A Pauson-Khand approach to the synthesis of ingenol.

PubMed

Winkler, Jeffrey D; Lee, Esther C Y; Nevels, LaToya I

2005-04-14

[reaction: see text] Pauson-Khand cyclization of dioxanone photoadduct 21 leads to the formation of a single product in good yield. However, retro-aldol fragmentation of the pentacyclic cyclopentenone 22 leads to the formation of 23, with cis C-8/C-10 intrabridgehead stereochemistry, unlike the target compound ingenol 1, which possesses C-8/C-10 trans intrabridgehead stereochemistry.

Molecular cloning of isoflavone reductase from pea (Pisum sativum L.): evidence for a 3R-isoflavanone intermediate in (+)-pisatin biosynthesis.

PubMed

Paiva, N L; Sun, Y; Dixon, R A; VanEtten, H D; Hrazdina, G

1994-08-01

Isoflavone reductase (IFR) reduces achiral isoflavones to chiral isoflavanones during the biosynthesis of chiral pterocarpan phytoalexins. A cDNA clone for IFR from pea (Pisum sativum) was isolated using the polymerase chain reaction and expressed in Escherichia coli. Analysis of circular dichroism (CD) spectra of the reduction product sophorol obtained using the recombinant enzyme indicated that the isoflavanone possessed the 3R stereochemistry, in contrast to previous reports indicating a 3S-isoflavanone as the product of the pea IFR. Analysis of CD spectra of sophorol produced using enzyme extracts of CuCl2-treated pea seedlings confirmed the 3R stereochemistry. Thus, the stereochemistry of the isoflavanone intermediate in (+)-pisatin biosynthesis in pea is the same as that in (-)-medicarpin biosynthesis in alfalfa, although the final pterocarpans have the opposite stereochemistry. At the amino acid level the pea IFR cDNA was 91.8 and 85.2% identical to the IFRs from alfalfa and chickpea, respectively. IFR appears to be encoded by a single gene in pea. Its transcripts are highly induced in CuCl2-treated seedlings, consistent with the appearance of IFR enzyme activity and pisatin accumulation.

A stereochemical examination of the equine metabolism of 17alpha-methyltestosterone.

PubMed

McKinney, Andrew R; Suann, Craig J; Stenhouse, Allen M

2007-01-09

An investigation was conducted into the stereochemistry of the equine urinary metabolites of 17alpha-methyltestosterone observed after oral administration. Standards of the complete range of C3/C5/C16 stereoisomeric 17alpha-methylandrostane-3,17beta-diols, 17alpha-methylandrostane-3,16,17beta-triols and 17alpha-hydroxymethylandrostane-3,17beta-diols were purchased or synthesised, and were used to unequivocally identify the absolute structures of the metabolites. Phase I metabolism was found to involve combinations of Delta(4)-3-ketone reduction with both 5alpha,3beta- and 5beta,3alpha-stereochemistry, hydroxylation at C16 with both 16alpha- and 16beta-stereochemistry and hydroxylation of the 17alpha-methyl substituent. Phase II metabolism involved mainly sulfation with a lesser degree of beta-glucuronidation.

Theonellapeptolide IIIe, a new cyclic peptolide from the New Zealand deep water sponge, Lamellomorpha strongylata.

PubMed

Li, S; Dumdei, E J; Blunt, J W; Munro, M H; Robinson, W T; Pannell, L K

1998-06-26

The structure, stereochemistry, and conformation of theonellapeptolide IIIe (1), a new 36-membered ring cyclic peptolide from the New Zealand deep-water sponge Lamellomorpha strongylata, is described. The sequence of the cytotoxic peptolide was determined through a combination of NMR and MS-MS techniques and confirmed by X-ray crystal structure analysis, which, with chiral HPLC, established the absolute stereochemistry.

Design and Implementation of a Self-Directed Stereochemistry Lesson Using Embedded Virtual Three-Dimensional Images in a Portable Document Format

ERIC Educational Resources Information Center

Cody, Jeremy A.; Craig, Paul A.; Loudermilk, Adam D.; Yacci, Paul M.; Frisco, Sarah L.; Milillo, Jennifer R.

2012-01-01

A novel stereochemistry lesson was prepared that incorporated both handheld molecular models and embedded virtual three-dimensional (3D) images. The images are fully interactive and eye-catching for the students; methods for preparing 3D molecular images in Adobe Acrobat are included. The lesson was designed and implemented to showcase the 3D…

Surfactant Effects on Structure and Mechanical Properties of Ultrahigh-Molecular-Weight Polyethylene/Layered Silicate Composites.

PubMed

Nikiforov, Leonid A; Okhlopkova, Tatinana A; Kapitonova, Iullia V; Sleptsova, Sardana A; Okhlopkova, Aitalina A; Shim, Ee Le; Cho, Jin-Ho

2017-12-05

In this study, the reinforcement of ultrahigh-molecular-weight polyethylene (UHMWPE) with biotite was investigated. The biotite filler was mechanically activated with different dry surfactants to improve its compatibility with UHMWPE and decrease agglomeration among biotite particles. Alkyldimethylbenzylammonium chloride (ADBAC) and cetyltrimethylammonium bromide (CTAB) were selected as cationic surfactants. The tensile strength of composites containing 1 wt % of CTAB-treated biotite was increased by 30% relative to those with untreated biotite, but was unchanged with ADBAC treatment of the same biotite content. The stereochemistry of the surfactant may be critical to the composite structure and mechanical properties of the material. The stereochemistry of CTAB was preferable to that of ADBAC in enhancing mechanical properties because the stereochemistry of ADBAC impedes favorable interactions with the biotite surface during mechanical activation.

Computationally Aided Absolute Stereochemical Determination of Enantioenriched Amines.

PubMed

Zhang, Jun; Gholami, Hadi; Ding, Xinliang; Chun, Minji; Vasileiou, Chrysoula; Nehira, Tatsuo; Borhan, Babak

2017-03-17

A simple and efficient protocol for sensing the absolute stereochemistry and enantiomeric excess of chiral monoamines is reported. Preparation of the sample requires a single-step reaction of the 1,1'-(bromomethylene)dinaphthalene (BDN) with the chiral amine. Analysis of the exciton coupled circular dichroism generated from the BDN-derivatized chiral amine sample, along with comparison to conformational analysis performed computationally, yields the absolute stereochemistry of the parent chiral monoamine.

A review of stereochemical implications in the generation of secondary organic aerosol from isoprene oxidation.

PubMed

Cash, James M; Heal, Mathew R; Langford, Ben; Drewer, Julia

2016-11-09

The atmospheric reactions leading to the generation of secondary organic aerosol (SOA) from the oxidation of isoprene are generally assumed to produce only racemic mixtures, but aspects of the chemical reactions suggest this may not be the case. In this review, the stereochemical outcomes of published isoprene-degradation mechanisms contributing to high amounts of SOA are evaluated. Despite evidence suggesting isoprene first-generation oxidation products do not contribute to SOA directly, this review suggests the stereochemistry of first-generation products may be important because their stereochemical configurations may be retained through to the second-generation products which form SOA. Specifically, due to the stereochemistry of epoxide ring-opening mechanisms, the outcome of the reactions involving epoxydiols of isoprene (IEPOX), methacrylic acid epoxide (MAE) and hydroxymethylmethyl-α-lactone (HMML) are, in principle, stereospecific which indicates the stereochemistry is predefined from first-generation precursors. The products from these three epoxide intermediates oligomerise to form macromolecules which are proposed to form chiral structures within the aerosol and are considered to be the largest contributors to SOA. If conditions in the atmosphere such as pH, aerosol water content, relative humidity, pre-existing aerosol, aerosol coatings and aerosol cation/anion content (and other) variables acting on the reactions leading to SOA affect the tacticity (arrangement of chiral centres) in the SOA then they may influence its physical properties, for example its hygroscopicity. Chamber studies of SOA formation from isoprene encompass particular sets of controlled conditions of these variables. It may therefore be important to consider stereochemistry when upscaling from chamber study data to predictions of SOA yields across the range of ambient atmospheric conditions. Experiments analysing the stereochemistry of the reactions under varying conditions of the above variables would help elucidate whether there is stereoselectivity in SOA formation from isoprene and if the rates of SOA formation are affected.

A new rearranged dolabellane diterpene from the soft coral Clavularia inflata.

PubMed

Alea, Glenn V; Bowden, Bruce F; Ragasa, Consolacion Y

2008-06-15

A new dolabellane type diterpene 1 has been isolated through its acetate 1a. The structure of 1a was elucidated by extensive 1D and 2D NMR spectroscopy and confirmed by mass spectrometry. The structure of 1 was deduced by comparison of its NMR spectral data with those of 1a, while its relative stereochemistry was deduced by NOESY. The absolute stereochemistry of C-7 was determined by analyses of 1 separately esterified with R and S O-mandelic acids.

Quinolizidine alkaloids from Lupinus lanatus

NASA Astrophysics Data System (ADS)

Neto, Alexandre T.; Oliveira, Carolina Q.; Ilha, Vinicius; Pedroso, Marcelo; Burrow, Robert A.; Dalcol, Ionara I.; Morel, Ademir F.

2011-10-01

In this study, one new quinolizidine alkaloid, lanatine A ( 1), together with three other known alkaloids, 13-α- trans-cinnamoyloxylupanine ( 2), 13-α-hydroxylupanine ( 3), and (-)-multiflorine ( 4) were isolated from the aerial parts of Lupinus lanatus (Fabaceae). The structures of alkaloids 1- 4 were elucidated by spectroscopic data analysis. The stereochemistry of 1 was determined by single crystal X-ray analysis. Bayesian statistical analysis of the Bijvoet differences suggests the absolute stereochemistry of 1. In addition, the antimicrobial potential of alkaloids 1- 4 is also reported.

Role of Chirality in Drugs… An Overview

PubMed

Alkadi, Hourieh; Jbeily, Rajwa

2017-03-29

Stereochemistry has been occupied a great role in manufacture and development of pharmaceuti-cals. Chiral properties play an important role in the determination of pharmacological actions of the drug. In recent years, there is a considerable interest in chiral separation to isolate and examine both enantiomers. This article provides an overview about the stereochemistry and its role in drugs, and also, offers approved isolation methods for enantiomeric pairs. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

DAG tales: the multiple faces of diacylglycerol--stereochemistry, metabolism, and signaling.

PubMed

Eichmann, Thomas Oliver; Lass, Achim

2015-10-01

The neutral lipids diacylglycerols (DAGs) are involved in a plethora of metabolic pathways. They function as components of cellular membranes, as building blocks for glycero(phospho)lipids, and as lipid second messengers. Considering their central role in multiple metabolic processes and signaling pathways, cellular DAG levels require a tight regulation to ensure a constant and controlled availability. Interestingly, DAG species are versatile in their chemical structure. Besides the different fatty acid species esterified to the glycerol backbone, DAGs can occur in three different stereo/regioisoforms, each with unique biological properties. Recent scientific advances have revealed that DAG metabolizing enzymes generate and distinguish different DAG isoforms, and that only one DAG isoform holds signaling properties. Herein, we review the current knowledge of DAG stereochemistry and their impact on cellular metabolism and signaling. Further, we describe intracellular DAG turnover and its stereochemistry in a 3-pool model to illustrate the spatial and stereochemical separation and hereby the diversity of cellular DAG metabolism.

Synthesis of new β-amidodehydroaminobutyric acid derivatives and of new tyrosine derivatives using copper catalyzed C-N and C-O coupling reactions.

PubMed

Pereira, G; Vilaça, H; Ferreira, P M T

2013-02-01

Several β-amidodehydroaminobutyric acid derivatives were prepared from N,C-diprotected β-bromodehydroaminobutyric acids and amides by a copper catalyzed C-N coupling reaction. The best reaction conditions include the use of a catalytic amount of CuI, N,N'-dimethylethylenediamine as ligand and K(2)CO(3) as base in toluene at 110 °C. The stereochemistry of the products was determined using NOE difference experiments and the results obtained are in agreement with an E-stereochemistry. Thus, the stereochemistry is maintained in the case of the E-isomers of β-bromodehydroaminobutyric acid derivatives, but when the Z-isomers were used as substrates the reaction proceeds with inversion of configuration. The use of β-bromodehydrodipeptides as substrates was also tested. It was found that the reaction outcome depend on the stereochemistry of the β-bromodehydrodipeptide and on the nature of the first amino acid residue. The products isolated were the β-amidodehydrodipeptide derivatives and/or the corresponding dihydropyrazines. The same catalytic system (CuI/N,N'-dimethylethylene diamine) was used in the C-O coupling reactions between a tyrosine derivative and aryl bromides. The new O-aryltyrosine derivatives were isolated in moderate to good yields. The photophysical properties of two of these compounds were studied in four solvents of different polarity. The results show that these compounds after deprotection can be used as fluorescence markers.

Structure elucidation of nigricanoside A through enantioselective total synthesis† †Electronic supplementary information (ESI) available: Complete experimental details and characterization data. See DOI: 10.1039/c5sc00281h Click here for additional data file.

PubMed Central

Chen, Jie; Koswatta, Panduka; DeBergh, J. Robb; Fu, Peng; Pan, Ende

2015-01-01

Nigricanoside A was isolated from green alga, and its dimethyl ester was found to display potent cytotoxicity. Its scarcity prevented a full structure elucidation, leaving total synthesis as the only means to determine its relative and absolute stereochemistry and to explore its biological activity. Here we assign the stereochemistry of the natural product through enantioselective total synthesis and provide initial studies of its cytotoxicity. PMID:26877863

Crown ether stereoisomerism: Implications in metal ion extraction and ionic liquid design

NASA Astrophysics Data System (ADS)

Pawlak, Alan J.

Since their discovery more than four decades ago, crown ethers (CEs) have been the subject of intense investigation in a number of fields. Although many of the structural features that govern the behavior of these compounds have been thoroughly explored, the effect of their stereochemistry has received relatively little attention. In the present work, crown ether stereochemistry is shown to have important implications in both the design of ternary (i.e., three-component) ionic liquids (TILs) and metal ion extraction. Specifically, as a first step toward the development of guidelines for the rational design of ternary ionic liquids employing crown ethers as the neutral extractant, a systematic examination of the effect of crown ether stereochemistry (employing dicyclohexano-18-crown-6 (DCH18C6) as a representative crown compound), along with ring size, the nature and number of donor atoms, and the presence of functional groups, on the thermal properties (i.e., melting point or glass transition; decomposition or evaporation) of these compounds was carried out. Stereochemistry was found to have no appreciable impact on the onset temperature for mass loss. Rather, molecular weight and aromaticity were found to be more influential. Stereochemistry was, however, found to significantly affect the melting point of a TIL prepared from it; while the metal-CE formation constant, which varies with stereoisomer was observed to determine the onset temperature for mass loss of the TIL. To explore the implications of crown ether stereoisomerism in metal ion extraction, the formation constants for alkaline earth cation complexes with the isomers of DCH18C6 and selected stereoisomers of di-tert-butylcyclohexano-18-crown-6 (DtBuCH18C6) were measured. These values were found to vary inversely with the ligand strain (i.e., reorganizational) energy for the isomer, as determined by molecular mechanics calculations. Using this relationship (along with additional identification methods), three isomers of DtBuCH18C6, which were separated by preparative LC, were definitively identified. Three additional isomers were partially identified.

Anti-Helicobacter pylori activity of derivatives of the phthalide-containing antibacterial agents spirolaxine methyl ether, CJ-12,954, CJ-13,013, CJ-13,102, CJ-13,104, CJ-13,108 and CJ-13,015.

PubMed

Radcliff, Fiona J; Fraser, John D; Wilson, Zoe E; Heapy, Amanda M; Robinson, James E; Bryant, Christina J; Flowers, Christopher L; Brimble, Margaret A

2008-06-01

The naturally occurring phthalide-containing antibiotics spirolaxine methyl ether, CJ-12,954, CJ-13,013, CJ-13,015, CJ-13,102, CJ-13,103, CJ-13,104 and CJ-13,108, have been reported to exhibit anti-H. pylori activity. However, the exact stereochemistry of spirolaxine methyl ether, CJ-12,954 or CJ-13,013, contributing to this observed activity has not been confirmed. The anti-H. pylori activity of several analogues of spirolaxine methyl ether, CJ-12,954 and CJ-13,013 of defined stereochemistry together with the anti-H. pylori activity of several indole analogues of the simpler phthalide-containing antibiotics CJ-13,102, CJ-13,104, CJ-13,108 and CJ-13,015 is reported herein. A 1:1 mixture of spiroacetals 5b and 6b in which the phthalide substituent exhibited (3R)-stereochemistry was sixty times more active than the corresponding 1:1 mixture of spiroacetals with (3S)-stereochemistry. Notably, the unnatural (2''S)-diastereomer of spirolaxine methyl ether exhibited more potent anti-H. pylori activity than the natural product spirolaxine methyl ether. The 4,6-dimethoxyindoles 9, 10, 11 and 13 were all found to be less active than their parent compounds 1, 2, 3 and 4, respectively. Chain-shortened 4,6-dimethoxyindole analogue 12 of CJ-13,108 3 and 4,6-dimethoxyindole-spiroacetal 13 exhibited weak anti-H. pylori activity thus providing future opportunity for drug discovery programs.

Single Stage Tandem Mass Spectrometry Assignment of the C-5 Uronic Acid Stereochemistry in Heparan Sulfate Tetrasaccharides using Electron Detachment Dissociation

NASA Astrophysics Data System (ADS)

Agyekum, Isaac; Zong, Chengli; Boons, Geert-Jan; Amster, I. Jonathan

2017-09-01

The analysis of heparan sulfate (HS) glycosaminoglycans presents many challenges, due to the high degree of structural heterogeneity arising from their non-template biosynthesis. Complete structural elucidation of glycosaminoglycans necessitates the unambiguous assignments of sulfo modifications and the C-5 uronic acid stereochemistry. Efforts to develop tandem mass spectrometric-based methods for the structural analysis of glycosaminoglycans have focused on the assignment of sulfo positions. The present work focuses on the assignment of the C-5 stereochemistry of the uronic acid that lies closest to the reducing end. Prior work with electron-based tandem mass spectrometry methods, specifically electron detachment dissociation (EDD), have shown great promise in providing stereo-specific product ions, such as the B3 ´ -CO2, which has been found to distinguish glucuronic acid (GlcA) from iduronic acid (IdoA) in some HS tetrasaccharides. The previously observed diagnostic ions are generally not observed with 2- O-sulfo uronic acids or for more highly sulfated heparan sulfate tetrasaccharides. A recent study using electron detachment dissociation and principal component analysis revealed a series of ions that correlate with GlcA versus IdoA for a set of 2- O-sulfo HS tetrasaccharide standards. The present work comprehensively investigates the efficacy of these ions for assigning the C-5 stereochemistry of the reducing end uronic acid in 33 HS tetrasaccharides. A diagnostic ratio can be computed from the sum of the ions that correlate to GlcA to those that correlate to IdoA. [Figure not available: see fulltext.

Synthesis, characterization and electrochemical studies of some Ni(II)Cu(II) heterobimetallic complexes derived from succinoyldihydrazones.

PubMed

Borthakur, R; Kumar, A; Lal, R A

2015-10-05

Synthesis, structural characterization and redox properties of three heterobimetallic complexes with formule {[NiCu(L(n))(CH3OH)3]·CH3OH} using [Cu(H2L(n))(H2O)] as metalloligand have been demonstrated in the present paper. Electronic spectroscopy suggests that the copper center has a pseudo square pyramidal stereochemistry in all the complexes while the nickel center has a distorted octahedral stereochemistry. The electron transfer reactions of the complexes have been investigated by cyclic voltammetry. Copyright © 2015 Elsevier B.V. All rights reserved.

Small-Molecule Inhibitor Leads of Ribosome-Inactivating Proteins Developed Using the Doorstop Approach

DTIC Science & Technology

2011-03-01

stereochemistry of R22 used in our virtual screen. R20 or R20b was prepared by coupling 4-formylbenzoic acid with a substituted pyrrole in the keto form for R20 or...a mixture of keto and enol forms for R20b according to a reported process [42] (Figure 4). The substituted pyrrole was obtained via cyclization of 2...1H- pyrrole -3-carboxylate—a close ana- log of R20b—has been reported to have the Z stereochemistry [45]. Therefore, identification of R20 as an active

Mechanism and stereochemistry for nucleophilic attack at carbon of platinum (iv) alkyls: Model reactions for hydrocarbon oxidation with aqueous platinum chlorides. Technical report

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

Luinstra, G.A.; Labinger, J.A.; Bercaw, J.E.

1992-10-01

Reactions of PtCl4(2-) with RI (R = CH3, CH2CH2OH) in water yield PtCl5R(2-) which were isolated as their NMe4 salts. They decompose in aqueous chloride solution to give ROH and RCL. erythro- and threo-PtCl5(CHDCHDOH)(2-) are obtained by oxidation of PtCl3(cis- and trans CHD=CHD)(-) respectively. Kinetic rate laws and stereochemistry support SN2 displacement by Cl(-) or H[sub 2]O as the mechanism of the decomposition reactions.

Sesquiterpene lactone stereochemistry influences herbivore resistance and plant fitness in the field

PubMed Central

Ahern, Jeffrey R.; Whitney, Kenneth D.

2014-01-01

Background and Aims Stereochemical variation is widely known to influence the bioactivity of compounds in the context of pharmacology and pesticide science, but our understanding of its importance in mediating plant–herbivore interactions is limited, particularly in field settings. Similarly, sesquiterpene lactones are a broadly distributed class of putative defensive compounds, but little is known about their activities in the field. Methods Natural variation in sesquiterpene lactones of the common cocklebur, Xanthium strumarium (Asteraceae), was used in conjunction with a series of common garden experiments to examine relationships between stereochemical variation, herbivore damage and plant fitness. Key Results The stereochemistry of sesquiterpene lactone ring junctions helped to explain variation in plant herbivore resistance. Plants producing cis-fused sesquiterpene lactones experienced significantly higher damage than plants producing trans-fused sesquiterpene lactones. Experiments manipulating herbivore damage above and below ambient levels found that herbivore damage was negatively correlated with plant fitness. This pattern translated into significant fitness differences between chemotypes under ambient levels of herbivore attack, but not when attack was experimentally reduced via pesticide. Conclusions To our knowledge, this work represents only the second study to examine sesquiterpene lactones as defensive compounds in the field, the first to document herbivore-mediated natural selection on sesquiterpene lactone variation and the first to investigate the ecological significance of the stereochemistry of the lactone ring junction. The results indicate that subtle differences in stereochemistry may be a major determinant of the protective role of secondary metabolites and thus of plant fitness. As stereochemical variation is widespread in many groups of secondary metabolites, these findings suggest the possibility of dynamic evolutionary histories within the Asteraceae and other plant families showing extensive stereochemical variation. PMID:24380844

Sesquiterpene lactone stereochemistry influences herbivore resistance and plant fitness in the field.

PubMed

Ahern, Jeffrey R; Whitney, Kenneth D

2014-03-01

Stereochemical variation is widely known to influence the bioactivity of compounds in the context of pharmacology and pesticide science, but our understanding of its importance in mediating plant-herbivore interactions is limited, particularly in field settings. Similarly, sesquiterpene lactones are a broadly distributed class of putative defensive compounds, but little is known about their activities in the field. Natural variation in sesquiterpene lactones of the common cocklebur, Xanthium strumarium (Asteraceae), was used in conjunction with a series of common garden experiments to examine relationships between stereochemical variation, herbivore damage and plant fitness. The stereochemistry of sesquiterpene lactone ring junctions helped to explain variation in plant herbivore resistance. Plants producing cis-fused sesquiterpene lactones experienced significantly higher damage than plants producing trans-fused sesquiterpene lactones. Experiments manipulating herbivore damage above and below ambient levels found that herbivore damage was negatively correlated with plant fitness. This pattern translated into significant fitness differences between chemotypes under ambient levels of herbivore attack, but not when attack was experimentally reduced via pesticide. To our knowledge, this work represents only the second study to examine sesquiterpene lactones as defensive compounds in the field, the first to document herbivore-mediated natural selection on sesquiterpene lactone variation and the first to investigate the ecological significance of the stereochemistry of the lactone ring junction. The results indicate that subtle differences in stereochemistry may be a major determinant of the protective role of secondary metabolites and thus of plant fitness. As stereochemical variation is widespread in many groups of secondary metabolites, these findings suggest the possibility of dynamic evolutionary histories within the Asteraceae and other plant families showing extensive stereochemical variation.

Synthesis of precursors to and spectroscopic characterization of highly unsaturated carbenes and diradicals and development and implementation of a web-based stereochemistry tutorial

NASA Astrophysics Data System (ADS)

Burrmann, Nicola Jean

A variety of substituted diynols, diynals, and diynones have been prepared en route to the synthesis of precursors to dialkynyl carbenes (R1--C≡C--C--C≡C--R 2). In light of the unique reactivity associated with these simple systems, several strategies were required to assemble the carbon backbones (Chapter I). Tosylhydrazone and trisylhydrazone precursors to 2-diazo-3-pentyne ( 1), 2-diazo-3-butyne (2), and Idiazo-2-butyne ( 3) were synthesized and then converted into their respective diazo compounds. Various attempts to study these diazo compounds using matrix isolation IR and EPR spectroscopy were made and proved to be unsuccessful. Computations were done to characterize the C5H6 potential energy surface, as well as to determine the IR vibrational frequencies of the isomers on this surface (Chapter 2). A web-based Stereochemistry Tutorial that details the core definitions and structural representations relevant to organic stereochemistry was designed and implemented into several introductory-level organic chemistry classes. This tutorial also allows for students to select their preferred structural representation and method for making stereochemical comparisons between molecules. The tutorial was evaluated, either qualitatively, quantitatively, or both, by students in three different introductory organic chemistry courses at the University of Wisconsin---Madison. The data show that students did use a variety of different methods for making stereochemical comparisons between molecules, and that prior exposure to lectures on stereochemistry by the course professor strongly influenced these choices. Furthermore, the level of improvement in stereochemical knowledge as a result of using only the tutorial was comparable to, or higher than, that achieved by students who were only exposed to lectures by the course professor, regardless of the method chosen for making stereochemical comparisons between molecules (Chapter 3)

Stereoselective synthesis of an active metabolite of the potent PI3 kinase inhibitor PKI-179.

PubMed

Chen, Zecheng; Venkatesan, Aranapakam M; Dos Santos, Osvaldo; Delos Santos, Efren; Dehnhardt, Christoph M; Ayral-Kaloustian, Semiramis; Ashcroft, Joseph; McDonald, Leonard A; Mansour, Tarek S

2010-03-05

The synthesis and stereochemical determination of 1-(4-(4-((1R,5R,6R)-6-hydroxy-3-oxa-8-azabicyclo[3.2.1]octan-8-yl)-6-morpholino-1,3,5-triazin-2-yl)phenyl)-3-(pyridin-4-yl)urea (2), an active metabolite of the potent PI3 kinase inhibitor PKI-179 (1), is described. Stereospecific hydroboration of the double bond of 2,5-dihydro-1H-pyrrole 8 gave the 2,3-trans alcohol 9 exclusively. The configuration of the 3-hydroxyl group in 9 was inverted by an oxidation and stereoselective reduction sequence to give the corresponding 2,3-cis isomer 23. Both exo (21) and endo (27) isomers of the metabolite 2 were prepared via a practical synthetic route from 9 and 23, respectively, and the stereochemistry of 2 was determined to be endo. The endo isomer (27) was separated into two enantiomers 28 and 29 by chiral HPLC. Compound 2 was found to be enantiomerically pure and identical to the enantiomer 28. The absolute stereochemistry of the enantiomer 28 was determined by Mosher's method, thus establishing the stereochemistry of the active metabolite 2.

Comparative analysis of the heme iron electronic structure and stereochemistry in tetrameric rabbit hemoglobin and monomeric soybean leghemoglobin a using Mössbauer spectroscopy with a high velocity resolution

NASA Astrophysics Data System (ADS)

Alenkina, I. V.; Kumar, A.; Berkovsky, A. L.; Oshtrakh, M. I.

2018-02-01

A comparative study of tetrameric rabbit hemoglobin and monomeric soybean leghemoglobin a in the oxy- and deoxy-forms was carried out using 57Fe Mössbauer spectroscopy with a high velocity resolution in order to analyze the heme iron electronic structure and stereochemistry in relation to the Mössbauer hyperfine parameters. The Mössbauer spectra of tetrameric rabbit hemoglobin in both forms were fitted using two quadrupole doublets related to the 57Fe in ɑ- and β-subunits. In contrast, the Mössbauer spectra of monomeric soybean leghemoglobin a were fitted using: (i) two quadrupole doublets for the oxy-form related to two conformational states of the distal His E7 imidazole ring and different hydrogen bonding of oxygen molecule in the oxy-form and (ii) using three quadrupole doublets for deoxy-form related to three conformational states of the proximal His F8 imidazole ring. Small variations of Mössbauer hyperfine parameters related to small differences in the heme iron electronic structure and stereochemistry in tetrameric rabbit hemoglobin and monomeric soybean leghemoglobin a are discussed.

Stereochemistry in subcomponent self-assembly.

PubMed

Castilla, Ana M; Ramsay, William J; Nitschke, Jonathan R

2014-07-15

CONSPECTUS: As Pasteur noted more than 150 years ago, asymmetry exists in matter at all organization levels. Biopolymers such as proteins or DNA adopt one-handed conformations, as a result of the chirality of their constituent building blocks. Even at the level of elementary particles, asymmetry exists due to parity violation in the weak nuclear force. While the origin of homochirality in living systems remains obscure, as does the possibility of its connection with broken symmetries at larger or smaller length scales, its centrality to biomolecular structure is clear: the single-handed forms of bio(macro)molecules interlock in ways that depend upon their handednesses. Dynamic artificial systems, such as helical polymers and other supramolecular structures, have provided a means to study the mechanisms of transmission and amplification of stereochemical information, which are key processes to understand in the context of the origins and functions of biological homochirality. Control over stereochemical information transfer in self-assembled systems will also be crucial for the development of new applications in chiral recognition and separation, asymmetric catalysis, and molecular devices. In this Account, we explore different aspects of stereochemistry encountered during the use of subcomponent self-assembly, whereby complex structures are prepared through the simultaneous formation of dynamic coordinative (N → metal) and covalent (N═C) bonds. This technique provides a useful method to study stereochemical information transfer processes within metal-organic assemblies, which may contain different combinations of fixed (carbon) and labile (metal) stereocenters. We start by discussing how simple subcomponents with fixed stereogenic centers can be incorporated in the organic ligands of mononuclear coordination complexes and communicate stereochemical information to the metal center, resulting in diastereomeric enrichment. Enantiopure subcomponents were then incorporated in self-assembly reactions to control the stereochemistry of increasingly complex architectures. This strategy has also allowed exploration of the degree to which stereochemical information is propagated through tetrahedral frameworks cooperatively, leading to the observation of stereochemical coupling across more than 2 nm between metal stereocenters and the enantioselective synthesis of a face-capped tetrahedron containing no carbon stereocenters via a stereochemical memory effect. Several studies on the communication of stereochemistry between the configurationally flexible metal centers in tetrahedral metal-organic cages have shed light on the factors governing this process, allowing the synthesis of an asymmetric cage, obtained in racemic form, in which all symmetry elements have been broken. Finally, we discuss how stereochemical diversity leads to structural complexity in the structures prepared through subcomponent self-assembly. Initial use of octahedral metal templates with facial stereochemistry in subcomponent self-assembly, which predictably gave rise to structures of tetrahedral symmetry, was extended to meridional metal centers. These lower-symmetry linkages have allowed the assembly of a series of increasingly intricate 3D architectures of varying functionality. The knowledge gained from investigating different aspects of the stereochemistry of metal-templated assemblies thus not only leads to new means of structural control but also opens pathways toward functions such as stereoselective guest binding and transformation.

Stereochemical studies of acyclic isoprenoids-XII. Lipids of methanogenic bacteria and possible contributions to sediments

USGS Publications Warehouse

Risatti, J.B.; Rowland, S.J.; Yon, D.A.; Maxwell, J.R.

1984-01-01

Abundant volatile lipids of Methanobacterium thermoautotrophicum and Methanosarcina barkeri include isoprenoid hydrocarbons (??? C30), and C15, C20 and C25 isoprenoid alcohols. M. barkeri contains 2,6,10,15,19-pentamethyleicosane, whose relative stereochemistry is the same as found in marine sediments, indicating that it is a marker of methanogenic activity. The C20, C30 and C25 alkenes in M. thermoautotrophicum also have a preferred sterochemistry; the latter have the 2,6,10,14,18-pentamethyleicosanyl skeleton, suggesting that the alkane in marine sediments may derive from methanogens. The stereochemistry of squalane in a marine sediment is also compatible with an origin in methanogens; in contrast, the stereochemistry of pristane in M. thermoautotrophicum indicates a fossil fuel contaminant origin, suggesting that this and certain other alkanes reported in archaebacteria might also be of contaminant origin. There is, therefore, little evidence at present that the pristane in immature marine sediments originates in methanogens. The C15 and C20 saturated alcohols in M. thermoautotrophicum have mainly the all-R configuration. If this is generally true for methanogens, the C20 alcohol in the Messel shale may originate mainly from methanogens, whereas that in the Green River shale may originate mainly from photosynthetic organisms. ?? 1984.

Correlations among experimental and theoretical NMR data to determine the absolute stereochemistry of darcyribeirine, a pentacyclic indole alkaloid isolated from Rauvolfia grandiflora

NASA Astrophysics Data System (ADS)

Cancelieri, Náuvia Maria; Ferreira, Thiago Resende; Vieira, Ivo José Curcino; Braz-Filho, Raimundo; Piló-Veloso, Dorila; Alcântara, Antônio Flávio de Carvalho

2015-10-01

Darcyribeirine (1) is a pentacyclic indole alkaloid isolated from Rauvolfia grandiflora. Stereochemistry of 1 was previously proposed based on 1D (coupling constant data) and 2D (NOESY correlations) NMR techniques, having been established a configuration 3R, 15S, and 20R (isomer 1a). Stereoisomers of 1 (i.e., 1a-1h) can be grouped into four sets of enantiomers. Carbon chemical shifts and hydrogen coupling constants were calculated using BLYP/6-31G* theory level for the eight isomers of 1. Calculated NMR data of 1a-1h were correlated with the corresponding experimental data of 1. The best correlations between theoretical and experimental carbon chemical shift data were obtained for the set of enantiomers 1e/1f to structures in the gaseous phase and considering solvent effects (using PCM and explicit models). Similar results were obtained when the same procedure was performed to correlations between theoretical and experimental coupling constant data. Finally, optical rotation calculations indicate 1e as its absolute stereochemistry. Orbital population analysis indicates that the hydrogen bonding between N-H of 1e and DMSO is due to contributions of its frontier unoccupied molecular orbitals, mainly LUMO+1, LUMO+2, and LUMO+3.

