modes of acivicin, a classical and an electrophilic active-site-directed glutamate analogue, to bacterial γ-glutamyltranspeptidases were found to be diverse. γ-Glutamyltranspeptidase (GGT) is an enzyme that plays a central role in glutathione metabolism, and acivicin is a classical inhibitor of GGT. Here, the structure of acivicin bound to Bacillus subtilis GGT determined by X-ray crystallography to 1.8 Å resolution is presented, in which it binds to the active site in a similar manner to that in Helicobacter pylori GGT, but in a different binding mode to that in Escherichia coli GGT. In B. subtilis GGT, acivicin is bound covalently through its C3 atom with sp{sup 2} hybridization to Thr403 O{sup γ}, the catalytic nucleophile of the enzyme. The results show that acivicin-binding sites are common, but the binding manners and orientations of its five-membered dihydroisoxazole ring are diverse in the binding pockets of GGTs.

  11. Quantitative Structure of an Acetate Dye Molecule Analogue at the TiO2–Acetic Acid Interface

    PubMed Central

    2016-01-01

    The positions of atoms in and around acetate molecules at the rutile TiO2(110) interface with 0.1 M acetic acid have been determined with a precision of ±0.05 Å. Acetate is used as a surrogate for the carboxylate groups typically employed to anchor monocarboxylate dye molecules to TiO2 in dye-sensitized solar cells (DSSC). Structural analysis reveals small domains of ordered (2 × 1) acetate molecules, with substrate atoms closer to their bulk terminated positions compared to the clean UHV surface. Acetate is found in a bidentate bridge position, binding through both oxygen atoms to two 5-fold titanium atoms such that the molecular plane is along the [001] azimuth. Density functional theory calculations provide adsorption geometries in excellent agreement with experiment. The availability of these structural data will improve the accuracy of charge transport models for DSSC. PMID:27110318

  12. NMR structure determination of a synthetic analogue of bacillomycin Lc reveals the strategic role of L-Asn1 in the natural iturinic antibiotics

    NASA Astrophysics Data System (ADS)

    Volpon, Laurent; Tsan, Pascale; Majer, Zsuzsa; Vass, Elemer; Hollósi, Miklós; Noguéra, Valérie; Lancelin, Jean-Marc; Besson, Françoise

    2007-08-01

    Iturins are a group of antifungal produced by Bacillus subtilis. All are cyclic lipopeptides with seven α-amino acids of configuration LDDLLDL and one β-amino fatty acid. The bacillomycin L is a member of this family and its NMR structure was previously resolved using the sequence Asp-Tyr-Asn-Ser-Gln-Ser-Thr. In this work, we carefully examined the NMR spectra of this compound and detected an error in the sequence. In fact, Asp1 and Gln5 need to be changed into Asn1 and Glu5, which therefore makes it identical to bacillomycin Lc. As a consequence, it now appears that all iturinic peptides with antibiotic activity share the common β-amino fatty acid 8- L-Asn1- D-Tyr2- D-Asn3 sequence. To better understand the conformational influence of the acidic residue L-Asp1, present, for example in the inactive iturin C, the NMR structure of the synthetic analogue SCP [cyclo ( L-Asp1- D-Tyr2- D-Asn3- L-Ser4- L-Gln5- D-Ser6- L-Thr7-β-Ala8)] was determined and compared with bacillomycin Lc recalculated with the corrected sequence. In both cases, the conformers obtained were separated into two families of similar energy which essentially differ in the number and type of turns. A detailed analysis of both cyclopeptide structures is presented here. In addition, CD and FTIR spectra were performed and confirmed the conformational differences observed by NMR between both cyclopeptides.

  13. Biological activity in Technosols as a key factor of their structure

    NASA Astrophysics Data System (ADS)

    Watteau, Françoise; Villemin, Geneviève; Bouchard, Adeline; Monserié, Marie-France; Séré, Geoffroy; Schwartz, Christophe; Morel, Jean-Louis

    2010-05-01

    )availability. HAP also contributed to the aggregation of technogenic constituents in Technosol 1. The biological activity generated by the presence of exogenous organic matter is thus in short (0-2 years) and mean (30 years) terms, a key factor of the structuration and by there of the pedogenesis of Technosols.