Synthesis of the ABC tricyclic fragment of the pectenotoxins via stereocontrolled cyclization of a gamma-hydroxyepoxide appended to the AB spiroacetal unit.

PubMed

Halim, Rosliana; Brimble, Margaret A; Merten, Jörn

2006-04-07

The stereocontrolled synthesis of the C1-C16 ABC spiroacetal-containing tricyclic fragment of pectenotoxin-7 6 has been accomplished. The key AB spiroacetal aldehyde 9 was successfully synthesized via acid catalyzed cyclization of protected ketone precursor 28 that was readily prepared from aldehyde 12 and sulfone 13. The syn stereochemistry in aldehyde 12 was installed using an asymmetric aldol reaction proceeding via a titanium enolate. The stereogenic centre in sulfone 13 was derived from (R)-(+)-glycidol. The absolute stereochemistry of the final spiroacetal aldehyde 9 was confirmed by NOE studies establishing the (S)-stereochemistry of the spiroacetal centre. Construction of the tetrahydrofuran C ring system began with Wittig olefination of the AB spiroacetal aldehyde 9 with (carbethoxyethylidene)triphenylphosphorane 10 affording the desired (E)-olefin 32. Appendage of a three carbon chain to the AB spiroacetal fragment was achieved via addition of acetylene 11 to the unstable allylic iodide 39. Epoxidation of (E)-enyne 8 via in situ formation of L-fructose derived dioxirane generated the desired syn-epoxide 36. Semi-hydrogenation of the resulting epoxide 36 followed by dihydroxylation of the alkene effected concomitant cyclization, thus completing the synthesis of the ABC spiroacetal ring fragment 6.

Conformational arm-wrestling: battles for stereochemical control in benzamides bearing matched and mismatched chiral 2- and 6-substituents.

PubMed

Clayden, Jonathan; Foricher, Yann J Y; Helliwell, Madeleine; Johnson, Paul; Mitjans, David; Vinader, Victoria

2006-02-07

The orientation of a tertiary amide group adjacent to an aromatic ring may be governed by the stereochemistry of an adjacent chiral substituent. With a chiral substituent in both ortho positions, matched/mismatched pairs of isomers result. Evidence for matched stereochemistry is provided by the clean NMR spectra of single conformers, while mismatching gives poor or unexpected selectivities in the formation of chiral substituents, or mixtures of amide conformers. Attempts to use the match-mismatch effect to select for racemic pairs of enantiomeric substituents, and hence develop a "racemate-sequestering" reagent, are described, along with the use of "matching" to scavenge a single enantiomer of a diamine from material of incomplete enantiomeric purity.

Inversion of Configuration at the Phosphorus Nucleophile in the Diastereoselective and Enantioselective Synthesis of P-Stereogenic syn-Phosphiranes from Chiral Epoxides.

PubMed

Muldoon, Jake A; Varga, Balázs R; Deegan, Meaghan M; Chapp, Timothy W; Eördögh, Ádám M; Hughes, Russell P; Glueck, David S; Moore, Curtis E; Rheingold, Arnold L

2018-04-23

Nucleophilic substitution results in inversion of configuration at the electrophilic carbon center (S N 2) or racemization (S N 1). The stereochemistry of the nucleophile is rarely considered, but phosphines, which have a high barrier to pyramidal inversion, attack electrophiles with retention of configuration at P. Surprisingly, cyclization of bifunctional secondary phosphine alkyl tosylates proceeded under mild conditions with inversion of configuration at the nucleophile to yield P-stereogenic syn-phosphiranes. DFT studies suggested that the novel stereochemistry results from acid-promoted tosylate dissociation to yield an intermediate phosphenium-bridged cation, which undergoes syn-selective cyclization. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The effect of fenoterol stereochemistry on the β2 adrenergic receptor system: ligand directed chiral recognition

PubMed Central

Jozwiak, Krzysztof; Plazinska, Anita; Toll, Lawrence; Jimenez, Lucita; Woo, Anthony Yiu-Ho; Xiao, Rui-Ping; Wainer, Irving W.

2011-01-01

The β2 adrenergic receptor (β2-AR) is a model system for studying the ligand recognition process in G-protein coupled receptors. Fenoterol (FEN) is a β2-AR selective agonist that has two centers of chirality and exists as four stereoisomers. Radioligand binding studies determined that stereochemistry greatly influences the binding affinity. Subsequent Van’t Hoff analysis shows very different thermodynamics of binding depending on the stereoconfiguration of the molecule. The binding of (S,x’)-isomers is almost entirely enthalpy controlled whereas binding of (R,x’)-isomers is purely entropy driven. Stereochemistry of FEN molecule also affects the coupling of the receptor to different G proteins. In a rat cardiomyocyte contractility model, (R,R’)-FEN was shown to selectively activate Gs protein signaling while the (S,R’)- isomer activated both Gi and Gs protein. The overall data demonstrate that the chirality at the two chiral centers of the FEN molecule influences the magnitude of binding affinity, thermodynamics of local interactions within the binding site and the global mechanism of β2-AR activation. Differences in thermodynamic parameters and non-uniform G-protein coupling suggest a mechanism of chiral recognition in which observed enantioselectivities arise from the interaction of the (R,x’)-FEN stereoisomers with a different receptor conformation than the one with which the (S,x’)-isomer interacts. PMID:21618615

Effect of fenoterol stereochemistry on the β2 adrenergic receptor system: ligand-directed chiral recognition.

PubMed

Jozwiak, Krzysztof; Plazinska, Anita; Toll, Lawrence; Jimenez, Lucita; Woo, Anthony Yiu-Ho; Xiao, Rui-Ping; Wainer, Irving W

2011-01-01

The β(2) adrenergic receptor (β(2)-AR) is a model system for studying the ligand recognition process in G protein-coupled receptors. Fenoterol (FEN) is a β(2)-AR selective agonist that has two centers of chirality and exists as four stereoisomers. Radioligand binding studies determined that stereochemistry greatly influences the binding affinity. Subsequent Van't Hoff analysis shows very different thermodynamics of binding depending on the stereoconfiguration of the molecule. The binding of (S,x')-isomers is almost entirely enthalpy controlled whereas binding of (R,x')-isomers is purely entropy driven. Stereochemistry of FEN molecule also affects the coupling of the receptor to different G proteins. In a rat cardiomyocyte contractility model, (R,R')-FEN was shown to selectively activate G(s) protein signaling while the (S,R')-isomer activated both G(i) and G(s) protein. The overall data demonstrate that the chirality at the two chiral centers of the FEN molecule influences the magnitude of binding affinity, thermodynamics of local interactions within the binding site, and the global mechanism of β(2)-AR activation. Differences in thermodynamic parameters and nonuniform G-protein coupling suggest a mechanism of chiral recognition in which observed enantioselectivities arise from the interaction of the (R,x')-FEN stereoisomers with a different receptor conformation than the one with which the (S,x')-isomer interacts. Copyright © 2011 Wiley-Liss, Inc.

Stereochemistry- and concentration-dependent effects of phosphatidylserine enrichment on platelet function.

PubMed

Meyer, Audrey F; Gruba, Sarah M; Kim, Donghyuk; Meyer, Ben M; Koseoglu, Secil; Dalluge, Joseph J; Haynes, Christy L

2017-08-01

Platelets are small (1-2μm in diameter), circulating anuclear cell fragments with important roles in hemostasis and thrombosis that provide an excellent platform for studying the role of membrane components in cellular communication. Platelets use several forms of communication including exocytosis of three distinct granule populations, formation of bioactive lipid mediators, and shape change (allowing for adhesion). This work explores the role of stereochemistry and concentration of exogenous phosphatidylserine (PS) on platelet exocytosis and adhesion. PS, most commonly found in the phosphatidyl-l-serine (l-PS) form, is exposed on the outer leaflet of the cell membrane after the platelet is activated. Knowledge about the impact of exogenous phosphatidylserine on cell-to-cell communication is limited (particularly concentration and stereochemistry effects). This study found that platelets incubated in l-PS or phosphatidyl-d-serine (d-PS) are enriched to the same extent with their respective incubated PS. All levels of l-PS enrichment also showed an increase in platelet cholesterol, but only the 50μM d-PS incubation showed an increase in cholesterol. The uptake of d-PS induced the secretion of granules and manufactured platelet activating factor (PAF) in otherwise unstimulated platelets. The uptake of l-PS had a greater impact on platelet stimulation by decreasing both the amount of δ-granule secretion and the amount of PAF that was manufactured. Copyright © 2017 Elsevier B.V. All rights reserved.

A rapid alternative to X-ray crystallography for chiral determination: case studies of vibrational circular dichroism (VCD) to advance drug discovery projects.

PubMed

Wesolowski, Steven S; Pivonka, Don E

2013-07-15

The absolute stereochemistry of chiral drugs is usually established via X-ray crystallography. However, vibrational circular dichroism (VCD) spectroscopy coupled with quantum mechanics simulations offers a rapid alternative to crystallography and is readily applied to both crystalline and non-crystalline samples. VCD is an effective complement to X-ray analysis of drug candidates, and it can be used as a high-throughput means of assessing absolute stereochemistry at all phases of the discovery process (hundreds of assignments per year). The practical implementation (or fee-for-service outsourcing) of VCD and selected case studies are illustrated with an emphasis on providing utility and impact to pharmaceutical discovery programs. Copyright © 2013 Elsevier Ltd. All rights reserved.

The effect of maturation on the configuration of pristane in sediments and petroleum

NASA Technical Reports Server (NTRS)

Patience, R. L.; Rowland, S. J.; Maxwell, J. R.

1978-01-01

The absolute stereochemistry of pristane in a sample of contemporary marine zooplankton, Messel shale (Germany) and Djatibarang (Java) crude has been determined by gas chromatographic methods. The relative stereochemistry in Irati shale (Brazil), Green River (U.S.) crude, Halibut (Australia) crude has also been determined, and confirmed for a sample of the Green River shale. The stereoisomer distributions indicate a loss of stereospecificity of the phytol-derived 6(R), 10(S) pristane with increasing geological maturation. For example, the least mature geological sample, the Eocene Messel shale, contains solely the 6(R), 10(S) isomer, whereas a mature sample, Djatibarange crude, contains 50% of the 6(R), 10(S) isomer and 25% of each of the 6(R), 10(R) and 6(S), 10(S) isomers.

Kinetics and stereochemistry of LinB-catalyzed δ-HBCD transformation: Comparison of in vitro and in silico results.

PubMed

Heeb, Norbert V; Mazenauer, Manuel; Wyss, Simon; Geueke, Birgit; Kohler, Hans-Peter E; Lienemann, Peter

2018-05-12

LinB is a haloalkane dehalogenase found in Sphingobium indicum B90A, an aerobic bacterium isolated from contaminated soils of hexachlorocyclohexane (HCH) dumpsites. We showed that this enzyme also converts hexabromocyclododecanes (HBCDs). Here we give new insights in the kinetics and stereochemistry of the enzymatic transformation of δ-HBCD, which resulted in the formation of two pentabromocyclododecanols (PBCDols) as first- (P 1δ , P 2δ ) and two tetrabromocyclododecadiols (TBCDdiols) as second-generation products (T 1δ , T 2δ ). Enzymatic transformations of δ-HBCD, α 1 -PBCDol, one of the transformation products, and α 2 -PBCDol, its enantiomer, were studied and modeled with Michaelis-Menten (MM) kinetics. Respective MM-parameters K M , v max , k cat /K M indicated that δ-HBCD is the best LinB substrate followed by α 2 - and α 1 -PBCDol. The stereochemistry of these transformations was modeled in silico, investigating respective enzyme-substrate (ES) and enzyme-product (EP) complexes. One of the four predicted ES-complexes led to the PBCDol product P 1δ , identical to α 2 -PBCDol with the 1R,2R,5S,6R,9R,10S-configuration. An S N 2-like substitution of bromine at C6 of δ-HBCD by Asp-108 of LinB and subsequent hydrolysis of the alkyl-enzyme led to α 2 -PBCDol. Modeling results further indicate that backside attacks at C1, C9 and C10 are reasonable too, selectively binding leaving bromide ions in a halide pocket found in LinB. Docking with α 2 -PBCDol, also allowed productive enzyme binding. A TBCD-1,5-diol with the 1S,2S,5R,6R,9S,10R-configuration is the predicted second-generation product T 1δ . In conclusion, in vitro- and in silico findings now allow a detailed description of step-wise enzymatic dehalohydroxylation reactions of δ-HBCD to specific PBCDols and TBCDdiols at Å-resolution and predictions of their stereochemistry. Copyright © 2018 Elsevier Ltd. All rights reserved.

Gold-catalyzed and N-iodosuccinimide-mediated cyclization of gamma-substituted allenamides.

PubMed

Hyland, Christopher J T; Hegedus, Louis S

2006-10-27

Chiral gamma-substituted allenamides have been shown to undergo efficient gold-catalyzed and N-iodosuccinimide-mediated cyclization to highly functionalized dihydrofurans. These reactions proceed rapidly and without loss of stereochemistry.

Carbohydrate Stereochemistry.

ERIC Educational Resources Information Center

Shallenberger, Robert S.; Wienen, Wanda J.

1989-01-01

Treats the development of general stereochemical principles in historical fashion. Discusses work by Pasteur, van't Hoff, and Le Bel. Considers sugars by configuration, anomeric forms, ring forms, and conformational isomers. Presents numerous diagrams and thorough explanations. (MVL)

Stereoselective Synthesis of 8,12-Furanoeudesmanes from Santonin. Absolute Stereochemistry of Natural Furanoeudesma-1,3-diene and Tubipofurane.

PubMed

Blay, Gonzalo; Cardona, Luz; García, Begoña; Pedro, José R.; Sánchez, Juan J.

1996-05-31

Ketobutenolide 3, easily obtained from santonin (1), has been transformed into two natural furanoeudesmanes 4 and 5, isolated from Commiphora molmol and Tubipora musica, respectively. trans- And cis-decalin systems were obtained by stereoselective reduction of the C(4)-C(5) double bond in 3 in the following way: hydrogenation of 3 over Pd/C followed by acidic treatment gave the cis isomer 10 as the major product; selective hydrogenation of the C(1)-C(2) double bond with the Wilkinson's catalyst followed by reduction with NaTeH yielded mainly the trans isomer 9. Compounds 9 and 10 were transformed into 4 and 5 in parallel sequences. Optical rotation and CD measurements of the synthetic products revealed that the stereochemistry of both natural products should be revised to their enantiomeric form.

A single active site residue directs oxygenation stereospecificity in lipoxygenases: Stereocontrol is linked to the position of oxygenation

PubMed Central

Coffa, Gianguido; Brash, Alan R.

2004-01-01

Lipoxygenases are a class of dioxygenases that form hydroperoxy fatty acids with distinct positional and stereo configurations. Several amino acid residues influencing regiospecificity have been identified, whereas the basis of stereocontrol is not understood. We have now identified a single residue in the lipoxygenase catalytic domain that is important for stereocontrol; it is conserved as an Ala in S lipoxygenases and a Gly in R lipoxygenases. Our results with mutation of the conserved Ala to Gly in two S lipoxygenases (mouse 8S-LOX and human 15-LOX-2) and the corresponding Gly–Ala substitution in two R lipoxygenases (human 12R-LOX and coral 8R-LOX) reveal that the basis for R or S stereo-control also involves a switch in the position of oxygenation on the substrate. After the initial hydrogen abstraction, antarafacial oxygenation at one end or the other of the activated pair of double bonds (pentadiene) gives, for example, 8S or 12R product. The Ala residue promotes oxygenation on the reactive pentadiene at the end deep in the substrate binding pocket and S stereochemistry of the product hydroperoxide, and a Gly residue promotes oxygenation at the proximal end of the reactive pentadiene resulting in R stereochemistry. A model of lipoxygenase reaction specificity is proposed in which product regiochemistry and stereochemistry are determined by fixed relationships between substrate orientation, hydrogen abstraction, and the Gly or Ala residue we have identified. PMID:15496467

Stereochemistry of quinoxaline antagonist binding to a glutamate receptor investigated by Fourier transform infrared spectroscopy.

PubMed

Madden, D R; Thiran, S; Zimmermann, H; Romm, J; Jayaraman, V

2001-10-12

The stereochemistry of the interactions between quinoxaline antagonists and the ligand-binding domain of the glutamate receptor 4 (GluR4) have been investigated by probing their vibrational modes using Fourier transform infrared spectroscopy. In solution, the electron-withdrawing nitro groups of both compounds establish a resonance equilibrium that appears to stabilize the keto form of one of the cyclic amide carbonyl bonds. Changes in the 6,7-dinitro-2,3-dihydroxyquinoxaline vibrational spectra on binding to the glutamate receptor, interpreted within the framework of a published crystal structure, illuminate the stereochemistry of the interaction and suggest that the binding site imposes a more polarized electronic bonding configuration on this antagonist. Similar spectral changes are observed for 6-cyano-7-dinitro-2,3-dihydroxyquinoxaline, confirming that its interactions with the binding site are highly similar to those of 6,7-dinitro-2,3-dihydroxyquinoxaline and leading to a model of the 6-cyano-7-dinitro-2,3-dihydroxyquinoxaline-S1S2 complex, for which no crystal structure is available. Conformational changes within the GluR ligand binding domain were also monitored. Compared with the previously reported spectral changes seen on binding of the agonist glutamate, only a relatively small change is detected on antagonist binding. This correlation between the functional effects of different classes of ligand and the magnitude of the spectroscopic changes they induce suggests that the spectral data reflect physiologically relevant conformational processes.

Teaching 1H NMR Spectrometry Using Computer Modeling.

ERIC Educational Resources Information Center

Habata, Yoichi; Akabori, Sadatoshi

2001-01-01

Molecular modeling by computer is used to display stereochemistry, molecular orbitals, structure of transition states, and progress of reactions. Describes new ideas for teaching 1H NMR spectroscopy using computer modeling. (Contains 12 references.) (ASK)

Diazo compounds in the chemistry of fullerenes

NASA Astrophysics Data System (ADS)

Tuktarov, Airat R.; Dzhemilev, Usein M.

2010-09-01

Experimental and theoretical data on the reactions of different diazo compounds (diazomethane, its derivatives, cyclic diazo compounds and diazocarbonyl compounds) with fullerenes are summarized. The structures and stereochemistry of cycloadducts formed in these reactions are considered.

Chemical Applications of Graph Theory: Part I. Fundamentals and Topological Indices.

ERIC Educational Resources Information Center

Hansen, Peter J.; Jurs, Peter C.

1988-01-01

Explores graph theory and use of topological indices to predict boiling points. Lists three indices: Wiener Number, Randic Branching Index and Molecular Connectivity, and Molecular Identification numbers. Warns of inadequacies with stereochemistry. (ML)

The effect of stereochemistry on the biological activity of natural phytotoxins, fungicides, insecticides and herbicides.

PubMed

Evidente, Antonio; Cimmino, Alessio; Andolfi, Anna

2013-02-01

Phytotoxins are secondary microbial metabolites that play an essential role in the development of disease symptoms induced by fungi on host plants. Although phytotoxins can cause extensive-and in some cases devastating-damage to agricultural crops, they can also represent an important tool to develop natural herbicides when produced by fungi and plants to inhibit the growth and spread of weeds. An alternative strategy to biologically control parasitic plants is based on the use of plant and fungal metabolites, which stimulate seed germination in the absence of the host plant. Nontoxigenic fungi also produce bioactive metabolites with potential fungicide and insecticide activity, and could be applied for crop protection. All these metabolites represent important tools to develop eco-friendly pesticides. This review deals with the relationships between the biological activity of some phytotoxins, seed germination stimulants, fungicides and insecticides, and their stereochemistry. Copyright © 2012 Wiley Periodicals, Inc.

Novel stereocontrolled approach to syn- and anti-oxepene-cyclogeranyl trans-fused polycyclic systems: asymmetric total synthesis of (-)-Aplysistatin, (+)-Palisadin A, (+)-Palisadin B, (+)-12-hydroxy-palisadin B, and the AB ring system of adociasulfate-2 and toxicol A.

PubMed

Couladouros, Elias A; Vidali, Veroniki P

2004-08-06

A new stereocontrolled method for the formation of trans-anti cyclogeranyl-oxepene systems is described. The demanding stereochemistry is secured by stereoselective coupling of a cyclogeranyl tertiary alcohol with a 1,2-unsymmetrically substituted epoxide, while the formation of the highly strained oxepene is achieved employing ring-closing metathesis. Since the stereochemistry of the trans-fused 6,7-ring system is determined by the epoxide, the method also allows the construction of trans-syn 6,7-ring systems. This approach leads to the synthesis of the AB fragment of Adociasulfate-2 and Toxicol A, for the first time. The flexibility and efficiency of the presented strategy is demonstrated by the total asymmetric synthesis of (-)-Aplysistatin, (+)-Palisadin A, (+)-12-hydroxy-Palisadin B, and (+)-Palisadin B, employing two similar key intermediates.

Buried chloride stereochemistry in the Protein Data Bank

PubMed Central

2014-01-01

Background Despite the chloride anion is involved in fundamental biological processes, its interactions with proteins are little known. In particular, we lack a systematic survey of its coordination spheres. Results The analysis of a non-redundant set (pairwise sequence identity?

Buried chloride stereochemistry in the Protein Data Bank.

PubMed

Carugo, Oliviero

2014-09-23

Despite the chloride anion is involved in fundamental biological processes, its interactions with proteins are little known. In particular, we lack a systematic survey of its coordination spheres. The analysis of a non-redundant set (pairwise sequence identity < 30%) of 1739 high resolution (<2 Å) crystal structures that contain at least one chloride anion shows that the first coordination spheres of the chlorides are essentially constituted by hydrogen bond donors. Amongst the side-chains positively charged, arginine interacts with chlorides much more frequently than lysine. Although the most common coordination number is 4, the coordination stereochemistry is closer to the expected geometry when the coordination number is 5, suggesting that this is the coordination number towards which the chlorides tend when they interact with proteins. The results of these analyses are useful in interpreting, describing, and validating new protein crystal structures that contain chloride anions.

Relative stability of radicals derived from artemisinin: A semiempirical and DFT study

NASA Astrophysics Data System (ADS)

Arantes, C.; de Araujo, M. T.; Taranto, A. G.; de M. Carneiro, J. W.

The semiempirical AM1 and PM3 methods, as well as the density functional (DFT/B3LYP) approach using the 6-31g(d) basis set, were employed to calculate the relative stability of intermediate radicals derived from artemisinin, a sesquiterpene lactone having an endoperoxide bridge that is essential for its antimalarial activity. The compounds studied have their nonperoxidic oxygen atom of the trioxane ring and/or the carbonyl group replaced by a CH2 unit. Relative stabilities were calculated by means of isodesmic equations using artemisinin as reference. It was found that replacement of oxygen atoms decreases the relative stability of the anionic radical intermediates. In contrast, for compounds with inverted stereochemistry the intermediate radicals were found to be more stable than those with the artemisinin-like stereochemistry. These relative stabilities may modulate the antimalarial potency. Radicals centered on carbon are always more stable than the corresponding radicals centered on oxygen.

Classroom Enters the Courtroom: Stereochemistry of SN1 and SN2 Reactions in Enantiomer Patent Litigations of the Antidepressant Escitalopram.

PubMed

Michman, Elisheva; Agranat, Israel

2016-01-01

The role of elementary stereochemistry is illustrated in the patent litigations of the blockbuster antidepressant drug escitalopram oxalate. An undergraduate student of organic chemistry would recognize the stereochemical courses of the intramolecular SN 2 and SN 1 reactions of the single-enantiomer (S)-diol intermediate in the synthesis of the blockbuster antidepressant drug escitalopram oxalate: retention of configuration of the chiral carbon atom under basic conditions and racemization under acidic conditions, respectively. He/she, in searching for a stereoselective ring-closure reaction of the enantiomeric diol, will think of an SN 2 reaction in a basic medium. From these points of view, the process claim in the enantiomer patents of escitalopram is obvious/lacks an inventive step. An organic chemistry examination problem based on this scenario is offered. © 2015 Wiley Periodicals, Inc.

Structural studies of naturally occurring toxicogenic compounds

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

Springer, J. P.

1977-10-01

The paralytic shellfish poison (PSP), saxitoxin, is a neurotoxin isolated from Alaska butter clams (Saxidomus giganteus), mussels (Mytilus californianus) and axenic cultures of the dinoflagellate Gonyaulax catenella. The structure of saxitoxin has been determined through the use of single crystal X-ray diffraction. It possesses a unique tricyclic arrangement of atoms containing two guanidinium moieties and also a hydrated ketone. The relative stereochemistry is presented as well as the absolute configuration. The chemical constitution of a tremorgenic metabolite, paxilline, isolated from extracts of the fungus Penicillium paxilli Bainier has been determined. Paxilline represents a previously unreported class of natural compounds formedmore » by the combination of tryptophan and mevalonate subunits. The complete stereostructure of two other fungal metabolites, paspaline and paspalicine, closely related to paxilline but isolated from Claviceps paspali Stammes have also been determined and are presented. The stereochemistries of paxilline, paspaline and paspalicine are identical at corresponding chiral centers.« less

Control of phosphorothioate stereochemistry substantially increases the efficacy of antisense oligonucleotides.

PubMed

Iwamoto, Naoki; Butler, David C D; Svrzikapa, Nenad; Mohapatra, Susovan; Zlatev, Ivan; Sah, Dinah W Y; Meena; Standley, Stephany M; Lu, Genliang; Apponi, Luciano H; Frank-Kamenetsky, Maria; Zhang, Jason Jingxin; Vargeese, Chandra; Verdine, Gregory L

2017-09-01

Whereas stereochemical purity in drugs has become the standard for small molecules, stereoisomeric mixtures containing as many as a half million components persist in antisense oligonucleotide (ASO) therapeutics because it has been feasible neither to separate the individual stereoisomers, nor to synthesize stereochemically pure ASOs. Here we report the development of a scalable synthetic process that yields therapeutic ASOs having high stereochemical and chemical purity. Using this method, we synthesized rationally designed stereopure components of mipomersen, a drug comprising 524,288 stereoisomers. We demonstrate that phosphorothioate (PS) stereochemistry substantially affects the pharmacologic properties of ASOs. We report that Sp-configured PS linkages are stabilized relative to Rp, providing stereochemical protection from pharmacologic inactivation of the drug. Further, we elucidated a triplet stereochemical code in the stereopure ASOs, 3'-SpSpRp, that promotes target RNA cleavage by RNase H1 in vitro and provides a more durable response in mice than stereorandom ASOs.

Antibiotic resistance versus small molecules, the chemical evolution.

PubMed

Lee, V J; Hecker, S J

1999-11-01

Two discovery approaches directed to addressing the problem of increasing bacterial resistance are described. The first is a program to build activity against methicillin-resistant Staphylococcus aureus (MRSA) into the cephalosporin class of antibacterials, by enhancing affinity for PBP2a, the penicillin-binding protein responsible for this resistance. Through stepwise improvement in potency, human serum binding, solubility, and betalactamase stability, a stable of new compounds with excellent potential as anti-MRSA agents was realized. From this set was chosen MC-02, 479 (RWJ-54428), which is now undergoing extensive preclinical evaluation. The second approach explores the uridyl peptide family of antibiotics, inhibitors of bacterial translocase (mraY), whose members include the pacidamycins, mureidomycins, and napsamycins. Access to a diverse set of analogs by total synthesis was catalyzed by the discovery that hydrogenation of the 4'-exoenamidofuranosyl moiety causes no loss in biological activity. Indepth exploration of SAR required (1) establishment of the absolute stereochemistry of the central diaminobutyric acid (DABA) moiety and (2) determination of the stereochemistry of the 4'-substituent on the deoxyfuranose unit. The former was accomplished by comparison of DABA derived from degradation of a natural product pacidamycin with a sample synthesized from L-threonine. The biological activity of one member of a synthesized library of possible stereoisomers of the natural product established the absolute stereochemistry of the remaining centers. A variety of analogs of the natural product were prepared utilizing the synthetic methods developed, and their biological activities provide important insights into the specificity and spectrum of the antibiotic class. Copyright 1999 John Wiley & Sons, Inc. Med Res Rev, 19, No. 6, 521-542, 1999

Antiviral agents of plant origin. III. Scopadulin, a novel tetracyclic diterpene from Scoparia dulcis L.

PubMed

Hayashi, T; Kawasaki, M; Miwa, Y; Taga, T; Morita, N

1990-04-01

The structure and stereochemistry of scopadulin, a novel aphidicolane-type diterpene isolated from Scoparia dulcis L. have been established from spectral data and single-crystal X-ray analysis of its acetone solvate.

An Easily Constructed Model of a Coordination Polyhedron that Represents the Hexagonal Closest-Packed Structure.

ERIC Educational Resources Information Center

Yamana, Shukichi

1987-01-01

Illustrates the 29 steps involved in the development of a model of a coordination polyhedron that represents the hexagonal closest packed structure. Points out it is useful in teaching stereochemistry. (TW)

Stereochemistry Considerations Can Improve Pesticide Safety and Sustainability

EPA Science Inventory

About 30% of pesticides are chiral molecules and therefore exist as two or more stereoisomers, which can differ significantly in their toxicity, biodegradation, and persistence. Such differences determine their relative safety to humans and environmental species. Enantiomers, mir...

How Stereochemistry Considerations can Improve Pesticide Safety

EPA Science Inventory

About 30% of pesticides are chiral molecules and therefore exist as two or more stereoisomers, which can differ significantly in their toxicity, biodegradation, and persistence. Such differences can impact their relative safety to humans and environmental species. Enantiomers, mi...

Guajadial: an unusual meroterpenoid from guava leaves Psidium guajava.

PubMed

Yang, Xiao-Long; Hsieh, Kun-Lung; Liu, Ji-Kai

2007-11-22

Guajadial (1), a novel caryophyllene-based meroterpenoid, was isolated from the Leaves of Psidium guajava (guava). The structure and relative stereochemistry of guajadial (1) were elucidated by extensive spectroscopic analysis. A possible biosynthetic pathway for 1 was proposed.

Organic Lecture Demonstrations.

ERIC Educational Resources Information Center

Silversmith, Ernest F.

1988-01-01

Provides a listing of 35 demonstrations designed to generate interest in organic chemistry and help put points across. Topics include opening lecture; molecular structure and properties; halogenation; nucleophilic substitution, alkenes and dienes, stereochemistry, spectroscopy, alcohols and phenols, aldehydes and ketones; carboxylic acids, amines,…

Total synthesis and stereochemical assignment of the spiroisoxazoline natural product (+)-calafianin.

PubMed

Bardhan, Sujata; Schmitt, Daniel C; Porco, John A

2006-03-02

Synthesis of the spiroisoxazoline natural product (+)-calafianin is reported using asymmetric nucleophilic epoxidation and nitrile oxide cycloaddition as key steps. Synthesis and spectral analysis of all calafianin stereoisomers led to unambiguous assignment of relative and absolute stereochemistry.

Demonstration of Enantiomer Specificity of Proteins and Drugs

ERIC Educational Resources Information Center

Anderson, Gretchen L.; Page, Shallee T.

2004-01-01

Classroom demonstrations and activities are used to illustrate the properties of enantiomer. During this activity, in a relatively short time students develop a working knowledge of the importance of stereochemistry in biochemistry and its effect on drug design and metabolism.

Secoiridoid components from Jasminum grandiflorum.

PubMed

Sadhu, Samir Kumar; Khan, Md Sojib; Ohtsuki, Takashi; Ishibashi, Masami

2007-07-01

Secoiridoid glucosides, 2''-epifraxamoside and demethyl-2''-epifraxamoside, and the secoiridoid, jasminanhydride were isolated from Jasminum grandiflorum together with four previously known phenolics and a triterpene. Structures were elucidated by detailed spectroscopic analysis. Stereochemistry of the compounds was determined by differential NOE experiment.

ELUCIDATION OF THE STEREOCHEMISTRY OF OCTAHYDROISOQUINOLINE DERIVATIVES BY NMR SPECTROSCOPY. (R826113)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

An Easily Constructed Model of a Coordination Polyhedron that Represents the Cubic Closest-Packed Structure.

ERIC Educational Resources Information Center

Yamana, Shukichi

1987-01-01

Illustrates the 18 steps to the development of a model of a coordination polyhedron that represents the cubic closest-packed structure. Uses a sealed, empty envelope in developing the model in teaching about stereochemistry. (TW)

Reaction mechanisms: Stripping down SN2

NASA Astrophysics Data System (ADS)

Orr-Ewing, Andrew J.

2012-07-01

The mechanism of the SN2 reaction is fundamental to understanding and controlling the stereochemistry of organic reactions, but surrounding solvent molecules may complicate the textbook picture. Micro-solvation studies have now explored the stereochemical consequences of the presence of one or two solvent molecules.

Synthesis, characterization and electrochemical studies of heterometallic manganese(IV)-zinc(II) and manganese(IV)-copper(II) complexes derived from bis(2-hydroxy-1-naphthaldehyde)oxaloyldihydrazone

NASA Astrophysics Data System (ADS)

Koch, Angira; Phukan, Arnab; Chanu, Oinam B.; Kumar, A.; Lal, R. A.

2014-02-01

Five manganese(IV) complexes [Mn(L)(bpy)] (1) and heterobimetallic complexes [MMn(L)Cl2(H2O)4]·1.5H2O (M = ZnII(2), CuII(3)) and [MnM(L)(bpy)Cl2] (M = ZnII(4), CuII(5)] have been synthesized from bis(2-hydroxy-1-naphthaldehyde)oxaloyldihydrazone (H4L) in methanol medium. The composition of the complexes have been established based on the data obtained from analytical, thermoanalytical and mass spectral studies. The structures of the complexes have been discussed in the light of molar conductance, magnetic moment, electronic, EPR, IR, FT-IR spectroscopic studies and transmission electron microscopies. The molar conductance values of these complexes in DMSO suggest their non-electrolytic nature. The μeff value for the complexes (1), (2) and (4) fall in the range 3.82-4.12 BM characteristic of the presence of the manganese(IV) in them. The complex (3) has μeff value of 3.70 BM at RT indicating considerable antiferromagnetic interaction between Mn(IV) and Cu(II). The μeff value of 4.72 BM for complex (5) is slightly lower than 4.90 BM for S = 2 ground state. In the complex (1) to (3), the ligand is coordinated to the metal centres as tetradentate ligand while in the complexes (4) and (5) as hexadentate ligand. Manganese(IV) has distorted octahedral stereochemistry in all complexes. Copper(II) has distorted octahedral and square planar stereochemistry in complexes (3) and (5) while zinc has distorted octahedral and tetrahedral stereochemistry, respectively. EPR studies of the complexes are also reported. The electron transfer reactions of the complexes have also been investigated by cyclic voltammetry.

Diastereoselective DNA Cleavage Recognition by Ni(II)•Gly-Gly-His Derived Metallopeptides

PubMed Central

Fang, Ya-Yin; Claussen, Craig A.; Lipkowitz, Kenny B.; Long, Eric C.

2008-01-01

Site-selective DNA cleavage by diastereoisomers of Ni(II)•Gly-Gly-His-derived metallopeptides was investigated through high-resolution gel analyses and molecular dynamics simulations. Ni(II)•L-Arg-Gly-His and Ni(II)•D-Arg-Gly-His (and their respective Lys analogues) targeted A/T-rich regions; however, the L-isomers consistently modified a sub-set of available nucleotides within a given minor groove site while the D-isomers differed in both their sites of preference and ability to target individual nucleotides within some sites. In comparison, Ni(II)•L-Pro-Gly-His and Ni(II)•D-Pro-Gly-His were unable to exhibit a similar diastereoselectivity. Simulations of the above systems, along with Ni(II)•Gly-Gly-His, indicated that the stereochemistry of the amino-terminal amino acid produces either an isohelical metallopeptide that associates stably at individual DNA sites (L-Arg or L-Lys) or, with D-Arg and D-Lys, a non-complementary metallopeptide structure that cannot fully employ its side chain nor amino-terminal amine as a positional stabilizing moiety. In contrast, amino-terminal Pro-containing metallopeptides of either stereochemistry, lacking an extended side chain directed toward the minor groove, did not exhibit a similar diastereoselectivity. While the identity and stereochemistry of amino acids located in the amino-terminal peptide position influenced DNA cleavage, metallopeptide diastereoisomers containing L- and D-Arg (or Lys) within the second peptide position did not exhibit diastereoselective DNA cleavage patterns; simulations indicated that a positively-charged amino acid in this location alters the interaction of the metallopeptide equatorial plane and the minor groove leading to an interaction similar to Ni(II)•Gly-Gly-His. PMID:16522100

Synthesis and assignment of the absolute configuration of the anti-Helicobacter pylori agents CJ-12,954 and CJ-13,014.

PubMed

Brimble, Margaret A; Bryant, Christina J

2007-09-07

The synthesis of the spiroacetal-containing anti-Helicobacter pylori agents (3S,2''S,5''S,7''S)- (ent-CJ-12,954) and (3S,2''S,5''R,7''S)- (ent-CJ-13,014) has been carried out based on the convergent union of a 1:1 mixture of heterocycle-activated spiroacetal sulfones and with (3S)-phthalide aldehyde . The synthesis of the (3R)-diastereomers (3R,2''S,5''S,7''S)- and (3R,2''S,5''R,7''S)- was also undertaken in a similar manner by union of (3R)-phthalide aldehyde with a 1:1 mixture of spiroacetal sulfones and . Comparison of the (1)H and (13)C NMR data, optical rotations and HPLC retention times of the synthetic compounds (3S,2''S,5''S,7''S)- and (3S,2''S,5''R,7''S)- and the (3R)-diastereomers (3R,2''S,5''S,7''S)- and (3R,2''S,5''R,7''S)-, with the naturally occurring compounds, established that the synthetic isomers and were in fact enantiomeric to the natural products CJ-12,954 and CJ-13,014. The (2S,8S)-stereochemistry in protected dihydroxyketone , the precursor to the mixture of spiroacetal sulfones and was established via union of readily available (S)-acetylene with aldehyde in which the (4S)-stereochemistry was established via asymmetric allylation. Deprotection and cyclization of protected dihydroxyketone afforded an inseparable 1:1 mixture of spiroacetal alcohols and that were converted into a 1:1 inseparable mixture of spiroacetal sulfones and . Phthalide-aldehyde was prepared via intramolecular acylation of bromocarbamate in which the (3S)-stereochemistry was established via asymmetric CBS reduction of ketone .

Mitomycin C and decarbamoyl mitomycin C induce p53-independent p21WAF1/CIP1 activation

PubMed Central

Cheng, Shu-Yuan; Seo, Jiwon; Huang, Bik Tzu; Napolitano, Tanya; Champeil, Elise

2016-01-01

Mitomycin C (MC), a commonly used anticancer drug, induces DNA damage via DNA alkylation. Decarbamoyl mitomycin C (DMC), another mitomycin lacking the carbamate at C10, generates similar lesions as MC. Interstrand cross-links (ICLs) are believed to be the lesions primarily responsible for the cytotoxicity of MC and DMC. The major ICL generated by MC (α-ICL) has a trans stereochemistry at the guanine-drug linkage whereas the major ICL from DMC (β-ICL) has the opposite, cis, stereochemistry. In addition, DMC can provoke strong p53-independent cell death. Our hypothesis is that the stereochemistry of the major unique β-ICL generated by DMC is responsible for this p53-independent cell death signaling. p53 gene is inactively mutated in more than half of human cancers. p21WAF1/CIP1 known as a major effector of p53 is involved in p53-dependent and -independent control of cell proliferation and death. This study revealed the role of p21WAF1/CIP1 on MC and DMC triggered cell damage. MCF-7 (p53-proficient) and K562 (p53-deficient) cells were used. Cell cycle distributions were shifted to the G1/S phase in MCF-7 treated with MC and DMC, but were shifted to the S phase in K562. p21WAF1/CIP1 activation was observed in both cells treated with MC and DMC, and DMC triggered more significant activation. Knocking down p53 in MCF-7 did not attenuate MC and DMC induced p21WAF1/CIP1 activation. The α-ICL itself was enough to cause p21WAF1/CIP1 activation. PMID:27666201

Differentiation of the Stereochemistry and Anomeric Configuration for 1-3 Linked Disaccharides Via Tandem Mass Spectrometry and 18O-labeling

NASA Astrophysics Data System (ADS)

Konda, Chiharu; Bendiak, Brad; Xia, Yu

2012-02-01

Collision-induced dissociation (CID) of deprotonated hexose-containing disaccharides ( m/z 341) with 1-2, 1-4, and 1-6 linkages yields product ions at m/z 221, which have been identified as glycosyl-glycolaldehyde anions. From disaccharides with these linkages, CID of m/z 221 ions produces distinct fragmentation patterns that enable the stereochemistries and anomeric configurations of the non-reducing sugar units to be determined. However, only trace quantities of m/z 221 ions can be generated for 1-3 linkages in Paul or linear ion traps, preventing further CID analysis. Here we demonstrate that high intensities of m/z 221 ions can be built up in the linear ion trap (Q3) from beam-type CID of a series of 1-3 linked disaccharides conducted on a triple quadrupole/linear ion trap mass spectrometer. 18O-labeling at the carbonyl position of the reducing sugar allowed mass-discrimination of the "sidedness" of dissociation events to either side of the glycosidic linkage. Under relatively low energy beam-type CID and ion trap CID, an m/z 223 product ion containing 18O predominated. It was a structural isomer that fragmented quite differently than the glycosyl-glycolaldehydes and did not provide structural information about the non-reducing sugar. Under higher collision energy beam-type CID conditions, the formation of m/z 221 ions, which have the glycosyl-glycolaldehyde structures, were favored. Characteristic fragmentation patterns were observed for each m/z 221 ion from higher energy beam-type CID of 1-3 linked disaccharides and the stereochemistry of the non-reducing sugar, together with the anomeric configuration, were successfully identified both with and without 18O-labeling of the reducing sugar carbonyl group.

DNA-Templated Polymerization of Side-Chain-Functionalized Peptide Nucleic Acid Aldehydes

PubMed Central

Kleiner, Ralph E.; Brudno, Yevgeny; Birnbaum, Michael E.; Liu, David R.

2009-01-01

The DNA-templated polymerization of synthetic building blocks provides a potential route to the laboratory evolution of sequence-defined polymers with structures and properties not necessarily limited to those of natural biopolymers. We previously reported the efficient and sequence-specific DNA-templated polymerization of peptide nucleic acid (PNA) aldehydes. Here, we report the enzyme-free, DNA-templated polymerization of side-chain-functionalized PNA tetramer and pentamer aldehydes. We observed that the polymerization of tetramer and pentamer PNA building blocks with a single lysine-based side chain at various positions in the building block could proceed efficiently and sequence-specifically. In addition, DNA-templated polymerization also proceeded efficiently and in a sequence-specific manner with pentamer PNA aldehydes containing two or three lysine side chains in a single building block to generate more densely functionalized polymers. To further our understanding of side-chain compatibility and expand the capabilities of this system, we also examined the polymerization efficiencies of 20 pentamer building blocks each containing one of five different side-chain groups and four different side-chain regio- and stereochemistries. Polymerization reactions were efficient for all five different side-chain groups and for three of the four combinations of side-chain regio- and stereochemistries. Differences in the efficiency and initial rate of polymerization correlate with the apparent melting temperature of each building block, which is dependent on side-chain regio- and stereochemistry, but relatively insensitive to side-chain structure among the substrates tested. Our findings represent a significant step towards the evolution of sequence-defined synthetic polymers and also demonstrate that enzyme-free nucleic acid-templated polymerization can occur efficiently using substrates with a wide range of side-chain structures, functionalization positions within each building block, and functionalization densities. PMID:18341334

Two-Dimensional Chirality in Three-Dimensional Chemistry.

ERIC Educational Resources Information Center

Wintner, Claude E.

1983-01-01

The concept of two-dimensional chirality is used to enhance students' understanding of three-dimensional stereochemistry. This chirality is used as a key to teaching/understanding such concepts as enaniotropism, diastereotopism, pseudoasymmetry, retention/inversion of configuration, and stereochemical results of addition to double bonds. (JN)

Grasping the Concepts of Stereochemistry.

ERIC Educational Resources Information Center

Barta, Nancy S.; Stille, John R.

1994-01-01

Presents an effective means of determining the R or S configuration of chiral molecules using the Cahn Ingold Prelog (CIP) sequence rules to establish substituent priority and use of the ultimate model of chirality, the hands, to aid in the direct correlation and assignment of relative configuration. (ZWH)

Effect of Stereochemistry on Directed Self-Assembly of Poly(styrene-b-lactide) Films on Chemical Patterns

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

Li, Xiao; Liu, Yadong; Wan, Lei

2016-03-15

We demonstrated here for the first time that the stereochemistry of polylactide (PLA) blocks affected the assembly behaviors of PS-b-PLA on chemical patterns. Two PS-b-PLA block copolymers, where the PLA block is either racemic (PDLLA) or left-handed (PLLA), were synthesized and directed to assemble on chemical patterns with a wide range of L-s/L-o. PS-b-PDLLA was stretched up to 70% on chemical patterns, while PS-b-PLLA was only stretched by 20%. The assembly behavior of PS-b-PDLLA was different from AB diblock copolymer, but similar to that of ABA triblock copolymer. The high stretchability might be attributed to the formation of stereocomplexes inmore » PDLLA blocks. Compared to ABA triblock copolymers, stereocomplexed diblock copolymers have much faster assembly kinetics. This observation provides a new concept to achieve large process windows by the introduction of specific interactions, for example, H-bonding, supramolecular interaction, and sterecomplexation, between polymer chains.« less

Solvent effects on the relative stability of radicals derived from artemisinin: DFT study using the PCM/COSMO approach

NASA Astrophysics Data System (ADS)

Araujo, M. T. De; Carneiro, J. W. De M.; Taranto, A. G.

The PCM/COSMO approach was employed to calculate the relative stability of radicals derived from the antimalarial artemisinin. The calculations were performed in polar (water) and apolar (THF) solvent at the density functional level [B3LYP/6-31g(d)]. Relative stabilities were calculated by means of isodesmic equations using artemisinin as reference. Replacement of oxygen atoms by CH2 unities was found to decrease the relative stability of the anionic radical intermediates. The degree of destabilization is reduced in the presence of solvent, being less in water than in THF. The dipole moment and the corresponding solvation free energies of these species modulate this effect. Derivatives with inverted stereochemistry are more stable than those with the artemisinin-like stereochemistry, although the solvent attenuates this stabilization effect. As was found in the in vacuo calculations, the radicals centered on carbon are always more stable than the corresponding radicals centered on oxygen.

Carbocation/Polyol Systems as Efficient Organic Catalysts for the Preparation of Cyclic Carbonates.

PubMed

Rulev, Yuri A; Gugkaeva, Zalina T; Lokutova, Anastasia V; Maleev, Victor I; Peregudov, Alexander S; Wu, Xiao; North, Michael; Belokon, Yuri N

2017-03-22

Carbocation/polyol systems are shown to be highly efficient catalysts for the synthesis of cyclic carbonates from epoxides and carbon dioxide at 50 °C and 5 MPa CO 2 pressure. The best activity was shown by the combination of crystal violet and 1,1'-bi-2-naphthol (BINOL), which could be recycled five times with no loss of activity. The presence of specific interactions between the amino groups of the carbocation and the hydroxyl protons was confirmed by NMR experiments. The Job plots for the crystal violet iodide/BINOL and brilliant green iodide/BINOL systems showed that the catalytic systems consist of one molecule of the carbocation and one molecule of BINOL. Mechanistic studies using a deuterated epoxide indicate that there was some loss of epoxide stereochemistry during the reaction, but predominant retention of stereochemistry is observed. On this basis, a catalytic cycle is proposed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fast, metadynamics-based method for prediction of the stereochemistry-dependent relative free energies of ligand-receptor interactions.

PubMed

Plazinska, Anita; Plazinski, Wojciech; Jozwiak, Krzysztof

2014-04-30

The computational approach applicable for the molecular dynamics (MD)-based techniques is proposed to predict the ligand-protein binding affinities dependent on the ligand stereochemistry. All possible stereoconfigurations are expressed in terms of one set of force-field parameters [stereoconfiguration-independent potential (SIP)], which allows for calculating all relative free energies by only single simulation. SIP can be used for studying diverse, stereoconfiguration-dependent phenomena by means of various computational techniques of enhanced sampling. The method has been successfully tested on the β2-adrenergic receptor (β2-AR) binding the four fenoterol stereoisomers by both metadynamics simulations and replica-exchange MD. Both the methods gave very similar results, fully confirming the presence of stereoselective effects in the fenoterol-β2-AR interactions. However, the metadynamics-based approach offered much better efficiency of sampling which allows for significant reduction of the unphysical region in SIP. Copyright © 2014 Wiley Periodicals, Inc.

Photochemical activity of a key donor-acceptor complex can drive stereoselective catalytic α-alkylation of aldehydes.

PubMed

Arceo, Elena; Jurberg, Igor D; Alvarez-Fernández, Ana; Melchiorre, Paolo

2013-09-01

Asymmetric catalytic variants of sunlight-driven photochemical processes hold extraordinary potential for the sustainable preparation of chiral molecules. However, the involvement of short-lived electronically excited states inherent to any photochemical reaction makes it challenging for a chiral catalyst to dictate the stereochemistry of the products. Here, we report that readily available chiral organic catalysts, with well-known utility in thermal asymmetric processes, can also confer a high level of stereocontrol in synthetically relevant intermolecular carbon-carbon bond-forming reactions driven by visible light. A unique mechanism of catalysis is proposed, wherein the catalyst is involved actively in both the photochemical activation of the substrates (by inducing the transient formation of chiral electron donor-acceptor complexes) and the stereoselectivity-defining event. We use this approach to enable transformations that are extremely difficult under thermal conditions, such as the asymmetric α-alkylation of aldehydes with alkyl halides, the formation of all-carbon quaternary stereocentres and the control of remote stereochemistry.

Correlation between the Stereochemistry and Bioactivity in Octahedral Rhodium Prolinato Complexes.

PubMed

Rajaratnam, Rajathees; Martin, Elisabeth K; Dörr, Markus; Harms, Klaus; Casini, Angela; Meggers, Eric

2015-08-17

Controlling the relative and absolute configuration of octahedral metal complexes constitutes a key challenge that needs to be overcome in order to fully exploit the structural properties of octahedral metal complexes for applications in the fields of catalysis, materials sciences, and life sciences. Herein, we describe the application of a proline-based chiral tridentate ligand to decisively control the coordination mode of an octahedral rhodium(III) complex. We demonstrate the mirror-like relationship of synthesized enantiomers and differences between diastereomers. Further, we demonstrate, using the established pyridocarbazole pharmacophore ligand as part of the organometallic complexes, the importance of the relative and absolute stereochemistry at the metal toward chiral environments like protein kinases. Protein kinase profiling and inhibition data confirm that the proline-based enantiopure rhodium(III) complexes, despite having all of the same constitution, differ strongly in their selectivity properties despite their unmistakably mutual origin. Moreover, two exemplary compounds have been shown to induce different toxic effects in an ex vivo rat liver model.

A Simple Method for Drawing Chiral Mononuclear Octahedral Metal Complexes

ERIC Educational Resources Information Center

Mohamadou, Aminou; Haudrechy, Arnaud

2008-01-01

Octahedral transition-metal complexes are involved in a number of reactions and octahedral coordination geometry, frequently observed for metallic centers, includes important topographical stereochemistry. Depending on the number and nature of different ligands, octahedral coordination units with at least two different monodentate ligands give…

Conformation analysis of oligomeric flavanoids

Treesearch

Jan P. Steynberg; E. Vincent Brandt; Daneel Ferreira; Carin A. Helfer; Wayne L. Mattice; Dominika Gornik; Richard W. Hemingway

1995-01-01

The profisetinidins are the most important polyflavanoids of commerce, making up the major constituents of wattle and quebracho tannins. Within the dimeric profisetinidins, substantial complexity exists because of stereo-, regio, rotational and conformational isomers. Definition of the stereochemistry of the upper and lower flavan units, the location of the...

Conformational analysis of oligomeric flavanoids

Treesearch

Jan P. Steynberg; E. Vincent Brandt; Daneel Ferreira; Carin A. Helfer; Wayne L. Mattice; Dominika Gornik; Richard W. Hemingway

1995-01-01

The profisetinidins are the most important polyflavanoids of commerce, making up the major constituents of wattle and quebracho tannins. Even within the dimeric profisetinidins, substantial complexity exists because of stereo-, regio-, rotational and conformational isomers. Definition of the stereochemistry of the upper and lower flavan units, the location of the...

Stereochemistry of Furfural Reduction by a Saccharomyces cerevisiae Aldehyde Reductase That Contributes to In Situ Furfural Detoxification

USDA-ARS?s Scientific Manuscript database

Ari1p from Saccharomyces cerevisiae, recently identified as an intermediate subclass short-chain dehydrogenase/reductase, contributes in situ to the detoxification of furfural. Furfural inhibits efficient ethanol production by the yeast, particularly when the carbon source is acid-treated lignocell...

The "Protocenter" Concept: A Method for Teaching Stereochemistry

ERIC Educational Resources Information Center

Lewis, David E.

2010-01-01

The "protocenter", defined as an atom carrying two different attached groups in a nonlinear arrangement, is proposed as a concept useful for the introduction of chirality and geometric isomerism in introductory organic chemistry classes. Two protocenters are the minimum requirement for stereoisomers of a compound to exist. Protocenters may be…

The Determination of the Stereochemistry of Erythro-1,2-Diphenyl-1,2-Ethanediol: An Undergraduate Organic Experiment.

ERIC Educational Resources Information Center

Rowland, Alex T.

1983-01-01

Describes an undergraduate organic chemistry experiment designed to illustrate the power of nuclear magnetic reasonance spectroscopy in a determination of the configurations at centers of chirality of various isomers of acyclic systems. Provides a background discussion and experimental procedure. (JM)

The Reception of J. H. van't Hoff's Theory of the Asymmetric Carbon Atom

ERIC Educational Resources Information Center

Snelders, H. A. M.

1974-01-01

Discusses Jacobus Henricus van't Hoff's revolutionary theory of the asymmetric carbon atom and its early reception among his contemporaries in the Netherlands. Indicates that the extension of the new idea to practical problems gives the impetus to the development of stereochemistry. (CC)

Further sesquiterpenoids and phenolics from Taraxacum officinale.

PubMed

Kisiel, W; Barszcz, B

2000-06-01

Five germacrane- and guaiane-type sesquiterpene lactones, including two previously described taraxinic acid derivatives, were isolated from the roots of Taraxacum officinale, together with benzyl glucoside, dihydroconiferin, syringin and dihydrosyringin. The other three lactones were identified as 11beta, 13-dihydrolactucin, ixerin D and ainslioside. Moreover, the stereochemistry at C-11 in dihydrotaraxinic acid was assigned.

Development of a stereoselective and scalable process for the preparation of a methylcyclobutanol-pyridyl ether.

PubMed

Kuethe, Jeffrey T; Basu, Kallol; Orr, Robert K; Ashley, Eric; Poirier, Marc; Tan, Lushi

2018-02-15

The evolution of a scalable process for the preparation of methylcyclobutanol-pyridyl ether 1 is described. Key aspects of this development including careful control of the stereochemistry, elimination of chromatography, and application to kilogram-scale synthesis are addressed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Determination of the stereochemistry of the aggregation pheromone of harlequin bug, Murgantia histrionica

USDA-ARS?s Scientific Manuscript database

Preparation of a complete stereoisomeric library of 1,10-bisaboladien-3-ols and selected 10,11-epoxy-1-bisabolen-3-ols was earlier pivotal for the identification of the aggregation pheromone of the brown marmorated stink bug, Halyomorpha halys. Herein, we describe syntheses of remaining10,11-epoxy-1...

Visualizing Molecular Chirality in the Organic Chemistry Laboratory Using Cholesteric Liquid Crystals

ERIC Educational Resources Information Center

Popova, Maia; Bretz, Stacey Lowery; Hartley, C. Scott

2016-01-01

Although stereochemistry is an important topic in second-year undergraduate organic chemistry, there are limited options for laboratory activities that allow direct visualization of macroscopic chiral phenomena. A novel, guided-inquiry experiment was developed that allows students to explore chirality in the context of cholesteric liquid crystals.…

The Metolachlor Herbicide: An Exercise in Today's Stereochemistry

ERIC Educational Resources Information Center

Mannschreck, Albrecht; von Angerer, Erwin

2009-01-01

Metolachlor is one of the most widely used agents registered for the protection of many cultivated plants against weeds. Because of axial and central chirality, this molecule forms four stereoisomers, the investigation of which by [superscript 1]H NMR and chromatography is described. It is shown that the isomers do not interconvert at room…

The Acquisition of Stereochemical Knowledge by Algerian Students Intending to Teach Physical Sciences

ERIC Educational Resources Information Center

Boukhechem, Mohamed-Salah; Dumon, Alain; Zouikri, Mohamed

2011-01-01

In this work we evaluated the level of difficulty found in learning stereochemistry concepts, by students intending to teach physical sciences at the Ecole Normale Superieure (ENS) Kouba (Algeria). A paper and pencil questionnaire was administered to 170 students to evaluate: their familiarity with Newman representations; their ability of linking…

NMR spectra of 3β-hydroxy-5α-cholane derivatives, zymosterol synthesis intermediates

NASA Astrophysics Data System (ADS)

Baranovsky, A. V.; Bolotin, A. A.; Kiselev, V. P.

2011-05-01

Proton and carbon resonances in NMR spectra of a number of derivatives of 3β-hydroxy-5α-cholanes, zymosterol synthesis intermediates, have been completely assigned using 2D NMR spectroscopy methods. The stereochemistry of the chiral centers and the structures of the molecules have been confirmed.

Impact of In Vitro System, Chemical Mistures, and Stereochemistry on the Intrinsic Clearance of 1,2,4-Triazole Fungicides in Human and Rat

EPA Science Inventory

The exposure of humans and ecologically important species to environmental chemicals typically occurs at unknown concentrations and for uncertain durations. Exposure becomes an internal dose when the chemical crosses the body barrier. Characterizing internal dose is important for...

Learning about Regiochemistry from a Hydrogen-Atom Abstraction Reaction in Water

ERIC Educational Resources Information Center

Sears-Dundes, Christopher; Huon, Yoeup; Hotz, Richard P.; Pinhas, Allan R.

2011-01-01

An experiment has been developed in which the hydrogen-atom abstraction and the coupling of propionitrile, using Fenton's reagent, are investigated. Students learn about the regiochemistry of radical formation, the stereochemistry of product formation, and the interpretation of GC-MS data, in a safe reaction that can be easily completed in one…

Synthesis of (R)- and (S)-10,16-dihydroxyhexadecanoic acid: cutin stereochemistry and fungal activation.

PubMed

Ahmed, Aqeel; Crawford, Terry; Gould, Stephanie; Ha, Y S; Hollrah, Monica; Noor-E-Ain, Farhana; Dickman, Martin B; Dussault, Patrick H

2003-05-01

The first asymmetric syntheses of the cutin monomers (R)- and (S)-10,16-dihydroxyhexadecanoic acid (10,16-DHPA) and confirmation of (S)(+)-absolute configuration for 10,16-DHPA derived from tomato are reported. The individual DHPA stereoisomers display differences in their ability to activate the fungal pathogen Colletotrichum trifolii.

Rehabilitation of faulty kinetic determinations and misassigned glycoside hydrolase family of retaining mechanism ß-xylosidases

USDA-ARS?s Scientific Manuscript database

We obtained Cx1 from a commercial supplier, whose catalog listed it as a ß-xylosidase of glycoside hydrolase family 43. NMR experiments indicate retention of anomeric configuration in its reaction stereochemistry, opposing the assignment of GH43, which follows an inverting mechanism. Partial protein...

Unravelling RNA-substrate interactions in a ribozyme-catalysed reaction using fluorescent turn-on probes.

PubMed

Gaffarogullari, Ece Cazibe; Greulich, Peter; Kobitski, Andrei Yu; Nierth, Alexander; Nienhaus, G Ulrich; Jäschke, Andres

2015-04-07

The Diels-Alder reaction is one of the most important C-C bond-forming reactions in organic chemistry, and much effort has been devoted to controlling its enantio- and diastereoselectivity. The Diels-Alderase ribozyme (DAse) catalyses the reaction between anthracene dienes and maleimide dienophiles with multiple-turnover, stereoselectivity, and up to 1100-fold rate acceleration. Here, a new generation of anthracene-BODIPY-based fluorescent probes was developed to monitor catalysis by the DAse. The brightness of these probes increases up to 93-fold upon reaction with N-pentylmaleimide (NPM), making these useful tools for investigating the stereochemistry of the ribozyme-catalysed reaction. With these probes, we observed that the DAse catalyses the reaction with >91% de and >99% ee. The stereochemistry of the major product was determined unambiguously by rotating-frame nuclear Overhauser NMR spectroscopy (ROESY-NMR) and is in agreement with crystallographic structure information. The pronounced fluorescence change of the probes furthermore allowed a complete kinetic analysis, which revealed an ordered bi uni type reaction mechanism, with the dienophile binding first. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Controlling the stereochemistry and regularity of butanethiol self-assembled monolayers on au(111).

PubMed

Yan, Jiawei; Ouyang, Runhai; Jensen, Palle S; Ascic, Erhad; Tanner, David; Mao, Bingwei; Zhang, Jingdong; Tang, Chunguang; Hush, Noel S; Ulstrup, Jens; Reimers, Jeffrey R

2014-12-10

The rich stereochemistry of the self-assembled monolayers (SAMs) of four butanethiols on Au(111) is described, the SAMs containing up to 12 individual C, S, or Au chiral centers per surface unit cell. This is facilitated by synthesis of enantiomerically pure 2-butanethiol (the smallest unsubstituted chiral alkanethiol), followed by in situ scanning tunneling microscopy (STM) imaging combined with density functional theory molecular dynamics STM image simulations. Even though butanethiol SAMs manifest strong headgroup interactions, steric interactions are shown to dominate SAM structure and chirality. Indeed, steric interactions are shown to dictate the nature of the headgroup itself, whether it takes on the adatom-bound motif RS(•)Au(0)S(•)R or involves direct binding of RS(•) to face-centered-cubic or hexagonal-close-packed sites. Binding as RS(•) produces large, organizationally chiral domains even when R is achiral, while adatom binding leads to rectangular plane groups that suppress long-range expression of chirality. Binding as RS(•) also inhibits the pitting intrinsically associated with adatom binding, desirably producing more regularly structured SAMs.

Study of the Stereochemistry and Oxidation Mechanism of Plant Polyphenols, Assisted by Computational Chemistry.

PubMed

Matsuo, Yosuke

2017-01-01

In recent years, plant polyphenols have attracted great attention due to their wide range of biological activities. Certain kinds of polyphenols have complex structures; therefore, it is difficult to elucidate their total structure, including stereochemistry. In this study, we reinvestigated the stereostructures of two major C-glycosidic ellagitannins contained in Quercus plants, vescalagin and castalagin, and revised their stereostructures based on theoretical calculations of spectroscopic data. We also determined the structures of quercusnins A and B, isolated from the sapwood of Quercus crispula, based on theoretical calculations of NMR data. The oxidation mechanism of polyphenols has not been entirely elucidated. Therefore, we have also studied the oxidation mechanism of tea catechins during black tea production. Our investigation of the oxidation mechanism of black tea pigment theaflavins revealed that the difference in the position of the galloyl ester affords different oxidation products of theaflavins. In addition, oxidation products of pyrogallol-type catechins could be classified into three types-dehydrotheasinensins, theacitrins, and proepitheaflagallins; their detailed production and degradation mechanisms were also examined.

Stereoselective synthesis of the 5'-hydroxy-5'-phosphonate derivatives of cytidine and cytosine arabinoside.

PubMed

Chen, Xuemei; Wiemer, Andrew J; Hohl, Raymond J; Wiemer, David F

2002-12-27

Both the (R)- and (S)-5'-hydroxy 5'-phosphonate derivatives of cytidine and cytosine arabinoside (ara-C) have been prepared via phosphite addition or a Lewis acid mediated hydrophosphonylation of appropriately protected 5'-nucleoside aldehydes. Phosphite addition to a cytosine aldehyde protected as the 2',3'-acetonide gave predominately the 5'R isomer, while phosphite addition to the corresponding 2',3'-bis TBS derivative favored the 5'S stereochemistry. In contrast, phosphite addition to the 2',3'-bis TBS protected aldehyde derived from ara-C gave only the 5'R adduct. However, TiCl(4)-mediated hydrophosphonylation of the same ara-C aldehyde favored the 5'S stereoisomer by a 2:1 ratio. Once all four of the diastereomers were in hand, the stereochemistry of these compounds could be assigned based on their spectral data or that obtained from their O-methyl mandelate derivatives. After hydrolysis of the phosphonate esters and various protecting groups, the four alpha-hydroxy phosphonic acids were tested for their ability to serve as substrates for the enzyme nucleoside monophosphate kinase and for their toxicity to K562 cells.

Cryogenic Vibrational Spectroscopy Provides Unique Fingerprints for Glycan Identification.

PubMed

Masellis, Chiara; Khanal, Neelam; Kamrath, Michael Z; Clemmer, David E; Rizzo, Thomas R

2017-10-01

The structural characterization of glycans by mass spectrometry is particularly challenging. This is because of the high degree of isomerism in which glycans of the same mass can differ in their stereochemistry, attachment points, and degree of branching. Here we show that the addition of cryogenic vibrational spectroscopy to mass and mobility measurements allows one to uniquely identify and characterize these complex biopolymers. We investigate six disaccharide isomers that differ in their stereochemistry, attachment point of the glycosidic bond, and monosaccharide content, and demonstrate that we can identify each one unambiguously. Even disaccharides that differ by a single stereogenic center or in the monosaccharide sequence order show distinct vibrational fingerprints that would clearly allow their identification in a mixture, which is not possible by ion mobility spectrometry/mass spectrometry alone. Moreover, this technique can be applied to larger glycans, which we demonstrate by distinguishing isomeric branched and linear pentasaccharides. The creation of a database containing mass, collision cross section, and vibrational fingerprint measurements for glycan standards should allow unambiguous identification and characterization of these biopolymers in mixtures, providing an enabling technology for all fields of glycoscience. Graphical Abstract ᅟ.

Stereochemistry of an agonist determines coupling preference of beta2-adrenoceptor to different G proteins in cardiomyocytes.

PubMed

Woo, Anthony Yiu-Ho; Wang, Tian-Bing; Zeng, Xiaokun; Zhu, Weizhong; Abernethy, Darrell R; Wainer, Irving W; Xiao, Rui-Ping

2009-01-01

A fundamental question regarding receptor-G protein interaction is whether different agonists can lead a receptor to different intracellular signaling pathways. Our previous studies have demonstrated that although most beta(2)-adrenoceptor agonists activate both G(s) and G(i) proteins, fenoterol, a full agonist of beta(2)-adrenoceptor, selectively activates G(s) protein. Fenoterol contains two chiral centers and may exist as four stereoisomers. We have synthesized a series of stereoisomers of fenoterol and its derivatives and characterized their receptor binding and pharmacological properties. We tested the hypothesis that the stereochemistry of an agonist determines selectivity of receptor coupling to different G protein(s). We found that the R,R isomers of fenoterol and methoxyfenoterol exhibited more potent effects to increase cardiomyocyte contraction than their S,R isomers. It is noteworthy that although (R,R)-fenoterol and (R,R)-methoxyfenoterol preferentially activate G(s) signaling, their S,R isomers were able to activate both G(s) and G(i) proteins as evidenced by the robust pertussis toxin sensitivities of their effects on cardiomyocyte contraction and on phosphorylation of extracellular signal-regulated kinase 1/2. The differential G protein selectivities of the fenoterol stereoisomers were further confirmed by photoaffinity labeling studies on G(s),G(i2), and G(i3) proteins. The inefficient G(i) signaling with the R,R isomers is not caused by the inability of the R,R isomers to trigger the protein kinase A (PKA)-mediated phosphorylation of the beta(2)-adrenoceptor, because the R,R isomers also markedly increased phosphorylation of the receptor at serine 262 by PKA. We conclude that in addition to receptor subtype and phosphorylation status, the stereochemistry of a given agonist plays an important role in determining receptor-G protein selectivity and downstream signaling events.