  14. Encoding complexity within supramolecular analogues of frustrated magnets.

    PubMed

    Cairns, Andrew B; Cliffe, Matthew J; Paddison, Joseph A M; Daisenberger, Dominik; Tucker, Matthew G; Coudert, François-Xavier; Goodwin, Andrew L

    2016-05-01

    The solid phases of gold(I) and/or silver(I) cyanides are supramolecular assemblies of inorganic polymer chains in which the key structural degrees of freedom-namely, the relative vertical shifts of neighbouring chains-are mathematically equivalent to the phase angles of rotating planar ('XY') spins. Here, we show how the supramolecular interactions between chains can be tuned to mimic different magnetic interactions. In this way, the structures of gold(I) and/or silver(I) cyanides reflect the phase behaviour of triangular XY magnets. Complex magnetic states predicted for this family of magnets-including collective spin-vortices of relevance to data storage applications-are realized in the structural chemistry of these cyanide polymers. Our results demonstrate how chemically simple inorganic materials can behave as structural analogues of otherwise inaccessible 'toy' spin models and also how the theoretical understanding of those models allows control over collective ('emergent') phenomena in supramolecular systems. PMID:27102677

  15. Electronic structure and photoelectron spectra of nickel (II) acetylacetonate and its thio- and amino-substituted analogues

    NASA Astrophysics Data System (ADS)

    Vovna, Vitaliy V.; Korochentsev, Vladimir V.; Komissarov, Aleksandr A.; L'vov, Igor B.; Myshakina, Nataliya S.

    2015-11-01

    Using ultraviolet photoelectron spectroscopy and electron density functional theory (DFT), we investigated the electronic structure of the d8 complex acetylacetonate Ni(a\\scsim a\\scsim)2 and its NH, S and NCH2-substitutes: nickel bis(acetylacetoneiminate) (Ni(acim)2), Ni(Sacac)2 and nickel N,N‧-Ethylene-bis(acetylacetoneiminate) (NiEcim), respectively. Based on the spectral regularities and calculated results for these four compounds, we interpreted the PE spectra to approximate the extended Koopmans' theorem IEi = -ɛi + δi using the δi relationship to the molecular orbital type, which differs substantially from earlier published interpretations. We determined the vertical ionization energies for the four pairs of ligand n- and π-levels and four d-type orbitals for the metal. We further discussed the regularities established both experimentally and theoretically for the influence that substituting S, NH and NCH2- for O exerted on the electronic and spatial structure of the complexes, effective atomic charges and intra-complex coordinate bonds.

  16. New bitter-masking compounds: hydroxylated benzoic acid amides of aromatic amines as structural analogues of homoeriodictyol.

    PubMed

    Ley, Jakob P; Blings, Maria; Paetz, Susanne; Krammer, Gerhard E; Bertram, Heinz-Jürgen

    2006-11-01

    Starting from the known bitter-masking flavanones eriodictyol and homoeriodictyol from herba santa some structurally related hydroxybenzoic acid amides of benzylamines were synthesized and evaluated as masking agents toward bitterness of caffeine by sensory methods. The closest structural relatives of homoeriodictyol, the hydroxybenzoic acid vanillylamides 5-9, were the most active and were able to reduce the bitterness of a 500 mg L(-1) caffeine solution by about 30% at a concentration of 100 mg L(-1). 2,4-Dihydroxybenzoic acid vanillylamide 7 showed a clear dose-dependent activity as inhibitor of the bitter taste of caffein between 5 and 500 mg L(-1). Additionally, it was possible to reduce the bitterness of quinine and salicine but not of the bitter peptide N-l-leucyl-l-tryptophan. Combinations of homoeriodictyol and amide 7 showed no synergistic or antagonistic changes in activity. The results for model compound 7 suggested that the hitherto unknown masking mechanism is probably the same for flavanones and the new amides. In the future, the new amides may be alternatives for the expensive flavanones to create flavor solutions to mask bitterness of pharmaceuticals or foodstuffs. PMID:17061836