Mechanistic, Mutational, and Structural Evaluation of a Taxus Phenylalanine Aminomutase

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

Feng, Lei; Wanninayake, Udayanga; Strom, Susan

The structure of a phenylalanine aminomutase (TcPAM) from Taxus canadensis has been determined at 2.4 {angstrom} resolution. The active site of the TcPAM contains the signature 4-methylidene-1H-imidazol-5(4H)-one prosthesis, observed in all catalysts of the class I lyase-like family. This catalyst isomerizes (S)-{alpha}-phenylalanine to the (R)-{beta}-isomer by exchange of the NH{sub 2}/H pair. The stereochemistry of the TcPAM reaction product is opposite of the (S)-{beta}-tyrosine made by the mechanistically related tyrosine aminomutase (SgTAM) from Streptomyces globisporus. Since TcPAM and SgTAM share similar tertiary- and quaternary-structures and have several highly conserved aliphatic residues positioned analogously in their active sites for substrate recognition,more » the divergent product stereochemistries of these catalysts likely cannot be explained by differences in active site architecture. The active site of the TcPAM structure also is in complex with (E)-cinnamate; the latter functions as both a substrate and an intermediate. To account for the distinct (3R)-{beta}-amino acid stereochemistry catalyzed by TcPAM, the cinnamate skeleton must rotate the C{sub 1}-C{sub {alpha}} and C{sub ipso}-C{sub {beta}} bonds 180{sup o} in the active site prior to exchange and rebinding of the NH{sub 2}/H pair to the cinnamate, an event that is not required for the corresponding acrylate intermediate in the SgTAM reaction. Moreover, the aromatic ring of the intermediate makes only one direct hydrophobic interaction with Leu-104. A L104A mutant of TcPAM demonstrated an 1.5-fold increase in k{sub cat} and a decrease in K{sub M} values for sterically demanding 3'-methyl-{alpha}-phenylalanine and styryl-{alpha}-alanine substrates, compared to the kinetic parameters for TcPAM. These parameters did not change significantly for the mutant with 4'-methyl-{alpha}-phenylalanine compared to those for TcPAM.« less

New phenolic esters from the resinous exudate of Haplopappus taeda.

PubMed

Faini, Francesca; Labbé, Cecilia; Torres, René; Rodilla, Jesús M; Silva, Lucía; Delle Monache, Franco

2007-12-01

Two new phenolic esters 9-trans-p-coumaroyloxy-alpha-terpineol (1) and 7-trans-p-coumaroyloxy-taedol (2), both endowed with free radical scavenger activity and cleroda-3,13 (E)-dien-15,18-diol (3) for which a cis stereochemistry at the decalin junction was found, were isolated from the resinous exudate from Haplopappus taeda upper parts.

Using One's Hands for Naming Optical Isomers and Other Stereochemical Positions.

ERIC Educational Resources Information Center

Mezl, Vasek A.

1996-01-01

Presents a method that allows students to use their hands to obtain the stereochemistry of chiral centers without redrawing the structure. Discusses the use of the model in: determining the configurations of amino acids, determining if sugars are D or L isomers, the sequence rule procedure, prochirality, naming the sides of trigonal carbons, and…

Rapid and Stereoselective Conversion of a "trans"-Cinnamic Acid to a beta-Bromostyrene

ERIC Educational Resources Information Center

Evans, Thomas A.

2006-01-01

The stereoselective synthesis of an aryl vinyl bromide is accomplished in a rapid microscale reaction of "trans"-4-methoxycinnamic acid with N-bromosuccinimide in dichloromethane. The product is purified by dry column vacuum chromatography and its stereochemistry is determined by [superscript 1]H NMR. TLC, GC and GC-MSD can also be used. This…

Exploring the Stereochemistry of the Wittig Reaction: The Unexpected Influence of a Nominal Spectator Ion

ERIC Educational Resources Information Center

Hanson, John; Dasher, Bill; Scharrer, Eric; Hoyt, Tim

2010-01-01

Students in the second-semester organic chemistry laboratory perform a Wittig reaction between butylidenetriphenylphosphorane (an ylide) and benzaldehyde and determine the relative percentages of the cis and trans isomers of the 1-phenyl-1-pentene product. Because of the highly reactive nature of this unstabilized ylide, students are introduced to…

De novo asymmetric synthesis and biological analysis of the daumone pheromones in Caenorhabditis elegans and in the soybean cyst nematode Heterodera glycines

USDA-ARS?s Scientific Manuscript database

The de novo asymmetric total syntheses of daumone 1, daumone 2 and analogs are described. The key steps of our approach are the diastereoselective palladium catalyzed glycosylation reaction, the Noyori reduction of a acetylfuran and a propargyl ketone, which introduce the absolute stereochemistry of...

Mosher Amides: Determining the Absolute Stereochemistry of Optically-Active Amines

ERIC Educational Resources Information Center

Allen, Damian A.; Tomaso, Anthony E., Jr.; Priest, Owen P.; Hindson, David F.; Hurlburt, Jamie L.

2008-01-01

The use of chiral reagents for the derivatization of optically-active amines and alcohols for the purpose of determining their enantiomeric purity or absolute configuration is a tool used by many chemists. Among the techniques used, Mosher's amide and Mosher's ester analyses are among the most reliable and one of the most often used. Despite this,…

The Pauson-Khand reaction of medium sized trans-cycloalkenes.

PubMed

Lledó, Agustí; Fuster, Aida; Revés, Marc; Verdaguer, Xavier; Riera, Antoni

2013-04-14

Medium sized trans-cycloalkenes are unusually reactive in the intermolecular Pauson-Khand reaction (PKR) with regard to typical monocyclic alkenes. This is due to the ring strain imparted by the E stereochemistry. The PKR of these alkenes offers a modular, regioselective and straightforward entry to trans fused [n.3.0] bicyclic scaffolds (n = 6-8).

Form Follows Function: Designer Chemistry at the 52nd Bürgenstock Conference.

PubMed

Heretsch, Philipp

2017-07-24

The 52nd Bürgenstock Conference on Stereochemistry took place from April 30-May 4, 2017, and showed how chemistry and design go hand-in-hand (as reflected in the image of the Bauhausarchiv in Berlin). In this Conference Report, Philipp Heretsch outlines the program. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chirality Made Simple: A 1 - and 2-Dimensional Introduction to Stereochemistry

ERIC Educational Resources Information Center

Gawley, Robert E.

2005-01-01

The introduction of chirality in one and two dimensions, along with the concepts of internal and external reflection, can be combined with concepts familiar to all students. Once familiar with 1-Dimensional and 2-Dimensional chirality, the same concepts can be extended to 3-Dimensional and by projecting 3-D back to two, it is possible to interpret…

Acquisition of HPLC-Mass Spectrometer

DTIC Science & Technology

2015-08-18

phenyl alanine. This dithiol is coordinated to the iron and all attempts to decompose the ionic coordination complex 56 to recover strictly the...sulfonation process of an asymmetric deprotonation providing a lithium complex with sparteine. This reaction scheme will also direct stereochemistry of...currently used in ointments for treatment of pain and inflammation. Capsaicin shows promise as an effective anti-cancer nutritional agent and

New erythritol derivatives from the fertile form of Roccella montagnei.

PubMed

Duong, Thuc Huy; Huynh, Bui Linh Chi; Chavasiri, Warinthorn; Chollet-Krugler, Marylene; Nguyen, Van Kieu; Nguyen, Thi Hoai Thu; Hansen, Poul Erik; Le Pogam, Pierre; Thüs, Holger; Boustie, Joël; Nguyen, Kim Phi Phung

2017-05-01

Chemical investigation of the methanol extract of the fertile form of Roccella montagnei collected in Vietnam afforded twelve secondary metabolites, including five new montagnetol derivatives, orsellinylmontagnetols A-D and a furanyl derivative together with seven known compounds. Their chemical structures were elucidated by analysis of 1D and 2D NMR and high resolution mass spectroscopic data. The relative stereochemistry of two chiral centers (C-2 and C-3) of orsellinylmontagnetols A and B was elucidated by comparison of their coupling constants and the specific rotation with those reported in the literature while the absolute stereochemistry was determined by the application of a modified Mosher method for the hydroxy group at C-3. The absolute configuration (2R,3S) of the butanetetraol moiety of these compounds is in accordance with that of erythrin, a recognized chemotaxonomic marker of the genus Roccella. Five of these compounds were evaluated for their cytotoxic activities against four cancer cell lines. Only orsellinylmontagnetol A exerted a moderate activity against MCF-7 cell line with an IC 50 value of 68.39 ± 3.46 μM. Copyright © 2017 Elsevier Ltd. All rights reserved.

Peptide- and proton-driven allosteric clamps catalyze anthrax toxin translocation across membranes

PubMed Central

Das, Debasis; Krantz, Bryan A.

2016-01-01

Anthrax toxin is an intracellularly acting toxin in which sufficient information is available regarding the structure of its transmembrane channel, allowing for detailed investigation of models of translocation. Anthrax toxin, comprising three proteins—protective antigen (PA), lethal factor (LF), and edema factor—translocates large proteins across membranes. Here we show that the PA translocase channel has a transport function in which its catalytic active sites operate allosterically. We find that the phenylalanine clamp (ϕ-clamp), the known conductance bottleneck in the PA translocase, gates as either a more closed state or a more dilated state. Thermodynamically, the two channel states have >300-fold different binding affinities for an LF-derived peptide. The change in clamp thermodynamics requires distant α-clamp and ϕ-clamp sites. Clamp allostery and translocation are more optimal for LF peptides with uniform stereochemistry, where the least allosteric and least efficiently translocated peptide had a mixed stereochemistry. Overall, the kinetic results are in less agreement with an extended-chain Brownian ratchet model but, instead, are more consistent with an allosteric helix-compression model that is dependent also on substrate peptide coil-to-helix/helix-to-coil cooperativity. PMID:27506790

Rate-limiting steps of stereochemistry retaining ß-D-xylosidase from Geobacillus stearothermophilus acting as substrates

USDA-ARS?s Scientific Manuscript database

Kinetic experiments of GSXynB2, a ß-xylosidase, acting on 2-nitrophenyl-ß-D-xylopyranoside (2NPX), 4-nitrophenyl-ß-D-xylopyranoside (4NPX), 4-methylumbelliferyl-ß-D-xylopyanoside (MuX) and xylobiose (X2) were conducted at pH 7.0 and 25 °C. Catalysis proceeds in two steps: E + substrate TO E-xylose ...

Verbalactone, a new macrocyclic dimer lactone from the roots of Verbascum undulatum with antibacterial activity.

PubMed

Magiatis, P; Spanakis, D; Mitaku, S; Tsitsa, E; Mentis, A; Harvala, C

2001-08-01

A novel macrocyclic dimer lactone, named verbalactone, was isolated from the roots of Verbascum undulatum and exhibited interesting antibacterial activity. It is the first time that 1,7-dioxacyclododecane is reported as the ring system of a natural product. The structure and the absolute stereochemistry of the new compound were determined by spectral methods and chemical correlation.

Biochemical changes in bone in a model of weightlessness

NASA Technical Reports Server (NTRS)

Mechanic, Gerald L.

1986-01-01

The amounts of nonmineralized and mineralized collagen in bone from control, immobilized, and immobilized reambulated monkeys were examined. In order to understand structure function relationships of bone collagen and the reponse of a variety of conditions on control of the three dimensional structure of the collagen fibril, the stereochemistry of the cross-linking reactions as well as the stereospecific packing of the collagen molecules were studied.

Stereoselective synthesis of conformationally constrained omega-amino acid analogues from pyroglutamic acid.

PubMed

Bentz, Emilie L; Goswami, Rajesh; Moloney, Mark G; Westaway, Susan M

2005-08-07

Bicyclic lactams derived from pyroglutamic acid provide a useful scaffold for synthesis of conformationally restricted analogues of lysine, ornithine and glutamine, as well as an Ala-Ala dipeptide analogue. Amino alcohol and carboxylic acid derivatives are accessible from a common intermediate. In this strategy, the bicyclic lactam system not only controls, but also facilitates the determination of the stereochemistry of the synthetic intermediates.

Piperidine Synthesis.

DTIC Science & Technology

1992-09-01

ORGANIZATION NAME(S) AND ADORESS(ES) B . PERFORMING ORGANIZATION CDR, CRDEC, ATTN: SMCCR-RSC-O, APG, MD REPORT NUMBER 21010-5423 CRDEC-TR-409 9. SPONSORING...hydroxypyridine with iodomethane or benzyl chloride followed by sodium borohydride reduction and HBr cleavage of the enol ether is yet another effective...Piperidine, Elsevier, New York, 1991. ( b ) Armardgo, W.L.F., "Stereochemistry of Heterocyclic Compounds, Part 1," John Wiley & Sons, New York, 1977. (c

Greening Wittig Reactions: Solvent-Free Synthesis of Ethyl Trans-Cinnamate and Trans-3-(9-Anthryl)-2-Propenoic Acid Ethyl Ester

ERIC Educational Resources Information Center

Nguyen, Kim Chi; Weizman, Haim

2007-01-01

Green procedure is used to create solvent-free alternatives for conventional Wittig reactions, which are widely used to install a double bond in a highly selective manner. Solvent-free reactions reduce health and environmental risks and provide a basis for an inquiry-based discussion of the stereochemistry of the Wittig reaction and the factors…

Stereospecific Ni-Catalyzed Cross-Coupling of Potassium Alkenyltrifluoroborates with Alkyl Halides

PubMed Central

2015-01-01

A general method for the alkenylation of alkyl electrophiles using nearly stoichiometric amounts of the air- and moisture-stable potassium organotrifluoroborates has been developed. Various functional groups were tolerated on both the nucleophilic and electrophilic partner. Reactions of highly substituted E- and Z-alkenyltrifluoroborates, as well as vinyl- and propenyltrifluoroborates, were successful, and no loss of stereochemistry or regiochemistry was observed. PMID:24666316

Dihydroberkleasmin A: a new eremophilane sesquiterpenoid from the fermentation broth of the plant endophytic fungus Pestalotiopsis photiniae.

PubMed

Yang, Xiao-Long; Zhang, Su; Zhu, Hua-Jie; Luo, Du-Qiang

2011-02-23

Dihydroberkleasmin A (1), a new ester-substituted sesquiterpenoid related to the eremophilane class, together with the known compound berkleasmin C (2), were isolated from the fermentation broth of the plant endophytic fungus Pestalotiopsis photiniae. The structure of dihydroberkleasmin A (1) was elucidated by extensive spectroscopic analysis. The stereochemistry was assigned by comparison of the NMR spectroscopic data with those of berkleasmin A.

Inducamides A–C, Chlorinated Alkaloids from an RNA Polymerase Mutant Strain of Streptomyces sp.

PubMed Central

2015-01-01

Inducamides A–C (1–3), three new chlorinated alkaloids featuring an amide skeleton generated by a tryptophan fragment and a 6-methylsalicylic acid unit, were isolated from a chemically induced mutant strain of Streptomyces sp. with the inducamides only being produced in the mutant strain. Their structures, including stereochemistry, were determined by spectroscopic analysis, Marfey’s method, and CD spectroscopy. PMID:25338006

Trap Type, Chirality of a-Pinene, and Geographic Region Affect Sampling Efficiency of Root and Lower Stem Insects in Pine

Treesearch

Nadir Erbilgin; Alex Szele; Kier Dean Klepzig; Kenneth Francis Raffa

2001-01-01

Root and lower stem insects cause significant damage to conifers, vector phytopathogenic fungi, and can predispose trees to bark beetle attacks. The development of effective sampling techniques is an important component in managing these cryptic insects. We tested the effects of trap type and stereochemistry of a-pinene, in combination with ethanol, on catches of the...

Stereochemistry of amino acids in surface samples of a marine sediment

NASA Technical Reports Server (NTRS)

Pollock, G. E.; Kvenvolden, K. A.

1978-01-01

In two surface samples of marine sediment, the percentages of D-alanine and D-aspartic acid are significantly higher than the other D-amino acids and are similar to the range found in soils. The percentage of D-glutamic acid is also higher than the other amino acids but less than D-alanine and D-aspartic acid. These D-amino acids may come mainly from bacteria.

Stereochemistry of amino acids in surface samples of a marine sediment

USGS Publications Warehouse

Pollock, G.E.; Kvenvolden, K.A.

1978-01-01

In two surface samples of marine sediment, the percentages of d-alanine and d-aspartic acid are significantly higher than the other d-amino acids and are similar to the range found in soils. The percentage of d-glutamic acid is also higher than the other amino acids but less than d-alanine and d-aspartic acid. These d-amino acids may come mainly from bacteria. ?? 1978.

Synthesis and characterization of heterobimetallic molybdenum and nickel complexes derived from polyfunctional disalicylaldehyde oxaloyldihydrazone

NASA Astrophysics Data System (ADS)

Kumar, Arvind; Borthakur, Rosmita; Koch, Angira; Chanu, Oinam B.; Choudhury, Sanjesh; Lemtur, Aka; Lal, Ram A.

2011-07-01

Heterobimetallic nickel and molybdenum complexes of the composition [Ni(L)MoO 2(A) 4]· nH 2O (A = H 2O (1), py (2), 2-pic (3), 3-pic (4), and 4-pic (5); n = 0, 2) and [Ni(L)(MoO 2)(BB) 2](BB = bpy (6) and (phen (7)) have been synthesized from the multidentate ligand disalicylaldehyde oxaloyldihydrazone (H 4L) in methanol. The composition of the complexes has been established based on data obtained from elemental analyses, thermoanalytical, mass spectral and molecular weight studies. The probable structures of the complexes have been discussed in the light of molar conductance, magnetic moment data and electronic, EPR and infrared spectral studies. In all of the complexes, the dihydrazone is present in enol form and coordinates to the metal centre as a tetrabasic hexadentate ligand. All of the complexes are normal paramagnetic to the extent of two unpaired electrons per nickel atom. The μeff values for the complexes lying in the region 2.87-3.07 B.M. are consistent with the octahedral stereochemistry of nickel(II) in the heterobimetallic complexes. The EPR and electronic spectral data also support the distorted octahedral stereochemistry of the nickel(II) centre. Both nickel and molybdenum have octahedral geometry in the complexes.

Sequence-Dependent Diastereospecific and Diastereodivergent Crosslinking of DNA by Decarbamoylmitomycin C.

PubMed

Aguilar, William; Paz, Manuel M; Vargas, Anayatzinc; Clement, Cristina C; Cheng, Shu-Yuan; Champeil, Elise

2018-04-20

Mitomycin C (MC), a potent antitumor drug, and decarbamoylmitomycin C (DMC), a derivative lacking the carbamoyl group, form highly cytotoxic DNA interstrand crosslinks. The major interstrand crosslink formed by DMC is the C1'' epimer of the major crosslink formed by MC. The molecular basis for the stereochemical configuration exhibited by DMC was investigated using biomimetic synthesis. The formation of DNA-DNA crosslinks by DMC is diastereospecific and diastereodivergent: Only the 1''S-diastereomer of the initially formed monoadduct can form crosslinks at GpC sequences, and only the 1''R-diastereomer of the monoadduct can form crosslinks at CpG sequences. We also show that CpG and GpC sequences react with divergent diastereoselectivity in the first alkylation step: 1"S stereochemistry is favored at GpC sequences and 1''R stereochemistry is favored at CpG sequences. Therefore, the first alkylation step results, at each sequence, in the selective formation of the diastereomer able to generate an interstrand DNA-DNA crosslink after the "second arm" alkylation. Examination of the known DNA adduct pattern obtained after treatment of cancer cell cultures with DMC indicates that the GpC sequence is the major target for the formation of DNA-DNA crosslinks in vivo by this drug. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure elucidation and absolute stereochemistry of isomeric monoterpene chromane esters.

PubMed

Batista, João M; Batista, Andrea N L; Mota, Jonas S; Cass, Quezia B; Kato, Massuo J; Bolzani, Vanderlan S; Freedman, Teresa B; López, Silvia N; Furlan, Maysa; Nafie, Laurence A

2011-04-15

Six novel monoterpene chromane esters were isolated from the aerial parts of Peperomia obtusifolia (Piperaceae) using chiral chromatography. This is the first time that chiral chromane esters of this kind, ones with a tethered chiral terpene, have been isolated in nature. Due to their structural features, it is not currently possible to assess directly their absolute stereochemistry using any of the standard classical approaches, such as X-ray crystallography, NMR, optical rotation, or electronic circular dichroism (ECD). Herein we report the absolute configuration of these molecules, involving four chiral centers, using vibrational circular dichroism (VCD) and density functional theory (DFT) (B3LYP/6-31G*) calculations. This work further reinforces the capability of VCD to determine unambiguously the absolute configuration of structurally complex molecules in solution, without crystallization or derivatization, and demonstrates the sensitivity of VCD to specify the absolute configuration for just one among a number of chiral centers. We also demonstrate the sufficiency of using the so-called inexpensive basis set 6-31G* compared to the triple-ζ basis set TZVP for absolute configuration analysis of larger molecules using VCD. Overall, this work extends our knowledge of secondary metabolites in plants and provides a straightforward way to determine the absolute configuration of complex natural products involving a chiral parent moiety combined with a chiral terpene adduct.

Investigation of the dynamic stereochemistry of dimesityl-2,4,6-trimethoxyphenylmethane by complete lineshape analysis and 2D EXSY NMR spectroscopy.

PubMed

Denkova, Pavletta; Vassilev, Nikolay; Van Lokeren, Luk; Willem, Rudolph

2008-04-01

The static and dynamic stereochemistry of dimesityl-2,4,6-trimethoxyphenylmethane in solution was investigated by lineshape analysis of 1D NMR spectra and cross-peak amplitude processing in 2D EXSY spectra, recorded at variable temperatures. Previous studies on this propeller-shaped chiral compound show that the stereomer threshold interconversion is associated with helicity reversal and occurs through [1,2]- and [1,3]-two ring flips of one mesityl and the 2,4,6-trimethoxyphenyl rings. In the present study, the experimental rate constants of the [1,2]- and [1,3]-two ring flips, which are identical, were determined at various temperatures by combining quantitative 2D EXSY spectra processing and complete lineshape analysis (CLSA) of 1D NMR spectra. The latter were subjected to reference deconvolution and linear prediction in order to eliminate the lineshape distortions due to magnetic field inhomogeneity. The activation parameters of these ring flips were determined by an Eyring equation analysis of the temperature dependence of the rate constant. The experimentally determined activation enthalpy and entropy for the two-ring flips, and those obtained from theoretical ab initio calculations at different levels of theory and basis sets, were found to be in good agreement. Copyright (c) 2008 John Wiley & Sons, Ltd.

Mechanistic Basis for High Stereoselectivity and Broad Substrate Scope in the (salen)Co(III)-Catalyzed Hydrolytic Kinetic Resolution

PubMed Central

Ford, David D.; Nielsen, Lars P. C.; Zuend, Stephan J.; Jacobsen, Eric N.

2013-01-01

In the (salen)Co(III)-catalyzed hydrolytic kinetic resolution (HKR) of terminal epoxides, the rate- and stereoselectivity-determining epoxide ring-opening step occurs by a cooperative bimetallic mechanism with one Co(III) complex acting as a Lewis acid and another serving to deliver the hydroxide nucleophile. In this paper, we analyze the basis for the extraordinarily high stereoselectivity and broad substrate scope observed in the HKR. We demonstrate that the stereochemistry of each of the two (salen)Co(III) complexes in the rate-determining transition structure is important for productive catalysis: a measurable rate of hydrolysis occurs only if the absolute stereochemistry of each of these (salen)Co(III) complexes is the same. Experimental and computational studies provide strong evidence that stereochemical communication in the HKR is mediated by the stepped conformation of the salen ligand, and not the shape of the chiral diamine backbone of the ligand. A detailed computational analysis reveals that the epoxide binds the Lewis acidic Co(III) complex in a well-defined geometry imposed by stereoelectronic, rather than steric effects. This insight serves as the basis of a complete stereochemical and transition structure model that sheds light on the reasons for the broad substrate generality of the HKR. PMID:24041239

Mechanistic basis for high stereoselectivity and broad substrate scope in the (salen)Co(III)-catalyzed hydrolytic kinetic resolution.

PubMed

Ford, David D; Nielsen, Lars P C; Zuend, Stephan J; Musgrave, Charles B; Jacobsen, Eric N

2013-10-16

In the (salen)Co(III)-catalyzed hydrolytic kinetic resolution (HKR) of terminal epoxides, the rate- and stereoselectivity-determining epoxide ring-opening step occurs by a cooperative bimetallic mechanism with one Co(III) complex acting as a Lewis acid and another serving to deliver the hydroxide nucleophile. In this paper, we analyze the basis for the extraordinarily high stereoselectivity and broad substrate scope observed in the HKR. We demonstrate that the stereochemistry of each of the two (salen)Co(III) complexes in the rate-determining transition structure is important for productive catalysis: a measurable rate of hydrolysis occurs only if the absolute stereochemistry of each of these (salen)Co(III) complexes is the same. Experimental and computational studies provide strong evidence that stereochemical communication in the HKR is mediated by the stepped conformation of the salen ligand, and not the shape of the chiral diamine backbone of the ligand. A detailed computational analysis reveals that the epoxide binds the Lewis acidic Co(III) complex in a well-defined geometry imposed by stereoelectronic rather than steric effects. This insight serves as the basis of a complete stereochemical and transition structure model that sheds light on the reasons for the broad substrate generality of the HKR.

Synthesis and anti-HBV activity of α-stereoisomer of aristeromycin based analogs.

PubMed

Kasula, Mohan; Toyama, Masaaki; Samunuri, Ramakrishnamraju; Rozy, Farhana; Yadav, Monika; Bal, Chandralata; Jha, Ashok Kumar; Baba, Masanori; Sharon, Ashoke

2016-08-15

The potential antiviral activity of aristeromycin type of derivatives (I) is limited by associated toxicity due to its possible 5'-O-phosphorylation and S-adenosyl-l-homocysteine hydrolase (SAHase) inhibitory activity. Aristeromycin structure has major pharmacophoric motif as 5'-OH and adenosine base, which may have significant role in enzyme binding followed by activity and or toxicity. Thus, the structural optimization to alter this major motif by replacing with its bioisostere and changing the 5'-O conformation through stereochemistry reversal was of interest. Thus, the inverted stereochemistry at 4'-position coupled with bioisostere of adenosine base in the target compounds (6-7) to access antiviral potential. The stereoselective formation of a key stereoisomer (2a) was achieved exclusively from neplanocin sugar (1a) by reduction in a single step. The novel target molecules (6-7) were synthesized in 4 steps with 55-62% yield. Compound 6 was analyzed by single crystal X-ray diffraction, which confirms the stereoselective formation of α-analogs with highly puckered cyclopentane ring and 2'-endo conformation. The compound 6 shown significant anti-hepatitis B virus activity of 6.5μM with CC50>100μM and yielded a promising lead with novel structural feature. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mechanisms for Breast Cancer Cell Resistance to Doxorubicin and Solutions to Resistance and Side Effects

DTIC Science & Technology

2001-10-01

doxorubicin and epidoxorubicin, doxoform and epidoxoform, respectively. The following results were obtained during the grant period: 1) The crystal structure ...diazadioxabicyclic structure . This structure contrasts with that of doxoform which is a dimeric conjugate with a bisoxazolidinylmethane structure . The... structural difference results from the stereochemistry at the 4’-position. Epidoxoform has a predicted half-life of more than 2 h in the vascular system

New isomalabaricane triterpenes from the marine sponge Stelletta globostellata that induce morphological changes in rat fibroblasts.

PubMed

Oku, N; Matsunaga, S; Wada, S i; Watabe, S; Fusetani, N

2000-02-01

Three new isomalabaricane triterpenes, 29-hydroxystelliferin D (2), 3-epi-29-hydroxystelliferin E (3), and 3-epi-29-hydroxystelliferin A (4), were isolated from the marine sponge Stelletta globostellata. Their structures, including absolute stereochemistry, were determined on the basis of spectral data and chemical methods. Rat fibroblasts treated with 0.2 microM of 2-4 exhibited unusual morphological characteristics, followed by death in 5 days.

Applications of ZVMo NMR spectroscopy. 17. ZVMo and UN relaxation time measurements confirming that (Mo(CN)8)U is dodecahedral in aqueous solution

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

Brownlee, R.T.; Shehan, B.P.; Wedd, A.G.

1987-07-01

Variable-temperature NMR line width measurements of ZVMo and UN in aqueous solutions of K4(Mo(CN)8) x 2H2O indicate that the stereochemistry of the (Mo(CN)8)U ion in solution is dodecahedral. A value for the ZVMo quadrupole coupling constant of 3.61 MHz is obtained. 27 references, 1 figure, 1 table.

Selective electrocatalytic oxidation of sorbitol to fructose and sorbose.

PubMed

Kwon, Youngkook; de Jong, Ed; van der Waal, Jan Kees; Koper, Marc T M

2015-03-01

A new electrocatalytic method for the selective electrochemical oxidation of sorbitol to fructose and sorbose is demonstrated by using a platinum electrode promoted by p-block metal atoms. By the studying a range of C4, C5 and C6 polyols, it is found that the promoter interferes with the stereochemistry of the polyol and thereby modifies its reactivity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Diastereoselective synthesis of enantiopure morpholines by electrophilic selenium-induced 6-exo cyclizations on chiral 3-allyl-2-hydroxymethylperhydro-1,3-benzoxazine derivatives.

PubMed

Pedrosa, Rafael; Andrés, Celia; Mendiguchía, Pilar; Nieto, Javier

2006-11-10

Enantiopure morpholine derivatives have been prepared by selenocyclofunctionalization of chiral 3-allyl-2-hydroxymethyl-substituted perhydro-1,3-benzoxazine derivatives. The cyclization occurs in high yields and diastereoselection, although the temperature of the reaction and the structure of the substituent at C-2 and the substitution pattern of the double bond can modify the regio- and stereochemistry of the final products.

Mo(CO)6-mediated intramolecular Pauson-Khand reaction of substituted diethyl 3-allyloxy-1-propynylphosphonates.

PubMed

Moradov, Dorit; Al Quntar, Abed Al Aziz; Youssef, Manar; Smoum, Reem; Rubinstein, Abraham; Srebnik, Morris

2009-02-06

Cyclisation of diethyl 3-allyloxy-1-propynylphosphonates with Mo(CO)(6) under PK conditions to give 3-substituted-5-oxo-3,5,6,6a-tetrahydro-1H-cyclopenta[c]furan-4-ylphosphonate, 2a-h, in 45-88% isolated yields was done. The R groups are always syn with H(b) (where applicable). The stereochemistry was determined via both NMR and crystal X-ray analysis.

1H and 13C NMR spectra of C-6 and C-9 substituted 3-azabicyclco[3.3.1]nonanes.

PubMed

Goodall, Kirsten; Brimble, Margaret; Barker, David

2008-01-01

The 1H and 13C NMR data for 3-azabicyclo[3.3.1]nonanes with OH and OMe substituents at C-6 and C-9 were measured using 1D (DEPT) and 2D (COSY, HSQC, HMBC, NOESY) experiments. Comparison of this NMR data illustrates the effects of stereochemistry and substitution at these positions. Copyright (c) 2007 John Wiley & Sons, Ltd.

The use of ene adducts to study and engineer enoyl-thioester reductases.

PubMed

Rosenthal, Raoul G; Vögeli, Bastian; Quade, Nick; Capitani, Guido; Kiefer, Patrick; Vorholt, Julia A; Ebert, Marc-Olivier; Erb, Tobias J

2015-06-01

An improved understanding of enzymes' catalytic proficiency and stereoselectivity would further enable applications in chemistry, biocatalysis and industrial biotechnology. We use a chemical probe to dissect individual catalytic steps of enoyl-thioester reductases (Etrs), validating an active site tyrosine as the cryptic proton donor and explaining how it had eluded definitive identification. This information enabled the rational redesign of Etr, yielding mutants that create products with inverted stereochemistry at wild type-like turnover frequency.

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

Nagaoka, Masataka; Core Research for Evolutional Science and Technology; ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520

A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

FeCl3-Catalyzed aminohalogenation of arylmethylenecyclopropanes and arylvinylidenecyclopropanes and corresponding mechanistic studies.

PubMed

Li, Qingjiang; Shi, Min; Timmons, Cody; Li, Guigen

2006-02-16

[reaction: see text] The aminochlorination of methylenecyclopropanes (MCPs) 1 and vinylidenecyclopropanes (VCPs) has been explored with use of FeCl(3) (20 mol %) as a Lewis acid catalyst in acetonitrile under convenient mild conditions. The stereochemistry has been unambiguously confirmed by X-ray structural analysis. The aziridinium-based mechanism, accounting for both regio- and stereoselectivity, has been carefully studied. A linear free-energy relationship study of this reaction confirms consistency with the Hammet equation.

7-endo selenocyclization reactions on chiral 3-prenyl and 3-cinnamyl-2-hydroxymethylperhydro-1,3-benzoxazine derivatives. A way to enantiopure 1,4-oxazepanes.

PubMed

Nieto, Javier; Andrés, Celia; Pérez-Encabo, Alfonso

2015-09-14

Enantiopure 1,4-oxazepane derivatives have been prepared by selenocyclofunctionalization of chiral 3-prenyl- and 3-cinnamyl-2-hydroxymethyl-substituted perhydro-1,3-benzoxazine derivatives. The 7-endo-cyclization occurs in high yields and diastereoselection. The regio- and stereochemistry of the cyclization products was dependent on the substitution pattern of the double bond, the nature of the hydroxyl group and the experimental conditions.

Diastereo- and regioselective addition of thioamide dianions to imines and aziridines: synthesis of N-thioacyl-1,2-diamines and N-thioacyl-1,3-diamines.

PubMed

Shibahara, Fumitoshi; Kobayashi, Shun-ichiro; Maruyama, Toshifumi; Murai, Toshiaki

2013-01-02

Addition reactions of thioamide dianions that were derived from N-arylmethyl thioamides to imines and aziridines were carried out. The reactions of imines gave the addition products of N-thioacyl-1,2-diamines in a highly diastereoselective manner in good-to-excellent yields. The diastereomeric purity of these N-thioacyl-1,2-diamines could be enriched by simple recrystallization. The reduction of N-thioacyl-1,2-diamines with LiAlH(4) gave their corresponding 1,2-diamines in moderate-to-good yields with retention of their stereochemistry. The oxidative-desulfurization/cyclization of an N-thioacyl-1,2-diamine in CuCl(2)/O(2) and I(2)/pyridine systems gave the cyclized product in moderate yield and the trans isomer was obtained as the sole product. On the other hand, a similar cyclization reaction with antiformin (aq. NaClO) as an oxidant gave the cis isomer as the major product. The reactions of N-tosylaziridines gave the addition products of N-thioacyl-1,3-diamines with low diastereoselectivity but high regioselectivity and in good-to-excellent yields. The use of AlMe(3) as an additive improved the efficiency and regioselectivity of the reaction. The stereochemistry of the obtained products was determined by X-ray diffraction. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stereochemistry of Furfural Reduction by a Saccharomyces cerevisiae Aldehyde Reductase That Contributes to In Situ Furfural Detoxification▿

PubMed Central

Bowman, Michael J.; Jordan, Douglas B.; Vermillion, Karl E.; Braker, Jay D.; Moon, Jaewoong; Liu, Z. Lewis

2010-01-01

Ari1p from Saccharomyces cerevisiae, recently identified as an intermediate-subclass short-chain dehydrogenase/reductase, contributes in situ to the detoxification of furfural. Furfural inhibits efficient ethanol production by yeast, particularly when the carbon source is acid-treated lignocellulose, which contains furfural at a relatively high concentration. NADPH is Ari1p's best known hydride donor. Here we report the stereochemistry of the hydride transfer step, determined by using (4R)-[4-2H]NADPD and (4S)-[4-2H]NADPD and unlabeled furfural in Ari1p-catalyzed reactions and following the deuterium atom into products 2-furanmethanol or NADP+. Analysis of the products demonstrates unambiguously that Ari1p directs hydride transfer from the si face of NADPH to the re face of furfural. The singular orientation of substrates enables construction of a model of the Michaelis complex in the Ari1p active site. The model reveals hydrophobic residues near the furfural binding site that, upon mutation, may increase specificity for furfural and enhance enzyme performance. Using (4S)-[4-2H]NADPD and NADPH as substrates, primary deuterium kinetic isotope effects of 2.2 and 2.5 were determined for the steady-state parameters kcatNADPH and kcat/KmNADPH, respectively, indicating that hydride transfer is partially rate limiting to catalysis. PMID:20525870

DNA-fiber EPR investigation of the influence of amino-terminal residue stereochemistry on the DNA binding orientation of Cu(II)•Gly-Gly-His-derived metallopeptides

PubMed Central

Hamada, Hirokazu; Abe, Yuko; Nagane, Ryoichi; Fang, Ya-Yin; Lewis, Mark A.; Long, Eric C.; Chikira, Makoto

2007-01-01

DNA fiber EPR was used to investigate the DNA binding stabilities and orientations of Cu(II)•Gly-Gly-His-derived metallopeptides containing d- vs. l-amino acid substitutions in the first peptide position. This examination included studies of Cu(II)•d-Arg-Gly-His and Cu(II)•d-Lys-Gly-His for comparison to metallopeptides containing l-Arg/Lys substitutions, and also the diastereoisomeric pairs Cu(II)•d/l-Pro-Gly-His and Cu(II)•d/l-Pro-Lys-His. Results indicated that l-Arg/Lys to d-Arg/Lys substitutions considerably randomized the orientation of the metallopeptides on DNA whereas the replacement of l-Pro by d-Pro in Cu(II)•l-Pro-Gly-His caused a decrease in randomness. The difference in the extent of randomness of d- vs. l-Pro-Gly-His complexes was diminished through the substitution of Gly for Lys in the middle peptide position, supporting the notion that the ε-amino group of Lys triggered further randomization, likely through hydrogen bonding or electrostatic interactions that disrupt binding of the metallopeptide equatorial plane and the DNA. The relationship between the stereochemistry of amino acid residues and the binding and reaction of M(II)•Xaa-Xaa’-His metallopeptides with DNA are also discussed. PMID:17706784

Trans -cyclopropanation of mycolic acids on trehalose dimycolate suppresses Mycobacterium tuberculosis –induced inflammation and virulence

PubMed Central

Rao, Vivek; Gao, Feng; Chen, Bing; Jacobs, William R.; Glickman, Michael S.

2006-01-01

Recent studies have shown that fine structural modifications of Mycobacterium tuberculosis cell envelope lipids mediate host cell immune activation during infection. One such alteration in lipid structure is cis-cyclopropane modification of the mycolic acids on trehalose dimycolate (TDM) mediated by proximal cyclopropane synthase of α mycolates (pcaA), a proinflammatory lipid modification during early infection. Here we examine the pathogenetic role and immunomodulatory function of mycolic acid cyclopropane stereochemistry by characterizing an M. tuberculosis cyclopropane–mycolic acid synthase 2 (cmaA2) null mutant (ΔcmaA2) that lacks trans-cyclopropanation of mycolic acids. Although titers of WT and ΔcmaA2 organisms were identical during mouse infection, ΔcmaA2 bacteria were hypervirulent while inducing larger granulomas than WT M. tuberculosis. The hypervirulence of the ΔcmaA2 strain depended on host TNF-α and IFN-γ. Loss of trans-cyclopropanation enhanced M. tuberculosis–induced macrophage inflammatory responses, a phenotype that was transferable with petroleum ether extractable lipids. Finally, purified TDM lacking trans-cyclopropane rings was 5-fold more potent in stimulating macrophages. These results establish cmaA2-dependent trans-cyclopropanation of TDM as a suppressor of M. tuberculosis–induced inflammation and virulence. In addition, cyclopropane stereochemistries on mycolic acids interact directly with host cells to both positively and negatively influence host innate immune activation. PMID:16741578

Cytotoxic steroids from Monascus purpureus-fermented rice.

PubMed

Shang, Xiao-Ya; Li, Jin-Jie; Liu, Ming-Tao; Li, Shuai; Liu, Ying; Wang, Ye-Feng; Huang, Xiao; Jin, Zong-Lian

2011-01-01

Bioassay-guided fractionation of an EtOH extract of Monascus purpureus-fermented rice led to the isolation of two new steroids (22S, 23R, 24S)-20β,23α,25α-trihydroxy-16,22-epoxy-4,6,8(14)-trienergosta-3-one (1), the first example of a steroid possessing both a conjugated triene ketone system and a fused 4H-furan ring side chain within one molecule, and (22E, 24R)-3β,5α-dihydroxyergosta-23-methyl-7,22-dien-6-one (2), as well as two known compounds (22E, 24R)-3β,5α-dihydroxyergosta-7,22-dien-6-one (3) and (22E, 24R)-6β-methoxy-ergosta-7,22-diene-3β,5α-diol (4). Their structures were assigned by detailed interpretation of HRESIMS, 1D and 2D NMR spectroscopic data. The absolute stereochemistry of 1 was determined by single-crystal X-ray crystallography while the absolute stereochemistry of 2 was established by CD. Compounds 1-4 showed cytotoxic activity against the lung adenocarcinoma (A549) with IC(50) values of 0.08, 0.94, 12.6 and 13.5 μM, respectively. In addition, compounds 1 and 2 exhibited moderate activities against human ovarian cancer (A2780), with IC(50) values of 2.8 and 5.1 μM. Copyright © 2011 Elsevier Inc. All rights reserved.

Structural basis for the D-stereoselectivity of human DNA polymerase β

PubMed Central

Vyas, Rajan; Reed, Andrew J.; Raper, Austin T.; Zahurancik, Walter J.; Wallenmeyer, Petra C.

2017-01-01

Abstract Nucleoside reverse transcriptase inhibitors (NRTIs) with L-stereochemistry have long been an effective treatment for viral infections because of the strong D-stereoselectivity exhibited by human DNA polymerases relative to viral reverse transcriptases. The D-stereoselectivity of DNA polymerases has only recently been explored structurally and all three DNA polymerases studied to date have demonstrated unique stereochemical selection mechanisms. Here, we have solved structures of human DNA polymerase β (hPolβ), in complex with single-nucleotide gapped DNA and L-nucleotides and performed pre-steady-state kinetic analysis to determine the D-stereoselectivity mechanism of hPolβ. Beyond a similar 180° rotation of the L-nucleotide ribose ring seen in other studies, the pre-catalytic ternary crystal structures of hPolβ, DNA and L-dCTP or the triphosphate forms of antiviral drugs lamivudine ((-)3TC-TP) and emtricitabine ((-)FTC-TP) provide little structural evidence to suggest that hPolβ follows the previously characterized mechanisms of D-stereoselectivity. Instead, hPolβ discriminates against L-stereochemistry through accumulation of several active site rearrangements that lead to a decreased nucleotide binding affinity and incorporation rate. The two NRTIs escape some of the active site selection through the base and sugar modifications but are selected against through the inability of hPolβ to complete thumb domain closure. PMID:28402499

Structure-delivery relationships of lysine-based gemini surfactants and their lipoplexes.

PubMed

Damen, Mark; Cristóbal-Lecina, Edgar; Sanmartí, Glòria Colom; van Dongen, Stijn F M; García Rodríguez, Cristina L; Dolbnya, Igor P; Nolte, Roeland J M; Feiters, Martin C

2014-08-21

The synthesis and properties of gemini surfactants of the type (R(1)(CO)-Lys(H)-NH)2(CH2)n are reported. For a spacer length of n = 6, the hydrophobic acyl tail was varied in length (R(1) = C8, C10, C12, C14, C16, and C18) and, for R(1) = C18, the degree of unsaturation. For R(1)(CO) = oleoyl (C18:1 Z) the spacer length (n = 2-8) and the stereochemistry of the lysine building block were varied; a 'half-gemini' derivative with a single oleoyl tail and head group was also prepared. The potential of the gemini surfactants to transfer polynucleotides across a cell membrane was investigated by transfection of HeLa cells with beta-galactosidase, both in the presence and absence of the helper lipid DOPE. Oleoyl was found to be by far the best hydrophobic tail for this biological activity, whereas the effect of the lysine stereochemistry was less pronounced. The effect of an optimum spacer length (n = 6) was observed only in the absence of helper lipid. The most active surfactant, i.e. the one with oleoyl chains and n = 6, formed liposomes with sizes in the range of 60-350 nm, and its lipoplex underwent a transition from a lamellar to a hexagonal morphology upon lowering the pH from 7 to 3.

Lignans from Arnica species.

PubMed

Schmidt, Thomas J; Stausberg, Sabine; Raison, Jeanette Von; Berner, Matthias; Willuhn, Günter

2006-05-10

From four Arnica species (A. angustifolia Vahl ssp. attenuata (Greene) Maguire, A. lonchophylla Greene ssp. lonchophylla Maguire (flowerheads), A. chamissonis Less. ssp. foliosa (Nutt.) Maguire, A. montana L. (roots and rhizomes)) a total of twelve lignans of the furofuran-, dibenzylbutyrolactone- and dibenzylbutyrolactol-type were isolated. No report on lignans as constituents of Arnica species exists so far. Besides the known pinoresinol, epipinoresinol, phillygenin, matairesinol, nortrachelogenin and nortracheloside, six dibenzylbutyrolactol derivatives with different stereochemistry and substitution at C-9 were isolated and their structures elucidated by NMR spectroscopic and mass spectral analysis.

tert-Butyl N-hydr­oxy-N-[(1S*,2R*)-2-(1-naphth­yl)cyclo­pent-3-en-1-yl]carbamate

PubMed Central

Lough, Alan J.; Machin, Ben P.; Tam, William

2009-01-01

The relative stereochemistry of the title compound, C20H23NO3, was established by X-ray analysis. The asymmetric unit contains two independent mol­ecules. In the crystal structure, each type of mol­ecule forms a centrosymmetric dimer via pairs of inter­molecular O—H⋯O hydrogen bonds, resulting in an R 2 2(10) loop in each case. PMID:21582783

Actinoranone, A Cytotoxic Meroterpenoid of Unprecedented Structure from a Marine Adapted Streptomyces sp

PubMed Central

Nam, Sang-Jip; Kauffman, Christopher A.; Paul, Lauren A.; Jensen, Paul R.

2014-01-01

The isolation and structure elucidation of a new meroterpenoid, actinoranone (1), produced by a marine bacterium closely related to the genus Streptomyces is reported. Actinoranone is composed of an unprecedented dihydronaphthalenone polyketide linked to a bicyclic diterpenoid. The stereochemistry of 1 was defined by application of the advanced Mosher's method and by interpretation of spectroscopic data. Actinoranone (1) is significantly cytotoxic to HCT-116 human colon cancer cells with an LD50 = 2.0 μg/mL. PMID:24152065

Haenamindole, an unusual diketopiperazine derivative from a marine-derived Penicillium sp. KCB12F005.

PubMed

Kim, Jong Won; Ko, Sung-Kyun; Son, Sangkeun; Shin, Kee-Sun; Ryoo, In-Ja; Hong, Young-Soo; Oh, Hyuncheol; Hwang, Bang Yeon; Hirota, Hiroshi; Takahashi, Shunji; Kim, Bo Yeon; Osada, Hiroyuki; Jang, Jae-Hyuk; Ahn, Jong Seog

2015-11-15

During the chemical investigation of marine-derived fungus, an unusual diketopiperazine (DKP) alkaloid, haenamindole (1), was isolated from a culture of the marine-derived fungus Penicillium sp. KCB12F005. The structure of 1, which possesses benzyl-hydroxypiperazindione and phenyl-pyrimidoindole rings system in the molecule, was elucidated by analysis of NMR and MS data. The stereochemistry of 1 was determined by ROESY and advanced Marfey's method. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dictyosphaeric acids A and B: new decalactones from an undescribed Penicillium sp. obtained from the alga Dictyosphaeria versluyii.

PubMed

Bugni, Tim S; Janso, Jeffrey E; Williamson, R Thomas; Feng, Xidong; Bernan, Valerie S; Greenstein, Michael; Carter, Guy T; Maiese, William M; Ireland, Chris M

2004-08-01

Fungal isolate F01V25 was obtained from the alga Dictyosphaeria versluyii collected near Dravuni, Fiji, in 2001 and represented a previously undescribed Penicillium sp. Fermentation of isolate F01V25 resulted in the production of two new polyketides, dictyosphaeric acids A and B, along with the known anthraquinone carviolin. The relative stereochemistry of dictyosphaeric acids A and B was determined using the J-based configuration analysis method in conjunction with ROE and NOE correlations.

New alkaloids of the sarpagine group from Rauvolfia serpentina hairy root culture.

PubMed

Sheludko, Yuri; Gerasimenko, Irina; Kolshorn, Heinz; Stöckigt, Joachim

2002-07-01

Three new monoterpenoid indole alkaloids, 19(S),20(R)-dihydroperaksine (1), 19(S),20(R)-dihydroperaksine-17-al (2), and 10-hydroxy-19(S),20(R)-dihydroperaksine (3), along with 16 known alkaloids 4-19 were isolated from hairy root culture of Rauvolfia serpentina, and their structures were elucidated by 1D and 2D NMR analyses. Taking into account the stereochemistry of the new alkaloids and results of preliminary enzymatical studies, the putative biosynthetical relationships between the novel alkaloids are discussed.

Enantioselective syntheses of cryptocarya triacetate, cryptocaryolone, and cryptocaryolone diacetate.

PubMed

Smith, Catherine M; O'Doherty, George A

2003-05-29

[reaction: see text] The enantioselective syntheses of three natural products from Cryptocarya latifolia have been achieved in 13-15 steps from ethyl sorbate. The route relies upon an enantio- and regioselective Sharpless dihydroxylation and a palladium-catalyzed reduction to establish the absolute stereochemistry. The route also relies upon a highly (E)-selective olefin cross-metathesis reaction to form trans-delta-hydroxy-1-enoates. The resulting delta-hydroxy-1-enoates were subsequently converted into cryptocarya triacetate, cryptocaryolone, and cryptocaryolone diacetate.

Total synthesis and structure-activity investigation of the marine natural product neopeltolide.

PubMed

Custar, Daniel W; Zabawa, Thomas P; Hines, John; Crews, Craig M; Scheidt, Karl A

2009-09-02

The total synthesis and biological evaluation of neopeltolide and analogs are reported. The key bond-forming step utilizes a Lewis acid-catalyzed intramolecular macrocyclization that installs the tetrahydropyran ring and macrocycle simultaneously. Independent of each other, neither the macrolide nor the oxazole side chain substituents of neopeltolide can inhibit the growth of cancer cell lines. The biological data of the analogs indicate that alterations to either the ester side chain or the stereochemistry of the macrolide result in a loss of biological activity.

Synthesis of Enantiomerically Pure 6-Substituted-Piperazine-2-Acetic Acid Esters as Intermediates for Library Production.

PubMed

Chamakuri, Srinivas; Jain, Prashi; Guduru, Shiva Krishna Reddy; Arney, Joseph Winston; MacKenzie, Kevin; Santini, Conrad; Young, Damian W

2018-05-11

Amino acids from the chiral pool have been used to produce a 24-member branch of 2,6-disubstituted piperazine scaffolds suitable for use in compound library production. Each scaffold was obtained as a single absolute stereoisomer in multi-gram quantities. Stereochemistry was confirmed by 2D NMR protocols and enantiomeric purity was determined by chiral HPLC. The scaffolds are intended for use as intermediates in parallel synthesis of small-molecule libraries.

Isotope chirality in long-armed multifunctional organosilicon ("Cephalopod") molecules.

PubMed

Barabás, Béla; Kurdi, Róbert; Zucchi, Claudia; Pályi, Gyula

2018-07-01

Long-armed multifunctional organosilicon molecules display self-replicating and self-perfecting behavior in asymmetric autocatalysis (Soai reaction). Two representatives of this class were studied by statistical methods aiming at determination of probabilities of natural abundance chiral isotopomers. The results, reported here, show an astonishing richness of possibilities of the formation of chiral isotopically substituted derivatives. This feature could serve as a model for the evolution of biological chirality in prebiotic and early biotic stereochemistry. © 2018 Wiley Periodicals, Inc.

NMR spectra of androstane analogs of brassinosteroids

NASA Astrophysics Data System (ADS)

Baranovskii, A. V.; Litvinovskaya, R. P.; Aver'kova, M. A.; Khripach, N. B.; Khripach, V. A.

2007-09-01

We have used two-dimensional NMR spectroscopy to make a complete assignment of signals from the nuclei of hydrogen and carbon atoms in the spectra of brassinosteroids in the androstane series. We have confirmed the stereochemistry of the chiral centers and the structure of the molecules. We have studied the effect of the configuration of the 2,3-diol groups in the A ring of the steroids on the chemical shift of adjacent atoms in the 13C and 1H NMR spectra.

α-Ketophosphonic Acid Esters — Synthesis, Structure, and Reactions

NASA Astrophysics Data System (ADS)

Zhdanov, Yu A.; Uzlova, L. A.; Glebova, Z. I.

1980-09-01

Studies on the synthesis and properties of α-ketophosphonic acid esters (KPE) — a class of highly reactive organophosphorus compounds — are surveyed. Data are presented concerning instances of the anomalous course of the process in the synthesis of KPE by the Arbuzov reaction. The reactions of KPE with nucleophiles, including those which lead to the rupture of the phosphorus-carbon bond, are examined in detail. The problems of the stereochemistry of KPE are dealt with briefly. The bibliography includes 162 references.

Isolation and structure determination of obyanamide, a novel cytotoxic cyclic depsipeptide from the marine cyanobacterium Lyngbya confervoides.

PubMed

Williams, Philip G; Yoshida, Wesley Y; Moore, Richard E; Paul, Valerie J

2002-01-01

Obyanamide (1) was isolated from a variety of the marine cyanobacterium Lyngbya confervoides collected in Saipan, Commonwealth of the Northern Mariana Islands. Gross structure elucidation of this novel cyclic depsipeptide relied on extensive application of 2D NMR techniques. The absolute stereochemistry was deduced by chiral chromatography of the hydrolysis products and comparison with authentic and synthetic standards. Obyanamide (1) was cytotoxic against KB cells with an IC(50) of 0.58 microg/mL.

Synthesis of Tricyclo[4,3,1,0(1,5)]decane Core of Plumisclerin A Using Pauson-Khand Annulation and SmI2-Mediated Radical Cyclization.

PubMed

Chen, Ji-Peng; He, Wei; Yang, Zhen-Yu; Yao, Zhu-Jun

2015-07-17

An efficient synthesis of the tricyclo[4,3,1,0(1, 5)]decane core (B/C/D rings) of plumisclerin A, a unique cytotoxic marine diterpenoid, is described. A Pauson-Khand reaction and a SmI2-mediated radical 1,4-conjugate addition successfully served as key reactions for construction of the fully functionalized 5,6-fused rings and the highly strained cyclobutanol moiety with correct relative stereochemistries, respectively.

Diastereoselective intermolecular Pauson-Khand reactions of chiral cyclopropenes.

PubMed

Pallerla, Mahesh K; Fox, Joseph M

2005-08-04

In this Letter, it is demonstrated that the unusual reactivity of cyclopropenes can increase the scope and utility of intermolecular Pauson-Khand reactions. The well-defined chiral environment of cyclopropenes has a powerful influence on the diastereoselectivity of the reactions and leads to the production of a single cyclopentenone in each of the described cases. The cyclopropane ring strongly influences the stereochemistry of reactions at the enone, and the three-membered ring can subsequently be cleaved under mild conditions. [reaction: see text

Static and dynamic stereochemistry of the conformational atropisomers of tetra(o-tolyl)benzene.

PubMed

Lunazzi, Lodovico; Mazzanti, Andrea; Minzoni, Mirko

2005-11-25

[graph: see text] Whereas only one atropisomer of 1,2,4,5-tetra(o-tolyl)benzene was observed by X-ray diffraction in the solid, five conformational atropisomers were detected by low-temperature NMR in solution. Their structures were assigned by a combination of NOE experiments, solvent effect, and ab initio calculations. Variable temperature dynamic NMR and bidimensional EXSY experiments allowed the barrier for the interconversion of these atropisomers to be determined (deltaG(double dagger) = 15.3 kcal mol(-1)).

Application of positive mode atmospheric chemical ionisation to distinguish epimeric oleanolic and ursolic acids.

PubMed

Townley, Chloe; Brettell, Rhea C; Bowen, Richard D; Gallagher, Richard T; Martin, William H C

2015-01-01

A new and more reliable method is reported for distinguishing the equatorial and axial epimers of oleanolic and ursolic acids and related triterpenoids based primarily on the relative abundance of the [M+H](+) and [M+-H(2)O](+) signals in their positive mode atmospheric pressure chemical ionisation mass spectra. The rate of elimination of water, which is the principal primary fragmentation of protonated oleanolic and ursolic acids, depends systematically on the stereochemistry of the hydroxyl group in the 3 position. For the b-epimer, in which the 3-hydroxyl substituent is in an equatorial position,[M+-H(2)O](+) is the base peak. In contrast, for the α-epimer, where the 3-hydroxyl group is axial, [M + H](+) is the base peak. This trend, which is general for a range of derivatives of oleanolic and ursolic acids, including the corresponding methyl esters, allows epimeric triterpenoids in these series to be securely differentiated. Confirmatory information is available from the collision-induced dissociation of the [M+-H(2)O](+) primary fragment ions, which follow different pathways for the species derived from axial and equatorial epimers of oleanolic and ursolic acids. These two pieces of independent spectral information permit the stereochemistry of epimeric oleanolic and ursolic acids (and selected derivatives) to be assigned with confidence without relying either on chromatographic retention times or referring to the spectra or other properties of authentic samples of these triterpenoids.

Interaction of model aryl- and alkyl-boronic acids and 1,2-diols in aqueous solution.

PubMed

Marinaro, William A; Prankerd, Richard; Kinnari, Kaisa; Stella, Valentino J

2015-04-01

The goal of this work was to quantitate ester formation between alkyl and aryl boronic acids and vicinal-diols or 1,2-diols in aqueous solution. As used here, 1,2-diols includes polyols with one or more 1,2-diol pairs. Multiple techniques were used including apparent pKa shifts of the boronic acids using UV spectrophotometry (for aryl acids) and titration (for aryl and alkyl acids). Isothermal microcalorimetry was also used, with all reactions being enthalpically favored. For all the acids and 1,2-diols and the conditions studied, evidence only supported 1:1 ester formation. All the esters formed were found to be significantly more acidic, as Lewis acids, by 3-3.5 pKa units than the corresponding nonesterified boronic acid. The equilibrium constants for ester formation increased with increasing number of 1,2-diol pairs but stereochemistry may also play a role as sorbitol with five possible 1,2-diol pairs and five isomers (taking into account the stereochemistry of the alcohol groups) was twice as efficient at ester formation compared with mannitol, also with five possible 1,2-diol pairs but only three isomers. Alkyl boronic acids formed esters to a greater extent than aryl acids. Although some quantitative differences were seen between the various techniques used, rank ordering of the structure/reactivity was consistent. Formulation implications of ester formation between boronic acids and 1,2-diols are discussed. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Stereochemical and conformational study on fenoterol by ECD spectroscopy and TD-DFT calculations.

PubMed

Tedesco, Daniele; Zanasi, Riccardo; Wainer, Irving W; Bertucci, Carlo

2014-03-01

Fenoterol and its derivatives are selective β2-adrenergic receptor (β2-AR) agonists whose stereoselective biological activities have been extensively investigated in the past decade; a complete stereochemical characterization of fenoterol derivatives is therefore crucial for a better understanding of the effects of stereochemistry on β2-AR binding. In the present project, the relationship between chiroptical properties and absolute stereochemistry of the stereoisomers of fenoterol (1) was investigated by experimental ECD spectroscopy and time-dependent density functional theory (TD-DFT). DFT geometry optimizations were carried out at the RI-B97D/TZVP/IEFPCM(MeOH) level and subsequent TD-DFT calculations were performed using the PBE0 hybrid functional. Despite the large pool of equilibrium conformers found for the investigated compounds and the known limitations of the level of theory employed, the computational protocol was able to reproduce the experimental ECD spectra of the stereoisomers of 1. The main contribution to the overall chiroptical properties was found to arise from the absolute configuration of the chiral center in α-position to the resorcinol moiety. Based on this evidence, a thorough conformational analysis was performed on the optimized DFT conformers, which revealed the occurrence of a different equilibrium between conformational patterns for the diastereomers of fenoterol: the (R,R')/(S,S') enantiomeric pair showed a higher population of folded conformations than the (R,S')/(S,R') pair. Copyright © 2013 Elsevier B.V. All rights reserved.

Isolation and determination of absolute configurations of insect-produced methyl-branched hydrocarbons

PubMed Central

Bello, Jan E.; McElfresh, J. Steven; Millar, Jocelyn G.

2015-01-01

Although the effects of stereochemistry have been studied extensively for volatile insect pheromones, little is known about the effects of chirality in the nonvolatile methyl-branched hydrocarbons (MBCHs) used by many insects as contact pheromones. MBCHs generally contain one or more chiral centers and so two or more stereoisomeric forms are possible for each structure. However, it is not known whether insects biosynthesize these molecules in high stereoisomeric purity, nor is it known whether insects can distinguish the different stereoisomeric forms of MBCHs. This knowledge gap is due in part to the lack of methods for isolating individual MBCHs from the complex cuticular hydrocarbon (CHC) blends of insects, as well as the difficulty in determining the absolute configurations of the isolated MBCHs. To address these deficiencies, we report a straightforward method for the isolation of individual cuticular hydrocarbons from the complex CHC blend. The method was used to isolate 36 pure MBCHs from 20 species in nine insect orders. The absolute stereochemistries of the purified MBCHs then were determined by digital polarimetry. The absolute configurations of all of the isolated MBCHs were determined to be (R) by comparison with a library of synthesized, enantiomerically pure standards, suggesting that the biosynthetic pathways used to construct MBCHs are highly conserved within the Insecta. The development of a straightforward method for isolation of specific CHCs will enable determination of their functional roles by providing pure compounds for bioassays. PMID:25583471

Versatile transformations of hydrocarbons in anaerobic bacteria: substrate ranges and regio- and stereo-chemistry of activation reactions†

PubMed Central

Jarling, René; Kühner, Simon; Basílio Janke, Eline; Gruner, Andrea; Drozdowska, Marta; Golding, Bernard T.; Rabus, Ralf; Wilkes, Heinz

2015-01-01

Anaerobic metabolism of hydrocarbons proceeds either via addition to fumarate or by hydroxylation in various microorganisms, e.g., sulfate-reducing or denitrifying bacteria, which are specialized in utilizing n-alkanes or alkylbenzenes as growth substrates. General pathways for carbon assimilation and energy gain have been elucidated for a limited number of possible substrates. In this work the metabolic activity of 11 bacterial strains during anaerobic growth with crude oil was investigated and compared with the metabolite patterns appearing during anaerobic growth with more than 40 different hydrocarbons supplied as binary mixtures. We show that the range of co-metabolically formed alkyl- and arylalkyl-succinates is much broader in n-alkane than in alkylbenzene utilizers. The structures and stereochemistry of these products are resolved. Furthermore, we demonstrate that anaerobic hydroxylation of alkylbenzenes does not only occur in denitrifiers but also in sulfate reducers. We propose that these processes play a role in detoxification under conditions of solvent stress. The thermophilic sulfate-reducing strain TD3 is shown to produce n-alkylsuccinates, which are suggested not to derive from terminal activation of n-alkanes, but rather to represent intermediates of a metabolic pathway short-cutting fumarate regeneration by reverse action of succinate synthase. The outcomes of this study provide a basis for geochemically tracing such processes in natural habitats and contribute to an improved understanding of microbial activity in hydrocarbon-rich anoxic environments. PMID:26441848

ns2np4 (n = 4, 5) lone pair triplets whirling in M*F2E3 (M* = Kr, Xe): Stereochemistry and ab initio analyses

NASA Astrophysics Data System (ADS)

Galy, Jean; Matar, Samir F.

2017-02-01

The stereochemistry of ns2np4 (n = 4, 5) lone pair LP characterizing noble gas Kr and Xe (labeled M*) in M*F2 difluorides is examined within coherent crystal chemistry and ab initio visualizations. M*2+ in such oxidation state brings three lone pairs (E) and difluorides are formulated M*F2E3. The analyses use electron localization function (ELF) obtained within density functional theory calculations showing the development of the LP triplets whirling {E3} quantified in the relevant chemical systems. Detailed ELF data analyses allowed showing that in α KrF2E3 and isostructural XeF2E3 difluorides the three E electronic clouds merge or hybridize into a torus and adopt a perfect gyration circle with an elliptical section, while in β KrF2 the network architecture deforms the whole torus into an ellipsoid shape. Original precise metrics are provided for the torus in the different compounds under study. In KrF2 the geometric changes upon β → α phase transition is schematized and mechanisms for the transformation with temperature or pressure are proposed. The results are further highlighted by electronic band structure calculations which show similar features of equal band gaps of 3 eV in both α and β KrF2 and a reorganization of frontier orbitals due to the different orientations of the F-Kr-F linear molecule in the two tetragonal structures.

The novel 13S,14S-epoxy-maresin is converted by human macrophages to maresin 1 (MaR1), inhibits leukotriene A4 hydrolase (LTA4H), and shifts macrophage phenotype

PubMed Central

Dalli, Jesmond; Zhu, Min; Vlasenko, Nikita A.; Deng, Bin; Haeggström, Jesper Z.; Petasis, Nicos A.; Serhan, Charles N.

2013-01-01

Maresins are produced by macrophages from docosahexaenoic acid (DHA) and exert potent proresolving and tissue homeostatic actions. Maresin 1 (MaR1; 7R,14S-dihydroxy-docosa-4Z,8E,10E,12Z,16Z,19Z-hexaenoic acid) is the first identified maresin. Here, we investigate formation, stereochemistry, and precursor role of 13,14-epoxy-docosahexaenoic acid, an intermediate in MaR1 biosynthesis. The 14-lipoxygenation of DHA by human macrophage 12-lipoxygenase (hm12-LOX) gave 14-hydro(peroxy)-docosahexaenoic acid (14-HpDHA), as well as several dihydroxy-docosahexaenoic acids, implicating an epoxide intermediate formation by this enzyme. Using a stereo-controlled synthesis, enantiomerically pure 13S,14S-epoxy-docosa-4Z,7Z,9E,11E,16Z,19Z-hexaenoic acid (13S,14S-epoxy-DHA) was prepared, and its stereochemistry was confirmed by NMR spectroscopy. When this 13S,14S-epoxide was incubated with human macrophages, it was converted to MaR1. The synthetic 13S,14S-epoxide inhibited leukotriene B4 (LTB4) formation by human leukotriene A4 hydrolase (LTA4H) ∼40% (P<0.05) to a similar extent as LTA4 (∼50%, P<0.05) but was not converted to MaR1 by this enzyme. 13S,14S-epoxy-DHA also reduced (∼60%; P<0.05) arachidonic acid conversion by hm12-LOX and promoted conversion of M1 macrophages to M2 phenotype, which produced more MaR1 from the epoxide than M1. Together, these findings establish the biosynthesis of the 13S,14S-epoxide, its absolute stereochemistry, its precursor role in MaR1 biosynthesis, and its own intrinsic bioactivity. Given its actions and role in MaR1 biosynthesis, this epoxide is now termed 13,14-epoxy-maresin (13,14-eMaR) and exhibits new mechanisms in resolution of inflammation in its ability to inhibit proinflammatory mediator production by LTA4 hydrolase and to block arachidonate conversion by human 12-LOX rather than merely terminating phagocyte involvement.—Dalli, J., Zhu, M., Vlasenko, N. A., Deng, B., Haeggström, J. Z., Petasis, N. A., Serhan, C. N. The novel 13S,14S-epoxy-maresin is converted by human macrophages to maresin 1 (MaR1), inhibits leukotriene A4 hydrolase (LTA4H) and shifts macrophage phenotype. PMID:23504711

A practical deca-gram scale ring expansion of (R)-(-)-carvone to (R)-(+)-3-methyl-6-isopropenyl-cyclohept-3-enone-1.

PubMed

Alves, Leandro de C; Desiderá, André L; de Oliveira, Kleber T; Newton, Sean; Ley, Steven V; Brocksom, Timothy J

2015-07-28

A route to enantiopure (R)-(+)-3-methyl-6-isopropenyl-cyclohept-3-enone-1, an intermediate for terpenoids, has been developed and includes a highly chemo- and regioselective Tiffeneau-Demjanov reaction. Starting from readily available (R)-(-)-carvone, this robust sequence is available on a deca-gram scale and uses flow chemistry for the initial epoxidation reaction. The stereochemistry of the addition of two nucleophiles to the carbonyl group of (R)-(-)-carvone has been determined by X-ray diffraction studies and chemical correlation.

mmpdb: An Open-Source Matched Molecular Pair Platform for Large Multiproperty Data Sets.

PubMed

Dalke, Andrew; Hert, Jérôme; Kramer, Christian

2018-05-29

Matched molecular pair analysis (MMPA) enables the automated and systematic compilation of medicinal chemistry rules from compound/property data sets. Here we present mmpdb, an open-source matched molecular pair (MMP) platform to create, compile, store, retrieve, and use MMP rules. mmpdb is suitable for the large data sets typically found in pharmaceutical and agrochemical companies and provides new algorithms for fragment canonicalization and stereochemistry handling. The platform is written in Python and based on the RDKit toolkit. It is freely available from https://github.com/rdkit/mmpdb .

Total Synthesis and Structure-Activity Investigation of the Marine Natural Product Neopeltolide

PubMed Central

Custar, Daniel W.; Zabawa, Thomas P.; Hines, John; Crews, Craig M.; Scheidt, Karl A.