  17. Crystal structure of farnesyl protein transferase complexed with a CaaX peptide and farnesyl diphosphate analogue.

    PubMed

    Strickland, C L; Windsor, W T; Syto, R; Wang, L; Bond, R; Wu, Z; Schwartz, J; Le, H V; Beese, L S; Weber, P C

    1998-11-24

    The crystallographic structure of acetyl-Cys-Val-Ile-selenoMet-COOH and alpha-hydroxyfarnesylphosphonic acid (alphaHFP) complexed with rat farnesyl protein transferase (FPT) (space group P61, a = b = 174. 13 A, c = 69.71 A, alpha = beta = 90 degrees, gamma = 120 degrees, Rfactor = 21.8%, Rfree = 29.2%, 2.5 A resolution) is reported. In the ternary complex, the bound substrates are within van der Waals contact of each other and the FPT enzyme. alphaHFP binds in an extended conformation in the active-site cavity where positively charged side chains and solvent molecules interact with the phosphate moiety and aromatic side chains pack adjacent to the isoprenoid chain. The backbone of the bound CaaX peptide adopts an extended conformation, and the side chains interact with both FPT and alphaHFP. The cysteine sulfur of the bound peptide coordinates the active-site zinc. Overall, peptide binding and recognition appear to be dominated by side-chain interactions. Comparison of the structures of the ternary complex and unliganded FPT [Park, H., Boduluri, S., Moomaw, J., Casey, P., and Beese, L. (1997) Science 275, 1800-1804] shows that major rearrangements of several active site side chains occur upon substrate binding. PMID:9843427

  18. A thiamin-bound, pre-decarboxylation reaction intermediate analogue in the pyruvate dehydrogenase E1 subunit induces large scale disorder-to-order transformations in the enzyme and reveals novel structural features in the covalently bound adduct.

    PubMed

    Arjunan, Palaniappa; Sax, Martin; Brunskill, Andrew; Chandrasekhar, Krishnamoorthy; Nemeria, Natalia; Zhang, Sheng; Jordan, Frank; Furey, William

    2006-06-01

    The crystal structure of the E1 component from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc) has been determined with phosphonolactylthiamin diphosphate (PLThDP) in its active site. PLThDP serves as a structural and electrostatic analogue of the natural intermediate alpha-lactylthiamin diphosphate (LThDP), in which the carboxylate from the natural substrate pyruvate is replaced by a phosphonate group. This represents the first example of an experimentally determined, three-dimensional structure of a thiamin diphosphate (ThDP)-dependent enzyme containing a covalently bound, pre-decarboxylation reaction intermediate analogue and should serve as a model for the corresponding intermediates in other ThDP-dependent decarboxylases. Regarding the PDHc-specific reaction, the presence of PLThDP induces large scale conformational changes in the enzyme. In conjunction with the E1-PLThDP and E1-ThDP structures, analysis of a H407A E1-PLThDP variant structure shows that an interaction between His-407 and PLThDP is essential for stabilization of two loop regions in the active site that are otherwise disordered in the absence of intermediate analogue. This ordering completes formation of the active site and creates a new ordered surface likely involved in interactions with the lipoyl domains of E2s within the PDHc complex. The tetrahedral intermediate analogue is tightly held in the active site through direct hydrogen bonds to residues His-407, Tyr-599, and His-640 and reveals a new, enzyme-induced, strain-related feature that appears to aid in the decarboxylation process. This feature is almost certainly present in all ThDP-dependent decarboxylases; thus its inclusion in our understanding of general thiamin catalysis is important. PMID:16531404

  19. Crystal Structure of Insulin-Regulated Aminopeptidase with Bound Substrate Analogue Provides Insight on Antigenic Epitope Precursor Recognition and Processing.