2009-01-01

The total synthesis and biological evaluation of neopeltolide and analogs are reported. The key bond-forming step utilizes a Lewis acid-catalyzed intramolecular macrocyclization that installs the tetrahydropyran ring and macrocycle simultaneously. Independent of each other, neither the macrolide nor the oxazole side chain substituents of neopeltolide can inhibit the growth of cancer cell lines. The biological data of the analogs indicate that alterations to either the ester side chain or the stereochemistry of the macrolide result in a loss of biological activity. PMID:19663512

Iminosugars as a new class of cholinesterase inhibitors.

PubMed

Decroocq, Camille; Stauffert, Fabien; Pamlard, Olivier; Oulaïdi, Farah; Gallienne, Estelle; Martin, Olivier R; Guillou, Catherine; Compain, Philippe

2015-02-15

To further extend the scope of iminosugar biological activity, a systematic structure-activity relationship investigation has been performed by synthesizing and evaluating as cholinesterase inhibitors a library of twenty-three iminoalditols with different substitutions and stereochemistry patterns. These compounds have been evaluated in vitro for the inhibition of cholinesterases (different sources of acetylcholinesterase and butyrylcholinesterase). Some compounds have IC50 values in the micromolar range and display significant inhibition selectivity for butyrylcholinesterase over acetylcholinesterase. These are the first examples of iminosugar-based inhibitors of cholinesterases. Copyright © 2015 Elsevier Ltd. All rights reserved.

Self-assembled three-dimensional chiral colloidal architecture

NASA Astrophysics Data System (ADS)

Ben Zion, Matan Yah; He, Xiaojin; Maass, Corinna C.; Sha, Ruojie; Seeman, Nadrian C.; Chaikin, Paul M.

2017-11-01

Although stereochemistry has been a central focus of the molecular sciences since Pasteur, its province has previously been restricted to the nanometric scale. We have programmed the self-assembly of micron-sized colloidal clusters with structural information stemming from a nanometric arrangement. This was done by combining DNA nanotechnology with colloidal science. Using the functional flexibility of DNA origami in conjunction with the structural rigidity of colloidal particles, we demonstrate the parallel self-assembly of three-dimensional microconstructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality.

Comparison of Insect Kinin Analogs With cis-Peptide Bond Motif 4-Aminopyroglutamate Identifies Optimal Stereochemistry for Diuretic Activity

DTIC Science & Technology

2006-01-01

Amino acid side-chain-protecting groups were Pbf for Arg and Boc for Trp. The coupling of Fmoc-4-amino- pyroglutamic acids (Fmoc-aPy-OH, Fmoc-apy-OH...Inc. Biopolymers (Pept Sci) 88:1–7, 2007. Keywords: 4-aminopyroglutamic acid ; cis-peptide bond; b-turn mimetic; constrained insect kinin analog...analogs containing three stereochemical var- iants of the (2S, 4S)-4-aminopyroglutamic acid (APy) com- ponent (see Figure 1), a mimic of the cis-peptide

New Meroterpenoids from the Endophytic Fungus Aspergillus flavipes AIL8 Derived from the Mangrove Plant Acanthus ilicifolius

PubMed Central

Bai, Zhi-Qiang; Lin, Xiuping; Wang, Junfeng; Zhou, Xuefeng; Liu, Juan; Yang, Bin; Yang, Xianwen; Liao, Shengrong; Wang, Lishu; Liu, Yonghong

2015-01-01

Four new meroterpenoids (2–5), along with three known analogues (1, 6, and 7) were isolated from mangrove plant Acanthus ilicifolius derived endophytic fungus Aspergillus flavipes. The structures of these compounds were elucidated by NMR and MS analysis, the configurations were assigned by CD data, and the stereochemistry of 1 was confirmed by X-ray crystallography analysis. A possible biogenetic pathway of compounds 1–7 was also proposed. All compounds were evaluated for antibacterial and cytotoxic activities. PMID:25574738

Synthesis of Pyrrolo[1,2-a]pyrimidine Enantiomers via Domino Ring-Closure followed by Retro Diels-Alder Protocol.

PubMed

Fekete, Beáta; Palkó, Márta; Haukka, Matti; Fülöp, Ferenc

2017-04-13

From 2-aminonorbornene hydroxamic acids, a simple and efficient method for the preparation of pyrrolo[1,2- a ]pyrimidine enantiomers is reported. The synthesis is based on domino ring-closure followed by microwave-induced retro Diels-Alder (RDA) protocols, where the chirality of the desired products is transferred from norbornene derivatives. The stereochemistry of the synthesized compounds was proven by X-ray crystallography. The absolute configuration of the product is determined by the configuration of the starting amino hydroxamic acid.

Determination of absolute configuration of an isopimarane-type diterpenoid by experimental and theoretical electronic circular dichroism and vibrational circular dichroism

NASA Astrophysics Data System (ADS)

Wang, Zhi-Qiang; Wu, Cheng-Jun; Wang, Zhen-Hui; Huang, Chao; Huang, Jian; Wang, Jin-Hui; Sun, Tie-Min

2017-10-01

In this study, the stereochemistry of a new isopimarane-type diterpenoid isolated from the Callicarpa macrophylla Vahl, Callicapene M3, was studied by experimental electronic circular dichroism and vibrational circular dichroism with the aid of TDDFT theoretical calculations. The good consistence between the experimental and simulated circular dichroism has clearly confirmed the absolute configuration of the title compound as (4S, 5S, 9S, 10S, 13S, 14S)-14α-hydroxy-7,15-isopimaradien-18-oic acid.

Stereoselective synthesis, spectral and antimicrobial studies of some cyanoacetyl hydrazones of 3-alkyl-2,6-diarylpiperidin-4-ones

NASA Astrophysics Data System (ADS)

Velayutham Pillai, M.; Rajeswari, K.; Vidhyasagar, T.

2014-11-01

A series of novel cyanoacetyl hydrazones of 3-alkyl-2,6-diarylpiperidin-4-ones were synthesized stereoselectively and characterized by IR, Mass, 1H NMR, 13C NMR, 1H-1H COSY and 1H-13C COSY spectra. The stereochemistry of the synthesized compounds was established using NMR spectra. Antimicrobial screening of the synthesized compounds revealed their antibacterial and antifungal potencies. Growth inhibition of Enterobacter Aerogenes by compound 15 was found to be superior to the standard drug.

Constant pH simulations of pH responsive polymers

NASA Astrophysics Data System (ADS)

Sharma, Arjun; Smith, J. D.; Walters, Keisha B.; Rick, Steven W.

2016-12-01

Polyacidic polymers can change structure over a narrow range of pH in a competition between the hydrophobic effect, which favors a compact state, and electrostatic repulsion, which favors an extended state. Constant pH molecular dynamics computer simulations of poly(methacrylic acid) reveal that there are two types of structural changes, one local and one global, which make up the overall response. The local structural response depends on the tacticity of the polymer and leads to different cooperative effects for polymers with different stereochemistries, demonstrating both positive and negative cooperativities.

Sophopterocarpan A, a novel pterocarpine derivative with a benzotetrahydrofuran-fused bicyclo [3.3.1] nonane from Sophora flavescens.

PubMed

Zhu, Hui; Yang, Ya-Nan; Xu, Kuo; Xie, Jing; Feng, Zi-Ming; Jiang, Jian-Shuang; Zhang, Pei-Cheng

2017-07-05

Sophopterocarpan A (1), with a novel benzotetrahydrofuran-fused bicyclo [3.3.1] nonane ring, was isolated from the roots of Sophora flavescens Ait. Its unusual structure, including its stereochemistry, was determined on the basis of a comprehensive spectroscopic data analysis. A plausible biogenetic pathway for 1 is presented. Sophopterocarpan A was identified as a potential autophagy activator. Additionally, it was found that 1 exhibited cytotoxic activity in MCF-7 cells with an IC 50 of 29.36 μM.

The Molecular Structure of Penicillin

NASA Astrophysics Data System (ADS)

Bentley, Ronald

2004-10-01

The chemical structure of penicillin was determined between 1942 and 1945 under conditions of secrecy established by the U.S. and U.K. governments. The evidence was not published in the open literature but as a monograph. This complex volume does not present a structure proof that can be readily comprehended by a student. In this article, a basic structural proof for the penicillin molecule is provided, emphasizing the chemical work. The stereochemistry of penicillin is also described, and various rearrangements are considered on the basis of the accepted β-lactam structure.

Environmental effects on the structure of β-amino acid based foldamers.

PubMed

Sussman, Fredy; Sanchez-Pedregal, Victor; Estévez, Juan Carlos; Balo, Lino; Jimenez-Barbero, Jesus; Arda, Ana; Gimeno, Ana; Royo, Miriam; Villaverde, M Carmen; Estevez, Ramon

2018-05-29

In this work we show that hybrid peptides formed by alternating trans-2-aminocyclopentanecarboxylic acid (trans-ACPC) and trans-2-aminocyclohexanecarboxylic acid (trans-ACHC) do not fold in the solvents typically used in the study of their homooligomers. Only when we chose to assay our peptides in SDS micelles we obtained the predicted helical structures. This indicates that the environment could play an equally important role (as the backbone stereochemistry) in determining their fold, possibly by providing a sequestered environment. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enantioselective Copper-Catalyzed Carboetherification of Unactivated Alkenes**

PubMed Central

Bovino, Michael T.; Liwosz, Timothy W.; Kendel, Nicole E.; Miller, Yan; Tyminska, Nina

2014-01-01

Chiral saturated oxygen heterocycles are important components of bioactive compounds. Cyclization of alcohols onto pendant alkenes is a direct route to their synthesis, but few catalytic enantioselective methods enabling cyclization onto unactivated alkenes exist. Herein is reported a highly efficient copper-catalyzed cyclization of γ-unsaturated pentenols that terminates in C-C bond formation, a net alkene carboetherification. Both intra- and intermolecular C-C bond formations are demonstrated, yielding functionalized chiral tetrahydrofurans as well as fused-ring and bridged-ring oxabicyclic products. Transition state calculations support a cis-oxycupration stereochemistry-determining step. PMID:24798697

The Missing Link in Leguminous Pterocarpan Biosynthesis is a Dirigent Domain-Containing Protein with Isoflavanol Dehydratase Activity

PubMed Central

Uchida, Kai; Akashi, Tomoyoshi

2017-01-01

Pterocarpan forms the basic structure of leguminous phytoalexins, and most of the isoflavonoid pathway genes encoding the enzymes responsible for its biosynthesis have been identified. However, the last step of pterocarpan biosynthesis is a ring closure reaction, and the enzyme that catalyzes this step, 2′-hydroxyisoflavanol 4,2′-dehydratase or pterocarpan synthase (PTS), remains as an unidentified ‘missing link’. This last ring formation is assumed to be the key step in determining the stereochemistry of pterocarpans, which plays a role in their antimicrobial activity. In this study, a cDNA clone encoding PTS from Glycyrrhiza echinata (GePTS1) was identified through functional expression fractionation screening of a cDNA library, which requires no sequence information, and orthologs from soybean (GmPTS1) and Lotus japonicus (LjPTS1) were also identified. These proteins were heterologously expressed in Escherichia coli and biochemically characterized. Surprisingly, the proteins were found to include amino acid motifs characteristic of dirigent proteins, some of which control stereospecific phenoxy radical coupling in lignan biosynthesis. The stereospecificity of substrates and products was examined using four substrate stereoisomers with hydroxy and methoxy derivatives at C-4′. The results showed that the 4R configuration was essential for the PTS reaction, and (−)- and (+)-pterocarpans were produced depending on the stereochemistry at C-3. In suspension-cultured soybean cells, levels of the GmPTS1 transcript increased temporarily prior to the peak in phytoalexin accumulation, strongly supporting the possible involvement of PTS in pterocarpan biosynthesis. PMID:28394400

Stereochemistry of C18 monounsaturated cork suberin acids determined by spectroscopic techniques including (1) H-NMR multiplet analysis of olefinic protons.

PubMed

Santos, Sara; Graça, José

2014-01-01

Suberin is a biopolyester responsible for the protection of secondary plant tissues, and yet its molecular structure remains unknown. The C18:1 ω-hydroxyacid and the C18:1 α,ω-diacid are major monomers in the suberin structure, but the configuration of the double bond remains to be elucidated. To unequivocally define the configuration of the C18:1 suberin acids. Pure C18:1 ω-hydroxyacid and C18:1 α,ω-diacid, isolated from cork suberin, and two structurally very close C18:1 model compounds of known stereochemistry, methyl oleate and methyl elaidate, were analysed by NMR spectroscopy, Fourier transform infrared (FTIR) and Raman spectroscopy, and GC-MS. The GC-MS analysis showed that both acids were present in cork suberin as only one geometric isomer. The analysis of dimethyloxazoline (DMOX) and picolinyl derivatives proved the double bond position to be at C-9. The FTIR spectra were concordant with a cis-configuration for both suberin acids, but their unambiguous stereochemical assignment came from the NMR analysis: (i) the chemical shifts of the allylic (13) C carbons were shielded comparatively to the trans model compound, and (ii) the complex multiplets of the olefinic protons could be simulated only with (3) JHH and long-range (4) JHH coupling constants typical of a cis geometry. The two C18:1 suberin acids in cork are (Z)-18-hydroxyoctadec-9-enoic acid and (Z)-octadec-9-enedoic acid. Copyright © 2013 John Wiley & Sons, Ltd.

Stereodivergent Synthesis of 1,3-Syn-Polyol Natural Product for Stereochemical-Based Structure Activity Relationship Studies

NASA Astrophysics Data System (ADS)

Zheng, Jiamin

The 1,3-syn-diol functionality is very common in many natural products. An important class containing this moiety are the 1,3-syn-polyol/pyranone natural products, which have been isolated from a variety of plant sources, and possess biological activities like plant growth inhibition as well as antifeedant, antifungal, antibacterial, and antitumor properties. The feature of this class is a 6-membered lactone where the lactoe oxygen is part of a 1,3-syn-diol motif. To pursue the 1,3-syn-polyol/pyranone natural products, an iterative hydration of polyene strategy was utilized to provide the 1,3- syn-diol functionality, and asymmetric synthetic strategies were explored to form the requisite stereochemistry. The versatility of the asymmetric approach was demonstrated in the synthesis of eupatorium pyranone and also in an ongoing project aimed at the synthesis of SIA7248. As an outgrowth of our work on the total syntheses of 1,3-syn -polyol natural products inspired a stereo-divergent synthesis of 1,3-syn-polyol natural products and their analogs for stereochemical-based structure-activity relationship (SSAR) studies. To identify the key structural factors important for the anticancer activity of the 1,3-syn-polyol/pyranones, a stereo-divergent 16-member library of pyranone/polyol congeners was designed, synthesized and tested with variations in both stereochemistry and numbers of polyol repeat units. Having access to stereochemical isomers of the biologically active natural products allowed us to design experiments that help illustrate their mechanisms of action.

Influence of major structural features of tocopherols and tocotrienols on their omega-oxidation by tocopherol-omega-hydroxylase.

PubMed

Sontag, Timothy J; Parker, Robert S

2007-05-01

Human cytochrome P450 4F2 (CYP4F2) catalyzes the initial omega-hydroxylation reaction in the metabolism of tocopherols and tocotrienols to carboxychromanols and is, to date, the only enzyme shown to metabolize vitamin E. The objective of this study was to characterize this activity, particularly the influence of key features of tocochromanol substrate structure. The influence of the number and positions of methyl groups on the chromanol ring, and of stereochemistry and saturation of the side chain, were explored using HepG2 cultures and microsomal reaction systems. Human liver microsomes and microsomes selectively expressing recombinant human CYP4F2 exhibited substrate activity patterns similar to those of HepG2 cells. Although activity was strongly associated with substrate accumulation by cells or microsomes, substantial differences in specific activities between substrates remained under conditions of similar microsomal membrane substrate concentration. Methylation at C5 of the chromanol ring was associated with markedly low activity. Tocotrienols exhibited much higher Vmax values than their tocopherol counterparts. Side chain stereochemistry had no effect on omega-hydroxylation of alpha-tocopherol (alpha-TOH) by any system. Kinetic analysis of microsomal CYP4F2 activity revealed Michaelis-Menten kinetics for alpha-TOH but allosteric cooperativity for other vitamers, especially tocotrienols. Additionally, alpha-TOH was a positive effector of omega-hydroxylation of other vitamers. These results indicate that CYP4F2-mediated tocopherol-omega-hydroxylation is a central feature underlying the different biological half-lives, and therefore biopotencies, of the tocopherols and tocotrienols.

Identification and sensory evaluation of dehydro- and deoxy-ellagitannins formed upon toasting of oak wood (Quercus alba L.).

PubMed

Glabasnia, Arne; Hofmann, Thomas

2007-05-16

Traditionally, spirits such as whiskey are matured in toasted wood barrels to improve the sensory quality of the final beverage. In order to gain first insight into the puzzling road map of thermal ellagitannin transformation chemistry and provide evidence for the changes in sensory active nonvolatiles in oak wood during toasting, the purified oak ellagitannins castalagin and vescalagin, their corresponding dimers roburin A and roburin D, and 33-carboxy-33-deoxyvescalagin were thermally treated in model experiments. Besides mouth-coating and golden-brown colored melanoidin-type polymers, individual major reaction products were produced as transient intermediates which were identified for the first time by means of LC-MS/MS and 1D/2D-NMR spectroscopy. Depending strongly on the stereochemistry, castalagin is oxidized to the previously unreported dehydrocastalagin, whereas its diastereomer vescalagin, differing only in the stereochemistry at carbon C-1, is most surprisingly converted into deoxyvescalagin. Comparative model experiments with 33-carboxy-33-deoxyvescalagin revealed castalagin, vescalagin, dehydrocastalagin, and deoxyvescalagin as typical reaction products, thus indicating decarboxylation as a key step in the thermal degradation of that ellagitannin. Similar to the ellagitannin monomers, LC-MS/MS analyses gave strong evidence that the corresponding dimer roburin A, containing the vescalagin configuration at C-1, was converted into the deoxyroburin A, whereas roburin D, exhibiting the castalagin configuration at C-1, was oxidized to give the dehydroroburin D. Human sensory experiments revealed that the ellagitannin derivatives imparted an astringent mouth-coating sensation with threshold concentrations ranging from 1.1 to 126.0 micromol/L, depending strongly on their chemical structure.

Assignment of the Stereochemistry and Anomeric Configuration of Sugars within Oligosaccharides Via Overlapping Disaccharide Ladders Using MSn

NASA Astrophysics Data System (ADS)

Konda, Chiharu; Londry, Frank A.; Bendiak, Brad; Xia, Yu

2014-08-01

A systematic approach is described that can pinpoint the stereo-structures (sugar identity, anomeric configuration, and location) of individual sugar units within linear oligosaccharides. Using a highly modified mass spectrometer, dissociation of linear oligosaccharides in the gas phase was optimized along multiple-stage tandem dissociation pathways (MSn, n = 4 or 5). The instrument was a hybrid triple quadrupole/linear ion trap mass spectrometer capable of high-efficiency bidirectional ion transfer between quadrupole arrays. Different types of collision-induced dissociation (CID), either on-resonance ion trap or beam-type CID could be utilized at any given stage of dissociation, enabling either glycosidic bond cleavages or cross-ring cleavages to be maximized when wanted. The approach first involves optimizing the isolation of disaccharide units as an ordered set of overlapping substructures via glycosidic bond cleavages during early stages of MSn, with explicit intent to minimize cross-ring cleavages. Subsequently, cross-ring cleavages were optimized for individual disaccharides to yield key diagnostic product ions ( m/ z 221). Finally, fingerprint patterns that establish stereochemistry and anomeric configuration were obtained from the diagnostic ions via CID. Model linear oligosaccharides were derivatized at the reducing end, allowing overlapping ladders of disaccharides to be isolated from MSn. High confidence stereo-structural determination was achieved by matching MSn CID of the diagnostic ions to synthetic standards via a spectral matching algorithm. Using this MSn ( n = 4 or 5) approach, the stereo-structures, anomeric configurations, and locations of three individual sugar units within two pentasaccharides were successfully determined.

Hydrophobic Tail Length, Degree of Fluorination and Headgroup Stereochemistry are Determinants of the Biocompatibility of (Fluorinated) Carbohydrate Surfactants

PubMed Central

Li, Xueshu; Turánek, Jaroslav; Knötigová, Pavlína; Kudláčková, Hana; Mašek, Josef; Parkin, Sean; Rankin, Stephen E; Knutson, Barbara L; Lehmler, Hans-Joachim

2009-01-01

A series of hydrocarbon and fluorocarbon carbohydrate surfactants with different headgroups (i.e., gluco-, galacto- and maltopyranoside) and (fluorinated) alkyl tails (i.e., C7 and C14 to C19) was synthesized to investigate trends in their cytotoxicity and haemolytic activity, and how surfactant-lipid interactions of selected surfactants contribute to these two measures of biocompatibility. All surfactants displayed low cytotoxicity (EC50 = 25 to > 250 μM) and low haemolytic activity (EC50 = 0.2 to > 3.3 mM), with headgroup structure, tail length and degree of fluorination being important structural determinants for both endpoints. The EC50 values of hydrocarbon and fluorocarbon glucopyranoside surfactants displayed a “cut-off” effect (i.e., a maximum with respect to the chain length). According to steady-state fluorescence anisotropy studies, short chain (C7) surfactants partitioned less readily into model membranes, which explains their low cytotoxicity and haemolytic activity. Interestingly, galactopyranosides were less toxic compared to glucopyranosides with the same hydrophobic tail. Although both surfactant types only differ in the stereochemistry of the 4-OH group, hexadecyl gluco- and galactopyranoside surfactants had similar apparent membrane partition coefficients, but differed in their overall effect on the phase behaviour of DPPC model membranes, as assessed using steady-state fluorescence anisotropy studies. These observations suggest that highly selective surfactant-lipid interactions may be responsible for the differential cytotoxicity and, possible, haemolytic activity of hydrocarbon and fluorocarbon carbohydrate surfactants intended for a variety of pharmaceutical and biomedical applications. PMID:19481909

Enantioselective copper-catalyzed carboetherification of unactivated alkenes.

PubMed

Bovino, Michael T; Liwosz, Timothy W; Kendel, Nicole E; Miller, Yan; Tyminska, Nina; Zurek, Eva; Chemler, Sherry R

2014-06-16

Chiral saturated oxygen heterocycles are important components of bioactive compounds. Cyclization of alcohols onto pendant alkenes is a direct route to their synthesis, but few catalytic enantioselective methods enabling cyclization onto unactivated alkenes exist. Herein reported is a highly efficient copper-catalyzed cyclization of γ-unsaturated pentenols which terminates in C-C bond formation, a net alkene carboetherification. Both intra- and intermolecular C-C bond formations are demonstrated, thus yielding functionalized chiral tetrahydrofurans as well as fused-ring and bridged-ring oxabicyclic products. Transition-state calculations support a cis-oxycupration stereochemistry-determining step. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Formal synthesis of berkelic acid: a lesson in α-alkylation chemistry.

PubMed

McLeod, Michael C; Wilson, Zoe E; Brimble, Margaret A

2012-01-06

The full details of our enantioselective formal synthesis of the biologically active natural product berkelic acid are described. The insertion of the C-18 methyl group proved challenging, with three different approaches investigated to install the correct stereochemistry. Our initial Horner-Wadsworth-Emmons/oxa-Michael approach to the berkelic acid core proved unsuccessful upon translation to the natural product itself. However, addition of a silyl enol ether to an oxonium ion, followed by a one-pot debenzylation/spiroketalisation/thermodynamic equilibration procedure, afforded the tetracyclic structure of the berkelic acid core as a single diastereoisomer.

Brocaenols A-C: novel polyketides from a marine derived Penicillium brocae.

PubMed

Bugni, Tim S; Bernan, Valerie S; Greenstein, Michael; Janso, Jeffrey E; Maiese, William M; Mayne, Charles L; Ireland, Chris M

2003-03-07

Chemical investigation of a Penicillium brocae, obtained from a tissue sample of a Fijian Zyzyya sp. sponge, yielded two known diketopiperazines and three novel cytotoxic polyketides, brocaenols A-C. The brocaenols contain an unusual enolized oxepine lactone ring system that to the best of our knowledge is unprecedented in the literature. The structures were elucidated by using 2D-NMR methods including an INADEQUATE experiment. The absolute stereochemistry of brocaenol A was established by using a modified Mosher method. The taxonomy of the producing fungus was elucidated by using both morphological and rDNA sequence analysis.

11-Step Total Synthesis of Araiosamines

PubMed Central

2016-01-01

A concise route to a small family of exotic marine alkaloids known as the araiosamines has been developed, and their absolute configuration has been assigned. The dense array of functionality, high polarity, and rich stereochemistry coupled with equilibrating topologies present an unusual challenge for chemical synthesis and an opportunity for innovation. Key steps involve the use of a new reagent for guanidine installation, a remarkably selective C–H functionalization, and a surprisingly simple final step that intersects a presumed biosynthetic intermediate. Synthetic araiosamines were shown to exhibit potency against Gram-positive and -negative bacteria despite a contrary report of no activity. PMID:27748593

13C NMR spectral characterization of epimeric rotenone and some related tetrahydrobenzopyranofurobenzopyranones

USGS Publications Warehouse

Abidi, S.L.; Abidi, M.S.

1983-01-01

The 13C nuclear magnetic resonance (nmr) spectra of epimers of rotenone and four 12a-hydroxy-analogues were examined to determine the stereochemical effect of the B/C ring fusion involving the 6a- and 12a-carbon centers. Chemical shift differences between the epimeric carbon resonances of cis- and trans-6a,12a-compounds were notably larger than those of diastereoisomers derived from the same B/C ring junction stereochemistry. Results of the spectral analysis have been useful for the quantification of mixtures of epimers and for the measurement of rates of epimerization and oxygenation.

Sesterterpenes from a common marine sponge, Hyrtios erecta.

PubMed

Crews, P; Bescansa, P

1986-01-01

Eleven sesterterpenes have been characterized from the biotoxic extracts of Hyrtios erecta. Their structures and stereochemistry were established by spectral properties or results from chemical interconversions. Especially valuable for establishing stereochemical features were 13C-nmr methyl shift correlations and analysis of 1H-nmr couplings and chemical shifts. The new scalarane sesterterpenes included 2, 3, 7, 9, and 10a (but 9 and 10a might be artifacts), and they were accompanied by five previously described scalaranes, 1, 4, 5a, 6, and 8, along with hyrtial (11), a novel norsesterterpene. Many of these sesterterpenes exhibited interesting biological activity.

Benzo(a)pyrene-7,8-dihydrodiol 9,10-oxide adenosine and deoxyadenosine adducts: structure and stereochemistry.

PubMed

Jeffrey, A M; Grzeskowiak, K; Weinstein, I B; Nakanishi, K; Roller, P; Harvey, R G

1979-12-14

The structure and absolute stereoconfigurations of four adenosine adducts with (+/-)-7 alpha,8 beta-dihydroxy-9 beta, 10 beta-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene (BPDE) and their deoxyadenosine analogs have been determined. They result from both cis and trans addition of the N6 amino group of ademine to the 10 position of both enantiomers of BDPE. This was determined from studies of the nuclear magnetic resonance spectra, mass spectra, and circular dichroism spectra, as well as from their pKa values and chemical reactivities.

Calibrating the coordination chemistry tool chest: metrics of bi- and tridentate ligands.

PubMed

Aguilà, David; Escribano, Esther; Speed, Saskia; Talancón, Daniel; Yermán, Luis; Alvarez, Santiago

2009-09-07

Bi- and multidentate ligands form part of the tools commonly used for designing coordination and supramolecular complexes with desired stereochemistries. Parameters and concepts usually employed include the normalized bite of bidentate ligands, their cis- or trans-coordinating ability, their rigidity or flexibility, or the duality of some ligands that can act in chelating or dinucleating modes. In this contribution we present a structural database study of over one hundred bi- and tridentate ligands that allows us to parametrize their coordinating properties and discuss the relevance of such parameters for the choice of coordination polyhedron or coordination sites.

Total synthesis and biological investigation of (-)-promysalin.

PubMed

Steele, Andrew D; Knouse, Kyle W; Keohane, Colleen E; Wuest, William M

2015-06-17

Compounds that specifically target pathogenic bacteria are greatly needed, and identifying the method by which they act would provide new avenues of treatment. Herein we report the concise, high-yielding total synthesis (eight steps, 35% yield) of promysalin, a natural product that displays antivirulence phenotypes against pathogenic bacteria. Guided by bioinformatics, four diastereomers were synthesized, and the relative and absolute stereochemistries were confirmed by spectral and biological analysis. Finally, we show for the first time that promysalin displays two antivirulence phenotypes: the dispersion of mature biofilms and the inhibition of pyoverdine production, hinting at a unique pathogenic-specific mechanism of action.

Emil Fischer and the "art of chemical experimentation".

PubMed

Jackson, Catherine M

2017-03-01

What did nineteenth-century chemists know? This essay uses Emil Fischer's classic study of the sugars in 1880s and 90s Germany to argue that chemists' knowledge was not primarily vested in the theories of valence, structure, and stereochemistry that have been the subject of so much historical and philosophical analysis of chemistry in this period. Nor can chemistry be reduced to a merely manipulative exercise requiring little or no intellectual input. Examining what chemists themselves termed the "art of chemical experimentation" reveals chemical practice as inseparable from its cognitive component, and it explains how chemists integrated theory with experiment through reason.

Iron Alkynyl Helicenes: Redox-Triggered Chiroptical Tuning in the IR and Near-IR Spectral Regions and Suitable for Telecommunications Applications.

PubMed

Shen, Chengshuo; Loas, Goulc'hen; Srebro-Hooper, Monika; Vanthuyne, Nicolas; Toupet, Loïc; Cador, Olivier; Paul, Frédéric; López Navarrete, Juan T; Ramírez, Francisco J; Nieto-Ortega, Belén; Casado, Juan; Autschbach, Jochen; Vallet, Marc; Crassous, Jeanne

2016-07-04

The combination of a bis-alkynyl-helicene moiety with two iron centers leads to novel electroactive species displaying unprecedented redox-triggered chiroptical switching. Upon oxidation, strong changes of vibrational modes (either local or extended coupled modes) are detected by vibrational circular dichroism and Raman optical activity. Remarkably, the sign of the optical rotation at 1.54 µm (that is, at wavelengths typically used for telecommunications) changes upon oxidation while the topology and stereochemistry of the helicene remain unchanged. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The three-dimensional crystal structure of cholera toxin

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

Zhang, Rong-Guang; Westbrook, M.L.; Nance, S.

1996-02-01

The clinical manifestations of cholera are largely attributable to the actions of a secreted hexameric AB{sub 5} enterotoxin (choleragen). We have solved the three-dimensional structure of choleragen at 2.5 {Angstrom} resolution and compared the refined coordinates with those of choleragenoid (isolated B pentamer) and the heat-labile enterotoxin from Escherichia coli (LT). The crystalline coordinates provide a detailed view of the stereochemistry implicated in binding to GM1 gangliosides and in carrying out ADP-ribosylation. The A2 chain of choleragen, in contrast to that of LT, is a nearly continuous {alpha}-helix with an interpretable carboxyl tail.

Facile total synthesis and antimicrobial activity of the marine fatty acids (Z)-2-methoxy-5-hexadecenoic acid and (Z)-2-methoxy-6-hexadecenoic acid.

PubMed

Carballeira, N M; Emiliano, A; Hernández-Alonso, N; González, F A

1998-12-01

The total synthesis of the naturally occurring (Z)-2-methoxy-5-hexadecenoic acid and (Z)-2-methoxy-6-hexadecenoic acid was accomplished using as a key step Mukaiyama's trimethylsilyl cyanide addition to 4- and 5-pentadecenal, respectively. These syntheses further confirm the structures of the natural marine fatty acids and corroborate their cis double-bond stereochemistry. The title compounds were antimicrobial against the Gram-positive bacteria Staphylococcus aureus (MIC 0.35 micromol/mL) and Streptococcus faecalis (MIC 0.35 micromol/mL).

Structure Elucidation of Verucopeptin, a HIF-1 Inhibitory Polyketide-Hexapeptide Hybrid Metabolite from an Actinomycete.

PubMed

Yoshimura, Aya; Nishimura, Shinichi; Otsuka, Saori; Hattori, Akira; Kakeya, Hideaki

2015-11-06

The transcriptional factor, hypoxia inducible factor-1 (HIF-1), is a promising target for cancer chemotherapy. From an actinomycete, verucopeptin (1) was identified as a HIF-1 signaling inhibitor. By a combination of chemical degradation and spectroscopic analyses, the absolute stereochemistry of metabolite 1 was determined to be 10R, 15S, 16S, 23S, 27S, 28R, 31S, 33S, 35R. Moreover, metabolite 1 was revealed to attenuate the HIF-1α and mTORC1 pathway, indicating that verucopeptin (1) would be a potent lead compound for anticancer chemotherapy.

Synthetic cathinones and stereochemistry: S enantiomer of mephedrone reduces anxiety- and depressant-like effects in cocaine- or MDPV-abstinent rats.

PubMed

Philogene-Khalid, Helene L; Hicks, Callum; Reitz, Allen B; Liu-Chen, Lee-Yuan; Rawls, Scott M

2017-09-01

The neuropharmacological profile of the synthetic cathinone mephedrone (MEPH) is influenced by stereochemistry. Both MEPH enantiomers are monoamine transporter substrates, but R-MEPH is primarily responsible for rewarding effects of MEPH as it produces greater locomotor activation and intracranial self-stimulation than S-MEPH. S-MEPH is a 50-fold more potent 5-HT releaser than R-MEPH and does not place preference in rats. MEPH is also structurally similar to the cathinone derivative bupropion, an antidepressant and smoking cessation medication, suggesting MEPH has therapeutic and addictive properties. We tested the hypothesis that S-MEPH reduces anxiety- and depression-like behaviors in rats withdrawn from chronic cocaine or methylenedioxypyrovalerone (MDPV) using the elevated plus maze (EPM) and forced swim test (FST), respectively. Rats were tested 48-h after a binge-like paradigm (3×/day for 10days in 1-h intervals) of cocaine (10mg/kg), MDPV (1mg/kg) or saline. In vitro studies assessed the receptor binding and activity of S-MEPH. Rats withdrawn from chronic cocaine or MDPV displayed an increase in anxiety- and depression-like behaviors that was antagonized by treatment with S-MEPH (10, 30mg/kg). S-MEPH displayed affinity, but not agonist activity, for 5-HT 2 receptors (2A-2C) and showed negligible affinity for dopaminergic, adrenergic and nicotinic receptors. S-MEPH attenuated withdrawal behaviors following chronic cocaine or MDPV, perhaps through 5-HT release and/or 5-HT 2 receptor interactions. The present data suggest S-MEPH may be a possible structural and pharmacological template to develop maintenance therapy for acute anxiety and depression during early withdrawal from psychostimulant abuse. Copyright © 2017 Elsevier B.V. All rights reserved.

Stereochemistry and solvent role in protein folding: nuclear magnetic resonance and molecular dynamics studies of poly-L and alternating-L,D homopolypeptides in dimethyl sulfoxide.

PubMed

Srivastava, Kinshuk Raj; Kumar, Anil; Goyal, Bhupesh; Durani, Susheel

2011-05-26

The competing interactions folding and unfolding protein structure remain obscure. Using homopolypeptides, we ask if poly-L structure may have a role. We mutate the structure to alternating-L,D stereochemistry and substitute water as the fold-promoting solvent with methanol and dimethyl sulfoxide (DMSO) as the fold-denaturing solvents. Circular dichroism and molecular dynamics established previously that, while both isomers were folded in water, the poly-L isomer was unfolded and alternating-L,D isomer folded in methanol. Nuclear magnetic resonance and molecular dynamics establish now that both isomers are unfolded in DMSO. We calculated energetics of folding-unfolding equilibrium with water and methanol as solvents. We have now calculated interactions of unfolded polypeptide structures with DMSO as solvent. Methanol was found to unfold and water fold poly-L structure as a dielectric. DMSO has now been found to unfold both poly-L and alternating-L,D structures by strong solvation of peptides to disrupt their hydrogen bonds. Accordingly, we propose that while linked peptides fold protein structure with hydrogen bonds they unfold the structure electrostatically due to the stereochemical effect of the poly-L structure. Protein folding to ordering of peptide hydrogen bonds with water as canonical solvent may thus involve two specific and independent solvent effects-one, strong screening of electrostatics of poly-L linked peptides, and two, weak dipolar solvation of peptides. Correspondingly, protein denaturation may involve two independent solvent effects-one, weak dielectric to unfold poly-L structure electrostatically, and two, strong polarity to disrupt peptide hydrogen bonds by solvation of peptides.

Z-sinapinic acid: the change of the stereochemistry of cinnamic acids as rational synthesis of a new matrix for carbohydrate MALDI-MS analysis.

PubMed

Salum, María L; Itovich, Lucia M; Erra-Balsells, Rosa

2013-11-01

Successful application of matrix-assisted laser desorption/ionization (MALDI) MS started with the introduction of efficient matrices such as cinnamic acid derivatives (i.e. 3,5-dimethoxy-4-hydroxycinnamic acid, SA; α-cyano-4-hydroxycinnamic acid). Since the empirical founding of these matrices, other commercial available cinnamic acids with different nature and location of substituents at benzene ring were attempted. Rational design and synthesis of new cinnamic acids have been recently described too. Because the presence of a rigid double bond in its molecule structure, cinnamic acids can exist as two different geometric isomers, the E-form and Z-form. Commercial available cinnamic acids currently used as matrices are the geometric isomers trans or E (E-cinnamic and trans-cinnamic acids). As a new rational design of MALDI matrices, Z-cinnamic acids were synthesized, and their properties as matrices were studied. Their performance was compared with that of the corresponding E-isomer and classical crystalline matrices (3,5-dihydroxybenzoic acid; norharmane) in the analysis of neutral/sulfated carbohydrates. Herein, we demonstrate the outstanding performance for Z-SA. Sulfated oligosaccharides were detected in negative ion mode, and the dissociation of sulfate groups was almost suppressed. Additionally, to better understand the quite different performance of each geometric isomer as matrix, the physical and morphological properties as well as the photochemical stability in solid state were studied. The influence of the E/Z photoisomerization of the matrix during MALDI was evaluated. Finally, molecular modeling (density functional theory study) of the optimized geometry and stereochemistry of E-cinnamic and Z-cinnamic acids revealed some factors governing the analyte-matrix interaction. Copyright © 2013 John Wiley & Sons, Ltd.

Synthesis, stereochemistry determination, pharmacological studies and quantum chemical analyses of bisthiazolidinone derivative

NASA Astrophysics Data System (ADS)

Mushtaque, Md.; Avecilla, Fernando; Hafeez, Zubair Bin; Jahan, Meriyam; Khan, Md. Shahzad; Rizvi, M. Moshahid A.; Khan, Mohd. Shahid; Srivastava, Anurag; Mallik, Anwesha; Verma, Saurabh

2017-01-01

A new compound (3) bisthaizolidinone derivative was synthesized by Knoevenagel condensation reaction. The structure of synthesized compound was elucidated by different spectral techniques and X-ray diffraction studies. The stereochemistry of the compound (3) was determined by 1Hsbnd 1H NOESY, 1Hsbnd 1H NMR COSY and single crystal X-ray diffraction studies as (Z, Z)-configuration. The computational quantum chemical studies of compound(3) like, IR, UV, NBO analysis were performed by DFT with Becke-3-Lee-Yang-Parr (B3LYP) exchange-correlation functional in combination with 6-311++G(d,p) basis sets. The DNA-binding of compound (3) exhibited a moderate binding constant (Kb = 1 × 105 Lmol-1) with hypochromic shift. The molecular docking displayed good binding affinity -7.18 kcal/mol. The MTT assay of compound (3) was screened against different cancerous cell lines, HepG2, Siha, Hela and MCF-7. Studies against these cell lines depicted that the screened compound (3) showed potent inhibitory activity against HepG2 cell (IC50 = 7.5 μM) followed by MCF-7 (IC50 = 52.0 μM), Siha (IC50 = 66.98 μM), Hela (IC50 = 74.83 μM) cell lines, and non-toxic effect against non-cancerous HEK-293 cells (IC50 = 287.89 μM) at the concentration range (0-300) μM. Furthermore, cell cycle perturbation was performed on HepG2 & Siha cell lines and observed that cells were arrested in G2/M in HepG2, and G0/G1 in Siha cell lines with respect to untreated control. Hence, compound (3) possesses potent anti-cancerous activity against HepG2 cell line.

The Missing Link in Leguminous Pterocarpan Biosynthesis is a Dirigent Domain-Containing Protein with Isoflavanol Dehydratase Activity.

PubMed

Uchida, Kai; Akashi, Tomoyoshi; Aoki, Toshio

2017-02-01

Pterocarpan forms the basic structure of leguminous phytoalexins, and most of the isoflavonoid pathway genes encoding the enzymes responsible for its biosynthesis have been identified. However, the last step of pterocarpan biosynthesis is a ring closure reaction, and the enzyme that catalyzes this step, 2'-hydroxyisoflavanol 4,2'-dehydratase or pterocarpan synthase (PTS), remains as an unidentified 'missing link'. This last ring formation is assumed to be the key step in determining the stereochemistry of pterocarpans, which plays a role in their antimicrobial activity. In this study, a cDNA clone encoding PTS from Glycyrrhiza echinata (GePTS1) was identified through functional expression fractionation screening of a cDNA library, which requires no sequence information, and orthologs from soybean (GmPTS1) and Lotus japonicus (LjPTS1) were also identified. These proteins were heterologously expressed in Escherichia coli and biochemically characterized. Surprisingly, the proteins were found to include amino acid motifs characteristic of dirigent proteins, some of which control stereospecific phenoxy radical coupling in lignan biosynthesis. The stereospecificity of substrates and products was examined using four substrate stereoisomers with hydroxy and methoxy derivatives at C-4'. The results showed that the 4R configuration was essential for the PTS reaction, and (-)- and (+)-pterocarpans were produced depending on the stereochemistry at C-3. In suspension-cultured soybean cells, levels of the GmPTS1 transcript increased temporarily prior to the peak in phytoalexin accumulation, strongly supporting the possible involvement of PTS in pterocarpan biosynthesis. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved.

CYP2C9 Amino Acid Residues Influencing Phenytoin Turnover and Metabolite Regio- and Stereochemistry

PubMed Central

Mosher, Carrie M.; Tai, Guoying; Rettie, Allan E.

2009-01-01

Phenytoin has been an effective anticonvulsant agent for over 60 years, although its clinical use is complicated by nonlinear pharmacokinetics, a narrow therapeutic index, and metabolically based drug-drug interactions. Although it is well established that CYP2C9 is the major cytochrome P450 enzyme controlling metabolic elimination of phenytoin through its oxidative conversion to (S)-5-(4-hydroxyphenyl)-5-phenylhydantoin (p-HPPH), nothing is known about the amino acid binding determinants within the CYP2C9 active site that promote metabolism and maintain the tight stereocontrol of hydroxy metabolite formation. This knowledge gap was addressed here through the construction of nine active site mutants at amino acid positions Phe100, Arg108, Phe114, Leu208, and Phe476 and in vitro analysis of the steady-state kinetics and stereochemistry of p-HPPH formation. The F100L and F114W mutants exhibited 4- to 5-fold increases in catalytic efficiency, whereas the F100W, F114L, F476L, and F476W mutants lost >90% of their phenytoin hydroxylation capacity. This pattern of effects differs substantially from that found previously for (S)-warfarin and (S)-flurbiprofen metabolism, suggesting that these three ligands bind within discrete locations in the CYP2C9 active site. Only the F114L, F476L, and L208V mutants altered phenytoin's orientation during catalytic turnover. The L208V mutant also uniquely demonstrated enhanced 6-hydroxylation of (S)-warfarin. These latter data provide the first experimental evidence for a role of the F-G loop region in dictating the catalytic orientation of substrates within the CYP2C9 active site. PMID:19258521

Microcionamides A and B, bioactive peptides from the philippine sponge Clathria (Thalysias) abietina.

PubMed

Davis, Rohan A; Mangalindan, Gina C; Bojo, Zenaida P; Antemano, Rowena R; Rodriguez, Nell O; Concepcion, Gisela P; Samson, Shiela C; de Guzman, Dennis; Cruz, Lourdes J; Tasdemir, Deniz; Harper, Mary Kay; Feng, Xidong; Carter, Guy T; Ireland, Chris M

2004-06-11

Microcionamides A (1) and B (2) have been isolated from the Philippine marine sponge Clathria (Thalysias) abietina. These new linear peptides are cyclized via a cystine moiety and have their C-terminus blocked by a 2-phenylethylenamine group. Their total structures, including absolute stereochemistry, were determined by a combination of spectral and chemical methods. Compound 1 was shown to slowly isomerize about the C-36/C-37 double bond when stored in DMSO. Microcionamides A (1) and B (2) exhibited significant cytotoxicity against the human breast tumor cells lines MCF-7 and SKBR-3 and displayed inhibitory activity against Mycobacterium tuberculosis H(37)Ra.

Spectroscopy and crystal structures of natural stereoisomers of neoclerodane diterpenoids from Teucrium yemense of Saudi medicinal plant

NASA Astrophysics Data System (ADS)

Nur-e-Alam, Mohammad; Kanthasamy, Gopikkaa; Yousaf, Muhammad; Alqahtani, Ali S.; Ghabbour, Hazem A.; Al-Rehaily, Adnan J.

2017-11-01

3-O-deacetylteugracilin (1) and teugracilin B (2), two natural stereoisomers, are isolated from Teucrium yemense (Defl). These two compounds are almost identical to each other, differing only at the C6 stereocenter. We now crystallise these two compounds and for the first time, determine the crystal structure through single crystal X-ray diffraction, and the stereochemistry for all positions using spectroscopic data. These techniques enable us to establish the difference between the two compounds. Careful interpretation of the results indicates that HRMS and 1 and 2D NMR spectroscopy, are in agreement with single crystal X-ray diffraction data.

Tigloylshikonin, a new minor Shikonin derivative, from the roots and the commercial root extract of lithospermum erythrorhizon.

PubMed

Ito, Yusai; Onobori, Kenichi; Yamazaki, Takeshi; Kawamura, Yoko

2011-01-01

Tigloylshikonin, a new shikonin derivative esterified with tiglic acid ((E)-2-methylbut-2-enoic acid), was isolated as a minor pigment from a food colorant "Shikon color," a commercial root extract from Lithospermum erythrorhizon SIEBOLD et ZUCCARINI. The structure of tigloylshikonin was elucidated using (1)H, (13)C, the difference nuclear Overhauser effect (NOE), and 2D NMR techniques. Its stereochemistry was determined by chiral-phase HPLC analysis. Tigloylshikonin was also found in the roots of L. erythrorhizon, which indicated that this new shikonin derivative is a typical component of naphthoquinone pigments in the roots of L. erythrorhizon.

Total synthesis of (±)-antroquinonol d.

PubMed

Sulake, Rohidas S; Jiang, Yan-Feng; Lin, Hsiao-Han; Chen, Chinpiao

2014-11-21

Total synthesis of (±)-antroquinonol D, which is isolated from very expensive and rarely found Antrodia camphorata and which has potential anticancer properties, was achieved from 4-methoxyphenol. In addition, a Michael addition to dimethoxy cyclohexadienones was studied. The main step involved chelation and substrate-controlled diastereoselective reduction of cyclohexenone and lactonization. Lactone synthesis facilitated the diastereoselective reduction of ketone, which help control the desired stereochemistry at the crucial stereogenic center in the natural product. Other key reactions in the synthesis involved a Michael addition of dimethyl malonate on cyclohexadienone, dihydroxylation, and Wittig olefination. A sesquiterpene side chain was synthesized through coupling with geranyl phenyl sulfide and Bouveault-Blanc reduction.

Alisiaquinones and alisiaquinol, dual inhibitors of Plasmodium falciparum enzyme targets from a New Caledonian deep water sponge.

PubMed

Desoubzdanne, Denis; Marcourt, Laurence; Raux, Roselyne; Chevalley, Séverine; Dorin, Dominique; Doerig, Christian; Valentin, Alexis; Ausseil, Frédéric; Debitus, Cécile

2008-07-01

Four new meroterpenes, alisiaquinones A-C (1-3) and alisiaquinol (4), were isolated from a New Caledonian deep water sponge. Their structures and relative stereochemistry were elucidated by spectroscopic data analysis. They are related to xestoquinone, but showed unusual substitution on a tetrahydrofuran junction. They displayed micromolar range activity on two enzymatic targets of importance for the control of malaria, the plasmodial kinase Pfnek-1 and a protein farnesyl transferase, as well as on different chloroquine-sensitive and -resistant strains of Plasmodium falciparum. Alisiaquinone C displayed a submicromolar activity on P. falciparum and a competitive selectivity index on the different plasmodial strains.

Asymmetric Synthesis of All the Known Phlegmarine Alkaloids

PubMed Central

Wolfe, Bradley H.; Libby, Adam H.; Al-awar, Rima S.; Foti, Christopher J.; Comins, Daniel L.

2010-01-01

The asymmetric synthesis of all four of the known natural phlegmarines and one synthetic derivative has been accomplished in 19 to 22 steps from 4-methoxy-3-(triisopropylsilyl)pyridine. Chiral N-acylpyridinium salt chemistry was used twice to set the stereocenters at the C-9 and C-2′ positions of the phlegmarine skeleton. Key reactions include the use of a mixed Grignard reagent for the second N-acylpyridinium salt addition, zinc/acetic acid reduction of a complex dihydropyridone, and a von Braun cyanogen bromide N-demethylation of a late intermediate. These syntheses confirmed the absolute stereochemistry of all the known phlegmarines. PMID:21077636

Chiral Sulfoxide-Induced Single Turn Peptide α-Helicity

PubMed Central

Zhang, Qingzhou; Jiang, Fan; Zhao, Bingchuan; Lin, Huacan; Tian, Yuan; Xie, Mingsheng; Bai, Guoyun; Gilbert, Adam M.; Goetz, Gilles H.; Liras, Spiros; Mathiowetz, Alan A.; Price, David A.; Song, Kun; Tu, Meihua; Wu, Yujie; Wang, Tao; Flanagan, Mark E.; Wu, Yun-Dong; Li, Zigang

2016-01-01

Inducing α-helicity through side-chain cross-linking is a strategy that has been pursued to improve peptide conformational rigidity and bio-availability. Here we describe the preparation of small peptides tethered to chiral sulfoxide-containing macrocyclic rings. Furthermore, a study of structure-activity relationships (SARs) disclosed properties with respect to ring size, sulfur position, oxidation state, and stereochemistry that show a propensity to induce α-helicity. Supporting data include circular dichroism spectroscopy (CD), NMR spectroscopy, and a single crystal X-ray structure for one such stabilized peptide. Finally, theoretical studies are presented to elucidate the effect of chiral sulfoxides in inducing backbone α-helicity. PMID:27934919

Vibrational Raman optical activity of ketose monosaccharides

NASA Astrophysics Data System (ADS)

Bell, Alasdair F.; Hecht, Lutz; Barron, Laurence D.

1995-07-01

The vibrational Raman optical activity (ROA) spectra of the four ketose sugars D-fructose, L-sorbose, D-tagatose and D-psicose in aqueous solution, which have been measured in backscattering in the range ≈250-1500 cm -1, are reported. These results are combined with those from a previous ROA study of aldose and pentose sugars in an attempt to establish new vibrational assignments and to verify old ones. The high information content of these spectra provides a new perspective on all the central features of monosaccharide stereochemistry including dominant anomeric configuration, ring conformation, exocyclic CH 2OH group conformation and relative disposition of the hydroxyl groups around the ring.

Mechanism and Stereochemistry of 5-Dehydroquinate Synthetase*

PubMed Central

Rotenberg, S. L.; Sprinson, D. B.

1970-01-01

3-Deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) labeled at C-7 randomly or stereospecifically with tritium and at C-1 with 14C was converted enzymically to 5-dehydroquinate. Tritium of all three substrates was completely retained in 5-dehydroquinate, in accord with formation of a non-ketonizing 6,7-enol intermediate. The 5-dehydroquinates were dehydrated to 5-dehydroshikimate by 5-dehydroquinate dehydratase, which is known to catalyze a cis-elimination. Only 5-dehydroquinate derived from [7-3H](7R)-DAHP lost its tritium in this dehydration, indicating that the configuration at C-7 was inverted in the conversion of DAHP to 5-dehydroquinate. PMID:5275368

Cytotoxic and antibacterial dihydrochalcones from Piper aduncum.

PubMed

Orjala, J; Wright, A D; Behrends, H; Folkers, G; Sticher, O; Rüegger, H; Rali, T

1994-01-01

Bioactivity-guided fractionation of a CH2Cl2 extract from the leaves of Piper aduncum afforded three new dihydrochalcones, piperaduncins A [3], B [4], and C [5], as well as two known dihydrochalcones, 2',6'-dihydroxy-4'-methoxydihydrochalcone [1] and 2',6',4-trihydroxy-4'-methoxydihydrochalcone [2] (asebogenin), together with sakuranetin, anodendroic acid methyl ester, and the carotenoid lutein. The structures of the isolates were elucidated by spectroscopic methods, mainly 1D- and 2D nmr spectroscopy. The proposed stereochemistry for compound 4 was deduced by NOESY spectroscopy and the corresponding energy minimum was established by molecular modelling calculations and translated into a 3D structure.

Biotransformation of tissue-specific hormone tibolone with fungal culture Trichothecium roseum

NASA Astrophysics Data System (ADS)

Shah, Syed Adnan Ali; Sultan, Sadia; Zaimi bin Mohd Noor, M.

2013-06-01

Whole cells based biotransformation is an important tool for bioconversion of steroids. It can be used to synthesize biologically potent compounds with diverse structures. Biotransformation of tissue-specific hormone tibolone (1) with Trichothecium roseum (ATCC 13411) has being carried out for the first time. Two new and three known metabolites 2-6 were isolated from fermentation of tibolone (1) with Trichothecium roseum and their structures were characterized by 2D NMR spectroscopy and mass spectrometry. The relative stereochemistry of new metabolites 5 and 6 was deduced by 2D NOESY experiments. The effect of cultures on tibolone structural modifications and time-course studies has also been conducted.

Diastereoselective Synthesis of a Strawberry Flavoring Agent by Epoxidation of Ethyl trans-b-Methylcinnamate

NASA Astrophysics Data System (ADS)

Pageau, Gayle J.; Mabaera, Rodwell; Kosuda, Kathryn M.; Sebelius, Tamara A.; Ghaffari, Ali H.; Kearns, Kenneth A.; McIntyre, Jean P.; Beachy, Tina M.; Thamattoor, Dasan M.

2002-01-01

The diastereoselective synthesis of ethyl (E)-3-methyl-3-phenylglycidate, a strawberry flavoring agent, is carried out by epoxidizing ethyl trans-b-methylcinnamate with m-chloroperbenzoic acid. This epoxidation is appropriate for the introductory organic laboratory and augments the small number of such experiments currently available for undergraduate education. In the course of performing this exercise, students are exposed to many important facets of organic chemistry such as synthesis, reaction mechanism, stereochemistry, chromatography, quantitative analysis, spectroscopy, and computational chemistry. The 1H NMR spectrum of this compound is especially interesting and presents instructive examples of diastereotopic protons and shielding effects of the aromatic ring current.

Spectral, coordination and thermal properties of 5-arylidene thiobarbituric acids

NASA Astrophysics Data System (ADS)

Masoud, Mamdouh S.; El-Marghany, Adel; Orabi, Adel; Ali, Alaa E.; Sayed, Reham

2013-04-01

Synthesis of 5-arylidine thiobarbituric acids containing different functional groups with variable electronic characters were described and their Co2+, Ni2+ and Cu2+ complexes. The stereochemistry and mode of bonding of 5-(substituted benzylidine)-2-TBA complexes were achieved based on elemental analysis, spectral (UV-VIS, IR, 1H NMR, MS), magnetic susceptibility and conductivity measurements. The ligands were of bidentate and tridentate bonding through S, N and O of pyrimidine nucleolus. All complexes were of octahedral configuration. The thermal data of the complexes pointed to their stability. The mechanism of the thermal decomposition is discussed. The thermodynamic parameters of the dissociation steps were evaluated and discussed.

Computational predictions of stereochemistry in asymmetric thiazolium- and triazolium-catalyzed benzoin condensations.

PubMed

Dudding, Travis; Houk, Kendall N

2004-04-20

The catalytic asymmetric thiazolium- and triazolium-catalyzed benzoin condensations of aldehydes and ketones were studied with computational methods. Transition-state geometries were optimized by using Morokuma's IMOMO [integrated MO (molecular orbital) + MO method] variation of ONIOM (n-layered integrated molecular orbital method) with a combination of B3LYP/6-31G(d) and AM1 levels of theory, and final transition-state energies were computed with single-point B3LYP/6-31G(d) calculations. Correlations between experiment and theory were found, and the origins of stereoselection were identified. Thiazolium catalysts were predicted to be less selective then triazolium catalysts, a trend also found experimentally.

Synthesis, absolute configuration and antimuscarinic activity of the enantiomers of [1-(2,2-diphenyl-[1,3]dioxolan-4-yl)-ethyl]-dimethyl-amine.

PubMed

Gulini, U; Angeli, P; Marucci, G; Buccioni, M; Giardinà, D; Antolini, L; Franchini, S; Sorbi, C; Brasili, L

2001-01-22

Methylation of the carbon atom C of compound 1, a potent and not selective muscarinic antagonist, was carried out. The resulting diastereomers were separated and the corresponding racemate further resolved to give four enantiomers, which were tested both as hydrogen oxalate and methiodide salts. The pharmacological results obtained at M1, M2 and M3 muscarinic receptor subtypes, show that methylation at C1, depending on the stereochemistry, increases antagonist potency, having thus the same effect of nitrogen quaternization. These results may well lead to the development of new potent antimuscarinic drugs lacking a cationic head.

On the helical arrangements of protein molecules.

PubMed

Dauter, Zbigniew; Jaskolski, Mariusz

2018-03-01

Helical structures are prevalent in biology. In the PDB, there are many examples where protein molecules are helically arranged, not only according to strict crystallographic screw axes but also according to approximate noncrystallographic screws. The preponderance of such screws is rather striking as helical arrangements in crystals must preserve an integer number of subunits per turn, while intuition and simple packing arguments would seem to favor fractional helices. The article provides insights into such questions, based on stereochemistry, trigonometry, and topology, and illustrates the findings with concrete PDB structures. Updated statistics of Sohncke space groups in the PDB are also presented. © 2017 The Protein Society.

Ammonificins C and D, Hydroxyethylamine Chromene Derivatives from a Cultured Marine Hydrothermal Vent Bacterium, Thermovibrio ammonificans

PubMed Central

Andrianasolo, Eric H.; Haramaty, Liti; Rosario-Passapera, Richard; Vetriani, Costantino; Falkowski, Paul; White, Eileen; Lutz, Richard

2012-01-01

Chemical and biological investigation of the cultured marine hydrothermal vent bacterium, Thermovibrio ammonifican led to the isolation of two hydroxyethylamine chromene derivatives, ammonificins C and D. Their structures were elucidated using combination of NMR and mass spectrometry. Absolute stereochemistry was ascertained by comparison of experimental and calculated CD spectra. Biological evaluation and assessment were determined using the patented ApopScreen cell-based screen for apoptosis-induction. Ammonificins C and D induce apoptosis in micromolar concentrations. To our knowledge, this finding is the first report of chemical compounds that induce apoptosis from the cultured deep-sea marine organism, hydrothermal vent bacterium, Thermovibrio ammonificans. PMID:23170085

seco-iridoids from Calycophyllum spruceanum (Rubiaceae).

PubMed

Cardona Zuleta, Luz Margarita; Cavalheiro, Alberto José; Siqueira Silva, Dulce Helena; Furlan, Maysa; Marx Young, Maria Claudia; Albuquerque, Sérgio; Castro-Gamboa, Ian; da Silva Bolzani, Vanderlan

2003-09-01

Three seco-iridoids 7-methoxydiderroside, 6'-O-acetyldiderroside and 8-O-tigloyldiderroside, were isolated from the wood bark of Calycophyllum spruceanum together with the known iridoids loganetin, loganin and the seco-iridoids secoxyloganin, kingiside and diderroside. Their structures were elucidated by means of NMR and MS spectral data analysis. Using NOE correlations and coupling constants, the relative stereochemistry of the new derivatives was established. 7-Methoxydiderroside, 6'-O-acetyldiderroside and the known secoxyloganin and diderroside showed in vitro activity against trypomastigote forms of Trypanosoma cruzi, with IC(50) values of 59.0, 90.2, 74,2 and 84.9 microg/mL, respectively and were compared to the standard gentian violet (IC(50) 7.5 microg/ml).

Semi-Microscale Williamson Ether Synthesis and Simultaneous Isolation of an Expectorant from Cough Tablets

NASA Astrophysics Data System (ADS)

Stabile, Ryan G.; Dicks, Andrew P.

2003-03-01

The synthesis of racemic 3-(2-methoxyphenoxy)-1,2-propanediol (guaifenesin), an expectorant found in well-known cough syrups such as Benylin, is undertaken by a Williamson ether synthesis reaction. The same compound is simultaneously isolated and characterized from commercially available Guai-Aid cough tablets. The experiment is well-suited towards the introductory part of an advanced organic laboratory course and complements typical lecture topics in a stimulating manner. Consideration is given towards reaction mechanisms, stereochemistry, optical activity, pharmaceutical synthesis, and spectroscopic analysis. Discussion of the merits or disadvantages of marketing a drug as a racemic mixture, with reference to the notorious thalidomide case study, and the concept of enantioselective synthesis is possible.

Elucidation of the absolute configuration of rhizopine by chiral supercritical fluid chromatography and vibrational circular dichroism.

PubMed

Krief, Alain; Dunkle, Melissa; Bahar, Masoud; Bultinck, Patrick; Herrebout, Wouter; Sandra, Pat

2015-07-01

The absolute configuration of rhizopine, an opine-like natural product present in nitrogen-fixing nodules of alfalfa infected by rhizobia, is elucidated using a combination of state-of-the-art analytical and semi-preparative supercritical fluid chromatography and vibrational circular dichroism spectroscopy. A synthetic peracetylated racemate was fractionated into its enantiomers and subjected to absolute configuration analysis revealing that natural rhizopine exists as a single enantiomer. The stereochemistry of non-derivatized natural rhizopine corresponds to (1R,2S,3R,4R,5S,6R)-4-amino-6-methoxycyclohexane-1,2,3,5-tetraol. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Isocoumarin Derivatives from the Sea Squirt-derived Fungus Penicillium stoloniferum QY2-10 and the Halotolerant Fungus Penicillium notatum B-52.

PubMed

Xin, Zhi-Hong; Tian, Li; Zhu, Tian-Jiao; Wang, Wen-Liang; Du, Lin; Fang, Yu-Chun; Gu, Qian-Qun; Zhu, Wei-Ming

2007-07-01

Two isocoumarin derivatives, stoloniferol A (1) and B (2), a known 5alpha, 8alpha-epidioxy-23-methyl-(22E, 24R)-ergosta-6, 22-dien-3beta-ol (3), and a known dihydrocitrinone (4) were isolated from the ethyl acetate extract of the sea squirt-derived fungus, Penicillium stoloniferum QY2-10, and a halophilic fungus, Penicillium notatum B-52, respectively. Their structures were elucidated by spectroscopic methods and optical rotation. The stereochemistry of 2 was determined on the basis of different NOE experiments and chemical transformation. Compound 3 showed cytotoxicity against P388 cells, with an IC50 value of 4.07 microM.

Mucor hiemalis mediated 14α-hydroxylation on steroids: in vivo and in vitro investigations of 14α-hydroxylase activity.

PubMed

Kolet, Swati P; Haldar, Saikat; Niloferjahan, Siddiqui; Thulasiram, Hirekodathakallu V

2014-07-01

Transformation of testosterone and progesterone into synthetically challenging 14α-hydroxy derivatives was achieved by using fungal strain Mucor hiemalis. Prolonged incubation led to the formation of corresponding 6β/7α,14α-dihydroxy metabolites. The position and stereochemistry of newly introduced hydroxyl group was determined by detailed spectroscopic analyses. The time course experiment indicated that fungal strain initiated transformation by hydroxylation at 14α-position followed by at 6β- or 7α-positions. Studies using cell-free extracts suggest that the 14α-hydroxylase activity is NADPH dependent and belongs to the cytochrome P450 family. Copyright © 2014 Elsevier Inc. All rights reserved.

Rauvolfianine, a new antimycobacterial glyceroglycolipid and other constituents from Rauvolfia caffra. Sond (Apocynaceae).

PubMed

Ebeh Messanga, Robert; Dominique Serge, Ngono Bikobo; Abouem A Zintchem, Auguste; Norbert, Mbabi Nyemeck Ii; Esther Del Florence, Moni Ndedi; Patrick Hervé, Betote Diboué; Maximilienne Ascension, Nyegue; Alex De Théodore, Atchadé; Dieudonné Emmanuel, Pegnyemb; Christian G, Bochet; Koert, Ulrich

2017-08-16

The chemical investigation of the extract of the dried leaves of Rauvolfia caffra (Sond) (synonym Rauvolfia macrophylla) (Apocynaceae) led to isolation of a new glycoside derivative, rauvolfianine (1) as well as six known compounds: oleanolic acid (2), sitosterol-3-O-β-D-glucopyranoside (3), betulinic acid (4), vellosimine (5), sarpagine (6) and D-fructofuranosyl-β-(2→1)-α-D-glucopyranoside (7). Compounds 1, 2, 3, 4 and 7 were evaluated for antitubercular activity. Compounds 1 and 2 were the most active (MIC = 7.8125 and 31.25 μg/mL) towards the Isoniazid resistant strain of Mycobacterium tuberculosis AC45. Their structures and relative stereochemistry were elucidated by spectroscopic methods.

First application of an efficient and versatile ligand for copper-catalyzed cross-coupling reactions of vinyl halides with N-heterocycles and phenols.

PubMed

Kabir, M Shahjahan; Lorenz, Michael; Namjoshi, Ojas A; Cook, James M

2010-02-05

2-Pyridin-2-yl-1H-benzoimidazole L3 is presented as a new, efficient, and versatile bidentate N-donor ligand suitable for the copper-catalyzed formation of vinyl C-N and C-O bonds. This inexpensive and easily prepared ligand facilitates copper-catalyzed cross-coupling reactions of alkenyl bromides and iodides with N-heterocycles and phenols to afford the desired cross-coupled products in good to excellent yields with full retention of stereochemistry. This method is particularly noteworthy given its efficiency, that is, mild reaction conditions, low catalyst loading, simplicity, versatility, and exceptional level of functional group tolerance.

First Application of An Efficient and Versatile Ligand for Copper-Catalyzed Cross-Coupling Reactions of Vinyl Halides with N-Heterocycles and Phenols

PubMed Central

Kabir, M. Shahjahan; Lorenz, Michael; Namjoshi, Ojas A.; Cook, James M.

2010-01-01

2-Pyridin-2-yl-1H-benzoimidazole L3 is presented as a new, efficient, and versatile bidentate N-donor ligand suitable for the copper-catalyzed formation of vinyl C-N and C-O bonds. This inexpensive and easily prepared ligand facilitates copper-catalyzed cross-coupling reactions of alkenyl bromides and iodides with N-heterocycles and phenols to afford the desired cross-coupled products in good to excellent yields with full retention of stereochemistry. This method is particularly noteworthy given its efficiency i.e., mild reaction conditions, low catalyst loading, simplicity, versatility, and exceptional level of functional group tolerance. PMID:20039699

Self-assembled three-dimensional chiral colloidal architecture.

PubMed

Ben Zion, Matan Yah; He, Xiaojin; Maass, Corinna C; Sha, Ruojie; Seeman, Nadrian C; Chaikin, Paul M

2017-11-03

Although stereochemistry has been a central focus of the molecular sciences since Pasteur, its province has previously been restricted to the nanometric scale. We have programmed the self-assembly of micron-sized colloidal clusters with structural information stemming from a nanometric arrangement. This was done by combining DNA nanotechnology with colloidal science. Using the functional flexibility of DNA origami in conjunction with the structural rigidity of colloidal particles, we demonstrate the parallel self-assembly of three-dimensional microconstructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Two new bioactive monotetrahydrofuran Annonaceous acetogenins from the bark of Xylopia aromatica.

PubMed

Colman-Saizarbitoria, T; Gu, Z M; McLaughlin, J L

1994-12-01

Xylopien [1] and xylomatenin [2], two new bioactive monotetrahydrofuran Annonaceous acetogenins, have been isolated from an EtOH extract of the bark of Xylopia aromatica, using bioactivity-directed fractionation employing lethality to brine shrimp. These new compounds each have a double bond in the hydrocarbon chain and have been identified as C-23, C-24 dehydro analogs of xylopiacin and xylomaticin. Their structures were elucidated by spectral analyses of the parent compounds and/or simple chemical derivatives. Their absolute stereochemistries have been established by 1H- and 2D nmr experiments utilizing the production of Mosher esters. These acetogenins showed cytotoxic potencies superior to adriamycin against three human solid tumor cell lines.