    PubMed

    Mpakali, Anastasia; Saridakis, Emmanuel; Harlos, Karl; Zhao, Yuguang; Papakyriakou, Athanasios; Kokkala, Paraskevi; Georgiadis, Dimitris; Stratikos, Efstratios

    2015-09-15

    Aminopeptidases that generate antigenic peptides influence immunodominance and adaptive cytotoxic immune responses. The mechanisms that allow these enzymes to efficiently process a vast number of different long peptide substrates are poorly understood. In this work, we report the structure of insulin-regulated aminopeptidase, an enzyme that prepares antigenic epitopes for cross-presentation in dendritic cells, in complex with an antigenic peptide precursor analog. Insulin-regulated aminopeptidase is found in a semiclosed conformation with an extended internal cavity with limited access to the solvent. The N-terminal moiety of the peptide is located at the active site, positioned optimally for catalysis, whereas the C-terminal moiety of the peptide is stabilized along the extended internal cavity lodged between domains II and IV. Hydrophobic interactions and shape complementarity enhance peptide affinity beyond the catalytic site and support a limited selectivity model for antigenic peptide selection that may underlie the generation of complex immunopeptidomes. PMID:26259583

  20. The role of structural inheritance in oblique rifting: Insights from analogue models and application to the Gulf of Aden

    NASA Astrophysics Data System (ADS)

    Autin, Julia; Bellahsen, Nicolas; Leroy, Sylvie; Husson, Laurent; Beslier, Marie-Odile; d'Acremont, Elia

    2013-11-01

    The geometry and kinematics of rifts are strongly controlled by pre-existing structures that may be present in both the crust and the mantle lithosphere. In the Gulf of Aden, the Tertiary oblique rift developed through inherited Mesozoic extensional basins that trend orthogonal to the direction of Oligo-Miocene divergence. Such inheritance may produce lateral variations in crustal thickness and thus in rheology of the crust and mantle lithosphere. How can such variations influence the present-day geometry of oblique rifts? May they locally overcome the impact of the oblique rheological weaknesses that in certain cases control the overall trend of the rift system? Moreover, we observe that major fracture zones systematically crosscut the inherited basins: may such inheritance influence the localization of major fracture zones by shifting the initial spreading centers?

  1. Simulated ΛCDM analogues of the thin plane of satellites around the Andromeda galaxy are not kinematically coherent structures

    NASA Astrophysics Data System (ADS)

    Buck, Tobias; Dutton, Aaron A.; Macciò, Andrea V.

    2016-08-01

    A large fraction of the dwarf satellites orbiting the Andromeda galaxy are surprisingly aligned in a thin, extended and apparently kinematically coherent planar structure. Such a structure is not easily found in simulations based on the cold dark matter model (ΛCDM). Using 21 high-resolution cosmological simulations, we analyse the kinematics of planes of satellites similar to the one around Andromeda. We find good agreement when co-rotation is characterized by the line-of-sight velocity. At the same time, when co-rotation is inferred by the angular momenta of the satellites, the planes are in agreement with the plane around our Galaxy. We find such planes to be common in our high-concentration haloes. The number of co-rotating satellites obtained from the sign of the line-of-sight velocity shows large variations depending on the viewing angle and is consistent with that obtained from a sample with random velocities. We find that the clustering of angular momentum vectors of the satellites in the plane is a better measure of the kinematic coherence. Thus we conclude that the line-of-sight velocity is not well suited as a proxy for the kinematical coherence of the plane. Analysis of the kinematics of our planes shows a fraction of ˜30 per cent chance-aligned satellites. Tracking the satellites in the plane back in time reveals that these planes are a transient feature and not kinematically coherent as would appear at first sight. Thus we expect some of the satellites in the plane around Andromeda to have high velocities perpendicular to the plane.

  2. Simulated ΛCDM analogues of the thin Plane of Satellites around the Andromeda galaxy are not kinematically coherent structures

    NASA Astrophysics Data System (ADS)

    Buck, Tobias; Dutton, Aaron A.; Macciò, Andrea V.

    2016-05-01

    A large fraction of the dwarf satellites orbiting the Andromeda galaxy are surprisingly aligned in a thin, extended and apparently kinematically coherent planar structure. Such a structure is not easily found in simulations based on the Cold Dark Matter model (ΛCDM). Using 21 high resolution cosmological simulations we analyse the kinematics of planes of satellites similar to the one around Andromeda. We find good agreement when co-rotation is characterized by the line-of-sight velocity. At the same time, when co-rotation is inferred by the angular momenta of the satellites, the planes are in agreement with the plane around our Galaxy. We find such planes to be common in our high concentration haloes. The number of co-rotating satellites obtained from the sign of the line-of-sight velocity shows large variations depending on the viewing angle and is consistent with that obtained from a sample with random velocities. We find that the clustering of angular momentum vectors of the satellites in the plane is a better measure of the kinematic coherence. Thus we conclude that the line-of-sight velocity is not well suited as a proxy for the kinematical coherence of the plane. Analysis of the kinematics of our planes shows a fraction of ˜30% chance aligned satellites. Tracking the satellites in the plane back in time reveals that these planes are a transient feature and not kinematically coherent as would appear at first sight. Thus we expect some of the satellites in the plane around Andromeda to have high velocities perpendicular to the plane.

  3. The fluorite related modulated structures of the Gd2(Zr2-xCex)O7 solid solution: An analogue for Pu disposition

    NASA Astrophysics Data System (ADS)

    Reid, D. P.; Stennett, M. C.; Hyatt, N. C.

    2012-07-01

    We present an overview of the Gd2(Zr2-xCex)O7 phase diagram, of interest as a model system for ceramic disposition of Pu (with Ce as a Pu surrogate). The fluorite related structures of this solid solution were determined using a modulated structure approach, to identify the underlying cation and vacancy ordering mechanisms from analysis of key satellite reflections in selected zone axis electron diffraction patterns. This revealed the formation of four structure types: pyrochlore for x<0.25, defect fluorite for 0.5structure for x=1.00, and a C-type structure for x>1.50. X-ray absorption (XAS) and electron energy loss (EELS) spectra confirmed the presence of Ce4+ as the dominant species in compositions across this system, remaining analogous to Pu4+.

  4. Syntheses of phosphatidyl-beta-D-glucoside analogues to probe antigen selectivity of monoclonal antibody 'DIM21'.

    PubMed

    Greimel, Peter; Lapeyre, Milaine; Nagatsuka, Yasuko; Hirabayashi, Yoshio; Ito, Yukishige

    2008-08-01

    Herein, we report the chemical syntheses of a series of phosphatidyl-beta-D-glucoside (PtdGlc) analogues, including 6-O-Ac, sn-2-O-Me, phosphorothioate as well as phosphatidylgalactoside and -mannoside derivatives. In the key step, beta-glycosyl H-phosphonate was condensed with enantiomerically pure diacylglycerol. Comparison of spectroscopic data with mono-acetylated PtdGlc from natural source confirmed the presence of an acetyl moiety at position 6. Furthermore, the reactivity of PtdGlc and its analogues toward monoclonal antibody 'DIM21' (MAb DIM21) was evaluated, revealing the crucial structural antigen features for successful MAb DIM21 binding. PMID:18625561

  5. Three Efficient Methods for Preparation of Coelenterazine Analogues.

    PubMed

    Shakhmin, Anton; Hall, Mary P; Walker, Joel R; Machleidt, Thomas; Binkowski, Brock F; Wood, Keith V; Kirkland, Thomas A

    2016-07-18

    The growing popularity of bioluminescent assays has highlighted the need for coelenterazine analogues possessing properties tuned for specific applications. However, the structural diversity of known coelenterazine analogues has been limited by current syntheses. Known routes for the preparation of coelenterazine analogues employ harsh reaction conditions that limit access to many substituents and functional groups. Novel synthetic routes reported here establish simple and robust methods for synthesis and investigation of structurally diverse marine luciferase substrates. Specifically, these new routes allow synthesis of coelenterazine analogues containing various heterocyclic motifs and substituted aromatic groups with diverse electronic substituents at the R(2) position. Interesting analogues described herein were characterized by their physicochemical properties, bioluminescent half-life, light output, polarity and cytotoxicity. Some of the analogues represent leads that can be utilized in the development of improved bioluminescent systems. PMID:27305599

  6. Novel Sorafenib-Based Structural Analogues: In Vitro Anticancer Evaluation of t-MTUCB and t-AUCMB

    PubMed Central

    Wecksler, Aaron T.; Hwang, Sung Hee; Wettersten, Hiromi I.; Gilda, Jennifer E.; Patton, Amy; Leon, Leonardo J.; Carraway, Kermit L.; Gomes, Aldrin V.; Baar, Keith; Weiss, Robert H.; Hammock, Bruce D.

    2014-01-01

    In the current study, we performed a mechanistic study on the cytotoxicity of two compounds, t-AUCMB and t-MTUCB, that are structurally similar to sorafenib. These compounds display strong cytotoxic responses in various cancer cell lines, despite significant differences in the induction of apoptotic events such as caspase activation and lactate dehydrogenase release in hepatoma cells. Both compounds induce autophagosome formation and LC3I cleavage, but there was little observable effect on mTORC1 or the downstream targets, S6K1 and 4E-BP1. In addition, there was an increase in activity of upstream signaling through the IRS1/PI3K/Akt signaling pathway, suggesting that unlike sorafenib, both compounds induce mTOR-independent autophagy. The observed autophagy correlates with mitochondrial membrane depolarization, AIF release, and oxidative stress-induced glutathione depletion. However, there were no observable changes in the ER-stress markers such as, Bip, IREα, p-eIP2, and the lipid peroxidation marker, 4-HNE, suggesting ER-independent oxidative stress. Finally, these compounds do not possess the multikinase inhibitory activity of sorafenib, which may be reflected in their difference in ability to halt cell cycle progression compared to sorafenib. Our findings indicate that both compounds have anti-cancer effects comparable to sorafenib in multiple cell line, but they induce significant differences in apoptotic responses and appear to induce mTOR-independent autophagy. t-AUCMB and t-MTUCB, represent novel chemical probes that are capable of inducing mTOR-independent autophagy and apoptosis to differing degrees, and thus may be potential tools for further understanding the link between these two cellular stress responses. PMID:24525589

  7. Novel sorafenib-based structural analogues: in-vitro anticancer evaluation of t-MTUCB and t-AUCMB.

    PubMed

    Wecksler, Aaron T; Hwang, Sung Hee; Wettersten, Hiromi I; Gilda, Jennifer E; Patton, Amy; Leon, Leonardo J; Carraway, Kermit L; Gomes, Aldrin V; Baar, Keith; Weiss, Robert H; Hammock, Bruce D

    2014-04-01

    In the current work, we carried out a mechanistic study on the cytotoxicity of two compounds, trans-4-[4-(3-adamantan-1-yl-ureido)-cyclohexyloxy]-N-methyl-benzamide (t-AUCMB) and trans-N-methyl-4-{4-[3-(4-trifluoromethoxy-phenyl)-ureido]-cyclohexyloxy}-benzamide (t-MTUCB), that are structurally similar to sorafenib. These compounds show strong cytotoxic responses in various cancer cell lines, despite significant differences in the induction of apoptotic events such as caspase activation and lactate dehydrogenase release in hepatoma cells. Both compounds induce autophagosome formation and LC3I cleavage, but there was little observable effect on mTORC1 or the downstream targets, S6K1 and 4E-binding protein. In addition, there was an increase in the activity of upstream signaling through the IRS1/PI3K/Akt-signaling pathway, suggesting that, unlike sorafenib, both compounds induce mammalian target of rapamycin (mTOR)-independent autophagy. The autophagy observed correlates with mitochondrial membrane depolarization, apoptosis-inducing factor release, and oxidative stress-induced glutathione depletion. However, there were no observable changes in the endoplasmic reticulum-stress markers such as binding immunoglobulin protein, inositol-requiring enzyme-α, phosphorylated eukaryotic initiation factor 2, and the lipid peroxidation marker, 4-hydroxynonenal, suggesting endoplasmic reticulum-independent oxidative stress. Finally, these compounds do not have the multikinase inhibitory activity of sorafenib, which may be reflected in their difference in the ability to halt cell cycle progression compared with sorafenib. Our findings indicate that both compounds have anticancer effects comparable with sorafenib in multiple cell lines, but they induce significant differences in apoptotic responses and appear to induce mTOR-independent autophagy. t-AUCMB and t-MTUCB represent novel chemical probes that are capable of inducing mTOR-independent autophagy and apoptosis to differing

  8. Planetary habitability: lessons learned from terrestrial analogues

    NASA Astrophysics Data System (ADS)

    Preston, Louisa J.; Dartnell, Lewis R.

    2014-01-01

    they emulate their intended target locale. We also outline key issues associated with the existing documentation of analogue research and the constraints this has on the efficiency of discoveries in this field. This review thus highlights the need for a global open access database for planetary analogues.

  9. U.S. Nuclear Regulatory Commission natural analogue research program

    SciTech Connect

    Kovach, L.A.; Ott, W.R.

    1995-09-01

    This article describes the natural analogue research program of the U.S. Nuclear Regulatory Commission (US NRC). It contains information on the regulatory context and organizational structure of the high-level radioactive waste research program plan. It also includes information on the conditions and processes constraining selection of natural analogues, describes initiatives of the US NRC, and describes the role of analogues in the licensing process.

  10. Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups.

    PubMed

    Le, Huong T; Ho, Cuong T; Trinh, Quan H; Trinh, Duc A; Luu, Minh T N; Tran, Hai S; Orange, Didier; Janeau, Jean L; Merroune, Asmaa; Rochelle-Newall, Emma; Pommier, Thomas

    2016-01-01

    Organic fertilizer application is often touted as an economical and effective method to increase soil fertility. However, this amendment may increase dissolved organic carbon (DOC) runoff into downstream aquatic ecosystems and may consequently alter aquatic microbial community. We focused on understanding the effects of DOC runoff from soils amended with compost, vermicompost, or biochar on the aquatic microbial community of a tropical reservoir. Runoff collected from a series of rainfall simulations on soils amended with different organic fertilizers was incubated for 16 days in a series of 200 L mesocosms filled with water from a downstream reservoir. We applied 454 high throughput pyrosequencing for bacterial 16S rRNA genes to analyze microbial communities. After 16 days of incubation, the richness and evenness of the microbial communities present decreased in the mesocosms amended with any organic fertilizers, except for the evenness in the mesocosms amended with compost runoff. In contrast, they increased in the reservoir water control and soil-only amended mesocosms. Community structure was mainly affected by pH and DOC concentration. Compared to the autochthonous organic carbon produced during primary production, the addition of allochthonous DOC from these organic amendments seemed to exert a stronger effect on the communities over the period of incubation. While the Proteobacteria and Actinobacteria classes were positively associated with higher DOC concentration, the number of sequences representing key bacterial groups differed between mesocosms particularly between the biochar runoff addition and the compost or vermi-compost runoff additions. The genera of Propionibacterium spp. and Methylobacterium spp. were highly abundant in the compost runoff additions suggesting that they may represent sentinel species of complex organic carbon inputs. Overall, this work further underlines the importance of studying the off-site impacts of organic fertilizers as