Straightforward synthesis of non-natural L-chalcogen and L-diselenide N-Boc-protected-γ-amino acid derivatives.

PubMed

Kawasoko, Cristiane Y; Foletto, Patricia; Rodrigues, Oscar E D; Dornelles, Luciano; Schwab, Ricardo S; Braga, Antonio L

2013-08-21

The synthesis of new chiral seleno-, telluro-, and thio-N-Boc-γ-amino acids is described herein. These new compounds were prepared through a simple and short synthetic route, from the inexpensive and commercially-available amino acid L-glutamic acid. The products, with a highly modular character, were obtained in good to excellent yields, via hydrolysis of chalcogen pyroglutamic derivatives with overall retention of the L-glutamic acid stereochemistry. Also, an L-diselenide-N-Boc-γ-amino acid was prepared in good yield. This new synthetic route represents an efficient method for preparing new L-chalcogen- and L-diselenide-γ-amino acids with biological potential.

A New Aggreceride analogue and a peltogynoid isolated from the stem bark of Entada abyssinica (Fabaceae).

PubMed

Melong, Raduis; Kapche, Deccaux G F W; Feussia, Michel T; Laatsch, Hartmut

2014-10-01

A new monoglyceride, l',26'-bis-[(S)-2,3-dihydroxypropyl] hexacosanedioate (1a) and the new peltogynoid, entadanin (3), along with eight known compounds, were isolated from the stem bark of Entada abyssinica (Fabaceae). The structures of the new compounds were determined by detailed analyses of 1D and 2D NMR spectra, in combination with high-resolution mass spectrometry data, and by comparison with related data from the literature. The stereochemistry of la was derived by comparison of the optical rotation with reference data. Peltogynoids have been reported previously from other Fabaceae, however this is the first report ofa peltogynoid from the genus Entada.

The influence of sulfur configuration in 1 H NMR chemical shifts of diasteromeric five-membered cyclic sulfites.

PubMed

Obregón-Mendoza, Marco A; Sánchez-Castellanos, Mariano; Cuevas, Gabriel; Gnecco, Dino; Cassani, Julia; Poveda-Jaramillo, Juan C; Reynolds, William F; Enríquez, Raúl G

2017-03-01

The effect of the stereochemistry of the sulfur atom on 1 H chemical shifts of the diasteromeric pair of cyclic sulfites of 4-[methoxy(4-nitrophenyl)methyl]-5-phenyl-1,3,2-dioxathiolan-2-oxide was investigated. The complete 1 H and 13 C NMR spectral assignment was achieved by the use of one-dimensional and two-dimensional NMR techniques in combination with X-ray data. A correlation of experimental data with theoretical calculations of chemical shift tensors using density functional theory and topological theory of atoms in molecules was made. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Three New Highly Oxygenated Germacranolides from Carpesium Divaricatum and Their Cytotoxic Activity.

PubMed

Zhang, Tao; Si, Jin-Guang; Zhang, Qiu-Bo; Chen, Jia-Huan; Ding, Gang; Zhang, Hong-Wu; Jia, Hong-Mei; Zou, Zhong-Mei

2018-05-03

Three new highly oxygenated ( 2 ⁻ 4 ), and two known ( 1 and 5 ) germacranolides, were isolated from the whole plant of Carpesium divaricatum . The planar structures and relative configurations of the new compounds were determined by detailed spectroscopic analysis. The absolute configuration of 1 was established using the circular dichroism (CD) method and X-ray diffraction, and the stereochemistry of the new compounds 2 ⁻ 4 were determined using similar CD spectra with 1 . The new compound 2 and the known compound 5 exhibited potent cytotoxicity against hepatocellular cancer (Hep G2) and human cervical cancer (HeLa) cells, superior to those of the positive control cis -platin.

Computational predictions of stereochemistry in asymmetric thiazolium- and triazolium-catalyzed benzoin condensations

PubMed Central

Dudding, Travis; Houk, Kendall N.

2004-01-01

The catalytic asymmetric thiazolium- and triazolium-catalyzed benzoin condensations of aldehydes and ketones were studied with computational methods. Transition-state geometries were optimized by using Morokuma's IMOMO [integrated MO (molecular orbital) + MO method] variation of ONIOM (n-layered integrated molecular orbital method) with a combination of B3LYP/6–31G(d) and AM1 levels of theory, and final transition-state energies were computed with single-point B3LYP/6–31G(d) calculations. Correlations between experiment and theory were found, and the origins of stereoselection were identified. Thiazolium catalysts were predicted to be less selective then triazolium catalysts, a trend also found experimentally. PMID:15079058

Synthesis and pharmacological evaluation of the individual stereoisomers of 3-[methyl(1,2,3,4-tetrahydro-2-naphthalenyl)amino]-1-indanone, a potent mast cell stabilising agent.

PubMed

Byrne, Adam J; Barlow, James W; Walsh, John J

2011-02-15

Each stereoisomer of 3-[methyl(1,2,3,4-tetrahydro-2-naphthalenyl)amino]-1-indanone, 1a-d, was prepared and evaluated in vitro for its ability to prevent mediator release induced by different degranulating agents from rodent mast cells and also in vivo against passive cutaneous anaphylaxis. The manner in which the stereoisomers prevented direct membrane activation was found to be highly dependent on the stereochemistry of the individual isomers. Stereoisomer 1b was the most active isomer in vivo, exhibiting superior activity to disodium cromoglycate. Copyright © 2010 Elsevier Ltd. All rights reserved.

A novel alkaloid isolated from Crotalaria paulina and identified by NMR and DFT calculations

NASA Astrophysics Data System (ADS)

Oliveira, Ramon Prata; Demuner, Antonio Jacinto; Alvarenga, Elson Santiago; Barbosa, Luiz Claudio Almeida; de Melo Silva, Thiago

2018-01-01

Pyrrolizidine alkaloids (PAs) are secondary metabolites found in Crotalaria genus and are known to have several biological activities. A novel macrocycle bislactone alkaloid, coined ethylcrotaline, was isolated and purified from the aerial parts of Crotalaria paulina. The novel macrocycle was identified with the aid of high resolution mass spectrometry and advanced nuclear magnetic resonance techniques. The relative stereochemistry of the alkaloid was defined by comparing the calculated quantum mechanical hydrogen and carbon chemical shifts of eight candidate structures with the experimental NMR data. The best fit between the eight candidate structures and the experimental NMR chemical shifts was defined by the DP4 statistical analyses and the Mean Absolute Error (MAE) calculations.

Thermodynamics of alpha-Cyclodextrin-p-Nitrophenyl Glycoside Complexes. A Simple System To Understand the Energetics of Carbohydrate Interactions in Water.

PubMed

Junquera, Elena; Laynez, José; Menéndez, Margarita; Sharma, Sunil; Penadés, Soledad

1996-10-04

Thermodynamic studies of the binding of a series of p-nitrophenyl glycosides (PNPGly) of varying stereochemistry to alpha-cyclodextrin (alpha-CD) were performed at three different temperatures (25, 35, and 42 degrees C) using a microcalorimetric technique. The system p-nitrophenol (PNP) at pH = 3 and alpha-CD was also studied for the sake of comparison. All these complexes were found to be enthalpy driven with a favorable enthalpic term clearly dominant over an unfavorable entropic term. A clear enthalpy-entropy compensation effect was observed at all the temperatures, with a slope close to unity (alpha = 1.02) and an intercept TDeltaS degrees (o) = 2.91 kcal mol(-)(1). This thermodynamic pattern is in agreement with those usually found for lectin-carbohydrate associations and for the binding processes of several host-guest systems. This pattern is explained in terms of the contribution of primarily two driving forces: the van der Waals interactions between the host and the guest, and the solvation/desolvation processes which accompany the association reaction. The presence of the carbohydrate molecule in the PNP ring causes a slight destabilization of the complex at 25 degrees C with respect to the alpha-CD-PNP (pH = 3) complex, although a different behavior has been observed depending on the axial/equatorial configuration of the glycoside and the temperature. This behavior is modulated by the stereochemistry of the glycoside. Differences were observed between the deoxy-derivatives (LAra and LFuc) and those derivatives with a hydroxymethyl group (Glc, Gal, Man). DeltaC(p) degrees values were obtained from the dependency of DeltaH degrees on temperature (=( partial differentialDeltaH degrees / partial differentialT)(p)). These values are small and negative except for alphaMan complex. For the latter complex, discrepancy between the calorimetric and the calculated van't Hoff enthalpies was observed. Parallels are drawn between the thermodynamics of our model and those proposed for carbohydrate-protein associations.

Low-spin manganese(II) and high-spin manganese(III) complexes derived from disalicylaldehyde oxaloyldihydrazone: Synthesis, spectral characterization and electrochemical studies

NASA Astrophysics Data System (ADS)

Syiemlieh, Ibanphylla; Kumar, Arvind; Kurbah, Sunshine D.; De, Arjune K.; Lal, Ram A.

2018-01-01

Low-spin manganese(II) complexes [MnII(H2slox)].H2O (1), [MnII(H2slox)(SL)] (where SL (secondary ligand) = pyridine (py, 2), 2-picoline (2-pic, 3), 3-picoline (3-pic, 4), and 4-picoline (4-pic, 5) and high-spin manganese(III) complex Na(H2O)4[MnIII(slox)(H2O)2].2.5H2O have been synthesized from disalicyaldehyde oxaloyldihydrazone in methanolic - water medium. The composition of complexes has been established by elemental analyses and thermoanalytical data. The structures of the complexes have been discussed on the basis of data obtained from molar conductance, UV visible, 1H NMR, infrared spectra, magnetic moment and electron paramagnetic resonance spectroscopic studies. Conductivity measurements in DMF suggest that the complexes (1-5) are non-electrolyte while the complex (6) is 1:1 electrolyte. The electronic spectral studies and magnetic moment data suggest five - coordinate square pyramidal structure for the complexes (2-5) and square planar geometry for manganese(II) in complex (1). In complex (6), both sodium and manganese(III) have six coordinate octahedral geometry. IR spectral studies reveal that the dihydrazone coordinates to the manganese centre in keto form in complexes (1-5) and in enol form in complex (6). In all complexes, the ligand is present in anti-cis configuration. Magnetic moment and EPR studies indicate manganese in +2 oxidation state in complexes (1-5), with low-spin square planar complex (1) and square pyramidal stereochemistries complexes (2-5) while in +3 oxidation state in high-spin distorted octahedral stereochemistry in complex (6). The complex (1) involves significant metal - metal interaction in the solid state. All of the complexes show only one metal centred electron transfer reaction in DMF solution in cyclic voltammetric studies. The complexes (1-5) involve MnII→MnI redox reaction while the complex (6) involves MnIII→MnII redox reaction, respectively.

The stereochemistry of chlorophyll-c₃ from the haptophyte Emiliania huxleyi: the (13²R)-enantiomers of chlorophylls-c are exclusively selected as the photosynthetically active pigments in chromophyte algae.

PubMed

Mizoguchi, Tadashi; Kimura, Yuki; Yoshitomi, Taichi; Tamiaki, Hitoshi

2011-11-01

Chlorophyll(Chl)-c pigments in algae, diatoms and some prokaryotes are characterized by the fully conjugated porphyrin π-system as well as the acrylate residue at the 17-position. The precise structural characterization of Chl-c(3) from the haptophyte Emiliania huxleyi was performed. The conformations of the π-conjugated peripheral substituents, the 3-/8-vinyl, 7-methoxycarbonyl and 17-acrylate moieties were evaluated, in a solution, using nuclear Overhauser enhancement correlations and molecular modeling calculations. The rotation of the 17-acrylate residue was considerably restricted, whereas the other three substituents readily rotated at ambient temperature. Moreover, the stereochemistry at the 13²-position was determined by combination of chiral high-performance liquid chromatography (HPLC) with circular dichroism (CD) spectroscopy. Compared with the CD spectra of the structurally related, synthetic (13²R)- and (13²S)-protochlorophyllide(PChlide)-a, naturally occurring Chl-c₃ had exclusively the (13²R)-configuration. To elucidate this natural selection of a single enantiomer, we analyzed the three major Chl-c pigments (Chl-c₁, c₂ and c₃) in four phylogenetically distinct classes of Chl-c containing algae, i.e., heterokontophyta, dinophyta, cryptophyta and haptophyta using chiral HPLC. All the photosynthetic organisms contained only the (13²R)-enantiomerically pure Chls-c, and lacked the corresponding enantiomeric (13²S)-forms. Additionally, Chl-c₂ was found in all the organisms as the common Chl-c. These results throw a light on the biosynthesis as well as photosynthetic function of Chl-c pigments: Chl-c₂ is derived from 8-vinyl-PChlide-a by dehydrogenation of the 17-propionate to acrylate residues as generally proposed, and the (13²R)-enantiomers of Chls-c function as photosynthetically active, light-harvesting pigments together with the principal Chl-a and carotenoids. 2011 Elsevier B.V. All rights reserved.

A Facile One-Pot Construction of Succinimide-Fused Spiro[Pyrrolidine-2,3'-Oxindoles] via 1,3-Dipolar Cycloaddition Involving 3-Amino Oxindoles and Maleimides.

PubMed

Jin, Lunqiang; Liang, Feng

2018-03-05

Increasing interests have been invested in the development of synthetic strategies toward the construction of spiro[pyrrolidine-2,3'-oxindole], which is the core structural skeleton in some compounds with diverse biological activities. In this work, an efficient diastereoselective 1,3-dipolar cycloaddition reaction of azomethine ylides generated in situ from 3-amino oxindoles and aldehydes with maleimides has been described. The protocol provides a facile and efficient access to structurally diverse succinimide-fused spiro[pyrrolidine-2,3'-oxindole] compounds in good to high yields (up to 93%) with moderate to excellent diastereoselectivities (up to >95:5). The relative stereochemistry of cycloaddition products has been assigned by X-ray diffraction analysis.

Four new cytotoxic tetrahydrofuranoid lignans from Sinopodophyllum emodi.

PubMed

Sun, Yan-Jun; Li, Zhan-Lin; Chen, Hong; Liu, Xiao-Qiu; Zhou, Wei; Hua, Hui-Ming

2012-03-01

Four new tetrahydrofuranoid lignans, (-)-tanegool-7'-methyl ether ( 1), (+)-7'-methoxylariciresinol (2), sinolignan C (3), and epipinoresinol-4,4'-di- O- β- D-glucopyranoside (4), were isolated from the roots and rhizomes of SINOPODOPHYLLUM EMODI together with one known lignan (5). Their structures and stereochemistry were elucidated on the basis of spectroscopic and mass spectrometric evidence. The isolation of compounds 1- 5 represents the first report of tetrahydrofuran lignans from the genus SINOPODOPHYLLUM. The cytotoxic activities of all isolated compounds were evaluated against HeLa and KB cell lines, and compound 1 showed the most potent cytotoxicity with IC₅₀ values of 9.7 µM and 4.7 µM, respectively. © Georg Thieme Verlag KG Stuttgart · New York.

Saccharin Aza Bioisosteres-Synthesis and Preclinical Property Comparisons.

PubMed

Chen, Yantao; Aurell, Carl-Johan; Pettersen, Anna; Lewis, Richard J; Hayes, Martin A; Lepistö, Matti; Jonson, Anna C; Leek, Hanna; Thunberg, Linda

2017-06-08

Saccharin is a well-known scaffold in drug discovery. Herein, we report the synthesis and preclinical property comparisons of three bioisosteres of saccharin: aza-pseudosaccharins (cluster B ), and two new types of aza-saccharins (clusters C and D ). We demonstrate a convenient protocol to selectively synthesize products in cluster C or D when primary amines are used. Preclinical characterization of selected matched-pair products is reported. Through comparison of two diastereomers, we highlight how stereochemistry affects the preclinical properties. Given that saccharin-based derivatives are widely used in many chemistry fields, we foresee that structures exemplified by clusters C and D offer new opportunities for novel drug design, creating a chiral center on the sulfur atom and the option of substitution at two different nitrogens.

Enantioselective photochemistry via Lewis acid catalyzed triplet energy transfer

PubMed Central

Blum, Travis R.; Miller, Zachary D.; Bates, Desiree M.; Guzei, Ilia A.; Yoon, Tehshik P.

2017-01-01

Relatively few catalytic systems are able to control the stereochemistry of electronically excited organic intermediates. Here we report the discovery that a chiral Lewis acid complex can catalyze triplet energy transfer from an electronically excited photosensitizer. This strategy is applied to asymmetric [2+2] photocycloadditions of 2′-hydroxychalcones using tris(bipyridyl) ruthenium(II) as a sensitizer. A variety of electrochemical, computational, and spectroscopic data rule out substrate activation via photoinduced electron transfer and instead support a mechanism in which Lewis acid coordination dramatically lowers the triplet energy of the chalcone substrate. We expect that this approach will enable chemists to more broadly apply their detailed understanding of chiral Lewis acid catalysis to stereocontrol in reactions of electronically excited states. PMID:27980203

A new approach to the side chain formation of 24-alkyl-22-hydroxy steroids: application to the preparation of early brassinolide biosynthetic precursors.

PubMed

Hurski, Alaksiej L; Zhabinskii, Vladimir N; Khripach, Vladimir A

2012-06-01

A new synthetic route to 22S-hydroxy-24R-methyl steroids has been developed and applied for the preparation of cathasterone, (22S)-hydroxycampesterol, and 6-deoxocathasterone, which are precursors in the early stages of the biosynthesis of brassinolide. The construction of the steroid side chain with the correct stereochemistry at C-24 is based on the use of Claisen rearrangement. The introduction of the 22-hydroxyl group has been achieved by epoxidation of the Δ(22)-double bond, nucleophilic opening of the intermediate mesyl epoxide with sodium sulfide, and desulfurization of the formed tetrahydrothiophenes with Raney nickel. Copyright © 2012 Elsevier Inc. All rights reserved.

Enantioselective Synthesis of All-Carbon Quaternary Centers Structurally Related to Amaryllidaceae Alkaloids.

PubMed

Mikušek, Jiří; Jansa, Petr; Jagtap, Pratap R; Vašíček, Tomáš; Císařová, Ivana; Matoušová, Eliška

2018-05-18

Enantioselective synthesis of all-carbon quaternary centers remains a considerable challenge for synthetic organic chemists. Here, we report a two-step protocol to synthesize such centers including tandem cyclization/Suzuki cross-coupling followed by halocarbocyclization. During this process, two rings, three new C-C bonds and a stereochemically defined all-carbon quaternary center are formed. The absolute configuration of this center is controlled by the stereochemistry of the adjacent stereocenter, which derives from an appropriate enantioenriched starting material. Using this method, we synthesized polycyclic compounds structurally similar to Amaryllidaceae alkaloids in high enantiomeric excesses. Because these products resemble naturally occurring compounds, our protocol can be used to synthesize various potentially bioactive compounds. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lanthanide tris(β-diketonates) as useful probes for chirality determination of biological amino alcohols in vibrational circular dichroism: ligand to ligand chirality transfer in lanthanide coordination sphere.

PubMed

Miyake, Hiroyuki; Terada, Keiko; Tsukube, Hiroshi

2014-06-01

A series of lanthanide tris(β-diketonates) functioned as useful chirality probes in the vibrational circular dichroism (VCD) characterization of biological amino alcohols. Various chiral amino alcohols induced intense VCD signals upon ternary complexation with racemic lanthanide tris(β-diketonates). The VCD signals observed around 1500 cm(-1) (β-diketonate IR absorption region) correlated well with the stereochemistry and enantiomeric purity of the targeted amino alcohol, while the corresponding monoalcohol, monoamine, and diol substrates induced very weak VCD signals. The high-coordination number and dynamic property of the lanthanide complex offer an effective chirality VCD probing of biological substrates. © 2014 Wiley Periodicals, Inc.

Synthesis of amino acid conjugates to 2-imino-3-methylene-5-carboxypyrrolidine and 2-imino-3-methylene-6-carboxypiperidine.

PubMed

Mitchell, Robin E

2010-03-15

The four stereomers of 2-imino-3-methylene-5-L(carboxy-L-valyl)pyrrolidine, a bacterial metabolite that is inhibitory to the fire blight bacterium Erwinia amylovora, were synthesised and compared for antibacterial activity. Several alternative amino acid conjugates with L,L-stereochemistry were also prepared, and the synthesis was extended to 3-methylenepiperidine-6-L-carboxylic acid and a selection of 2-imino-3-methylenepiperidine-6-L-carboxy-L-amino acid conjugates. All synthetic amino acid conjugates (L,L-stereomers) were inhibitory to the growth of E. amylovora. The likely participation of the conjugated iminomethylene moiety as a Michael acceptor is implicated. Copyright 2010 Elsevier Ltd. All rights reserved.

Stereocontrolled dopamine receptor binding and subtype selectivity of clebopride analogues synthesized from aspartic acid.

PubMed

Einsiedel, Jürgen; Weber, Klaus; Thomas, Christoph; Lehmann, Thomas; Hübner, Harald; Gmeiner, Peter

2003-10-06

Employing the achiral 4-aminopiperidine derivative clebopride as a lead compound, chiral analogues were developed displaying dopamine receptor binding profiles that proved to be strongly dependent on the stereochemistry. Compared to the D1 receptor, the test compounds showed high selectivity for the D2-like subtypes including D2(long), D2(short), D3 and D4. The highest D4 and D3 affinities were observed for the cis-3-amino-4-methylpyrrolidines 3e and the enantiomer ent3e resulting in K(i) values of 0.23 and 1.8 nM, respectively. The benzamides of type 3 and 5 were synthesized in enantiopure form starting from (S)-aspartic acid and its unnatural optical antipode.

Isolation and anti-hepatitis B virus activity of dibenzocyclooctadiene lignans from the fruits of Schisandra chinensis.

PubMed

Xue, Yongbo; Li, Xifeng; Du, Xue; Li, Xiaonian; Wang, Weiguang; Yang, Jianhong; Chen, Jijun; Pu, Jianxin; Sun, Handong

2015-08-01

Seven lignans with a dibenzocyclooctadiene skeleton, termed schinlignans A-G, and a 6,7-seco-homolignan, schischinone, together with seven known lignans, were isolated from the fruits of Schisandra chinensis (Turcz.) Baill. Their structures were elucidated by extensive spectroscopic methods, including HRESIMS, IR, UV, and 2D NMR (COSY, HMQC, COSY, and HMBC experiments). The stereochemistry at the chiral centers and the biphenyl moiety, were determined using ROESY, as well as via interpretation of their ECD spectra. Schinlignan G and methylgomisin O exhibited potent anti-hepatitis B virus activity against HBV DNA replication with IC50 values of 5.13 and 5.49μgmL(-1), respectively. Copyright © 2015 Elsevier Ltd. All rights reserved.

Insight into the stereospecificity of short-chain thermus thermophilus alcohol dehydrogenase showing pro-S hydride transfer and prelog enantioselectivity.

PubMed

Pennacchio, Angela; Giordano, Assunta; Esposito, Luciana; Langella, Emma; Rossi, Mosè; Raia, Carlo A

2010-04-01

The stereochemistry of the hydride transfer in reactions catalyzed by NAD(H)-dependent alcohol dehydrogenase from Thermus thermophilus HB27 was determined by means of (1)H-NMR spectroscopy. The enzyme transfers the pro-S hydrogen of [4R-(2)H]NADH and exhibits Prelog specificity. Enzyme-substrate docking calculations provided structural details about the enantioselectivity of this thermophilic enzyme. These results give additional insights into the diverse active site architectures of the largely versatile short-chain dehydrogenase superfamily enzymes. A feasible protocol for the synthesis of [4R-(2)H]NADH with high yield was also set up by enzymatic oxidation of 2-propanol-d(8) catalyzed by Bacillus stearothermophilus alcohol dehydrogenase.

NMR and X-ray structural characterization and conformational aspects of fluorinated (5Z)-3-benzil-5-arylidenofuran-2(5H)-ones

NASA Astrophysics Data System (ADS)

Teixeira, R. R.; Barbosa, L. C. A.; Kabeshov, M. A.; Maltha, C. R. A.; Corrêa, R. S.; Doriguetto, A. C.

2014-10-01

Herein we describe structural insights of (5Z)-3-benzyl-5-(2-fluorobenzylidene)furan-2(5H)-one (6) and (5Z)-3-benzyl-5-(pentafluorobenzylidene)furan-2(5H)-one (7), γ-alkylidenebutenolides analogues of the natural products nostoclides. Their structures were investigated by NMR spectroscopy and X-ray crystallography. The stereochemistry of the exocyclic double bond of these fluorinated compounds was determined to be Z by NMR analysis and confirmed by X-ray data. Compounds 6 and 7 crystallized in the monoclinic crystal system P21/c group. A comparison between structural features of (6) and (7) and nostoclide derivatives previously published by us is described.

Diastereoisomers of 2-benzyl-2, 3-dihydro-2-(1H-inden-2-yl)-1H-inden-1-ol: potential anti-inflammatory agents.

PubMed

Sheridan, Helen; Walsh, John J; Cogan, Carina; Jordan, Michael; McCabe, Tom; Passante, Egle; Frankish, Neil H

2009-10-15

The synthesis and biological activity of the novel diastereoisomers of 2-benzyl-2,3-dihydro-2-(1H-inden-2-yl)-1H-inden-1-ol is reported. The 2,2-coupled indane dimers were synthesised by coupling of the silyl enol ether of 1-indanone with the dimethyl ketal of 2-indanone. The coupled product was directly alkylated to give the racemic ketone which was reduced to the diastereoisomeric alcohols. The alcohols were separated and their relative stereochemistry was established by X-ray crystallography. These molecules demonstrate significant anti-inflammatory activity in vivo and in vitro and may represent a new class of anti-inflammatory agent.

The crystal structure of dihydrodipicolinate synthase from Escherichia coli with bound pyruvate and succinic acid semialdehyde: unambiguous resolution of the stereochemistry of the condensation product.

PubMed

Boughton, Berin A; Dobson, Renwick C J; Hutton, Craig A

2012-08-01

The crystal structure of Escherichia coli dihydrodipicolinate synthase with pyruvate and substrate analogue succinic acid semialdehyde condensed with the active site lysine-161 was solved to a resolution of 2.3 Å. Comparative analysis to a previously reported structure both resolves the configuration at the aldol addition center, where the final addition product clearly displays the (S)-configuration, and the final conformation of the adduct within the active site. Direct comparison to two other crystal structures found in the Protein Data Bank, 1YXC, and 3DU0, demonstrates significant similarity between the active site residues of these structures. Copyright © 2012 Wiley Periodicals, Inc.

Stereoselective Synthesis of α-Amino-C-phosphinic Acids and Derivatives.

PubMed

Viveros-Ceballos, José Luis; Ordóñez, Mario; Sayago, Francisco J; Cativiela, Carlos

2016-08-29

α-Amino-C-phosphinic acids and derivatives are an important group of compounds of synthetic and medicinal interest and particular attention has been dedicated to their stereoselective synthesis in recent years. Among these, phosphinic pseudopeptides have acquired pharmacological importance in influencing physiologic and pathologic processes, primarily acting as inhibitors for proteolytic enzymes where molecular stereochemistry has proven to be critical. This review summarizes the latest developments in the asymmetric synthesis of acyclic and phosphacyclic α-amino-C-phosphinic acids and derivatives, following in the first case an order according to the strategy used, whereas for cyclic compounds the nitrogen embedding in the heterocyclic core is considered. In addition selected examples of pharmacological implications of title compounds are also disclosed.

Investigation of Mechanistic Pathway for Trimethyl Borate Mediated Amidation of (R)-Mandelic Acid for the Synthesis of Mirabegron, an Antimuscarinic Agent.

PubMed

Deshmukh, Dattatray G; Bangal, Mukund N; Patekar, Mukunda R; Medhane, Vijay J; Mathad, Vijayavitthal Thippannachar

2018-03-01

The present work describes investigation of mechanistic pathway for trimethyl borate mediated amidation of (R)-mandelic acid (3) with 4-nitophenylethylamine (2) to provide (R)-2-hydroxy-N-[2-(4-nitrophenyl)ethyl]-2-phenylacetamide (4) during mirabegron synthesis. Plausible reaction mechanism is proposed by isolating and elucidating the active α-hydroxy ester intermediate 16 from the reaction mass. Trimethyl borate mediated approach proved to be selective in providing 4 without disturbing α-hydroxyl group and stereochemistry of the chiral center, and is also a greener, more economic and production friendly over the reported methods. The developed approach is rapid and efficient for the preparation of 4 with an overall yield of 85-87% and around 99.0% purity by HPLC at scale.

A dual-catalysis approach to enantioselective [2 + 2] photocycloadditions using visible light.

PubMed

Du, Juana; Skubi, Kazimer L; Schultz, Danielle M; Yoon, Tehshik P

2014-04-25

In contrast to the wealth of catalytic systems that are available to control the stereochemistry of thermally promoted cycloadditions, few similarly effective methods exist for the stereocontrol of photochemical cycloadditions. A major unsolved challenge in the design of enantioselective catalytic photocycloaddition reactions has been the difficulty of controlling racemic background reactions that occur by direct photoexcitation of substrates while unbound to catalyst. Here, we describe a strategy for eliminating the racemic background reaction in asymmetric [2 + 2] photocycloadditions of α,β-unsaturated ketones to the corresponding cyclobutanes by using a dual-catalyst system consisting of a visible light-absorbing transition-metal photocatalyst and a stereocontrolling Lewis acid cocatalyst. The independence of these two catalysts enables broader scope, greater stereochemical flexibility, and better efficiency than previously reported methods for enantioselective photochemical cycloadditions.

Tunneling and Parity Violation in Trisulfane (HSSSH): An Almost Ideal Molecule for Detecting Parity Violation in Chiral Molecules.

PubMed

Fábri, Csaba; Horný, Ľuboš; Quack, Martin

2015-12-01

Measuring the parity-violating energy difference Δpv E between the enantiomers of chiral molecules is a major challenge of current physical-chemical stereochemistry. An important step towards this goal is to identify suitable molecules for such experiments by means of theory. This step has been made by calculations for the complex dynamics of tunneling and electroweak quantum chemistry of parity violation in the "classic" molecule trisulfane, HSSSH, which satisfies the relevant conditions for experiments almost ideally, as the molecule is comparatively simple and parity violation clearly dominates over tunneling in the ground state. At the same time, the barrier for stereomutation is easily overcome by the S-H infrared chromophore. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.

PubMed

DiMaio, F; Chiu, W

2016-01-01

Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data. © 2016 Elsevier Inc. All rights reserved.

Erosion of stereochemical control with increasing nucleophilicity: O-glycosylation at the diffusion limit.

PubMed

Beaver, Matthew G; Woerpel, K A

2010-02-19

Nucleophilic substitution reactions of 2-deoxyglycosyl donors indicated that the reactivity of the oxygen nucleophile has a significant impact on stereoselectivity. Employing ethanol as the nucleophile resulted in a 1:1 (alpha:beta) ratio of diastereomers under S(N)1-like reaction conditions. Stereoselective formation of the 2-deoxy-alpha-O-glycoside was only observed when weaker nucleophiles, such as trifluoroethanol, were employed. The lack of stereoselectivity observed in reactions of common oxygen nucleophiles can be attributed to reaction rates of the stereochemistry-determining step that approach the diffusion limit. In this scenario, both faces of the prochiral oxocarbenium ion are subject to nucleophilic addition to afford a statistical mixture of diastereomeric products. Control experiments confirmed that all nucleophilic substitution reactions were performed under kinetic control.

Total synthesis and structural revision of the marine macrolide neopeltolide.

PubMed

Custar, Daniel W; Zabawa, Thomas P; Scheidt, Karl A

2008-01-23

The total synthesis and structural revision of the marine natural product neopeltolide is reported. The key bond-forming step involves a Lewis acid-catalyzed intramolecular cyclization to install the tetrahydropyran ring and the macrocycle simultaneously. This type of cyclization is the first of its kind and assembles the carbon backbone of the natural product efficiently. The synthesis of the reported structure revealed differences in the data between the natural and synthetic material. After significant investigation, the diastereomeric molecule with the C11 and C13 configurations inverted was synthesized using the initial route. This compound matches the data reported for neopeltolide (1H, 13C, HRMS, IR, NOESY, [alpha]), thereby establishing the correct overall structure for this potent macrolide natural product, including the relative and absolute stereochemistry.

Synthetic strategy for preparing chiral double-semicrystalline polyether block copolymers

DOE PAGES

McGrath, Alaina J.; Shi, Weichao; Rodriguez, Christina G.; ...

2014-12-11

Here, we report an effective strategy for the synthesis of semi-crystalline block copolyethers with well-defined architecture and stereochemistry. As an exemplary system, triblock copolymers containing either atactic (racemic) or isotactic ( R or S) poly(propylene oxide) end blocks with a central poly(ethylene oxide) mid-block were prepared by anionic ring-opening procedures. Stereochemical control was achieved by an initial hydrolytic kinetic resolution of racemic terminal epoxides followed by anionic ring-opening polymerization of the enantiopure monomer feedstock. The resultant triblock copolymers were highly isotactic (meso triads [ mm]% ~ 90%) with optical microscopy, differential scanning calorimetry, wide angle x-ray scattering and small anglemore » x-ray scattering being used to probe the impact of the isotacticity on the resultant polymer and hydrogel properties.« less

Stereochemical analysis of the elimination reaction catalyzed by D-amino-acid oxidase.

PubMed

Cheung, Y F; Walsh, C

1976-06-01

The stereochemistry of the intramolecular proton transfer catalyzed by the flavoenzyme, D-amino-acid oxidase, during the elimination reaction of beta-chloro-alpha-amino acid substrates (Walsh et al. (1973), J. Biol. Chem. 248, 1964) has been established. Both D-erythro- and D-threo-2-amino-3-chloro(2-3H) butyrate have been shown to yield (3R)-2-keto (3-3H)-2- butyrate predominantly. Tritium kinetic isotope effects on the rate of the reaction (4.7 for the D-erythro, and 3.8 for the D-threo compound) and percentages of intramolecular triton transfer (7.2% for the D-erythro- and 2.6% for the D-threo compound) have been measured. Their implications on the mechanism of this unusual elimination reaction are discussed.

Conformational studies of bacterial peptidoglycan: structure and stereochemistry of N-acetyl-β- D-glucosamine and N-acetyl-β- D-muramic acid

NASA Astrophysics Data System (ADS)

Yadav, P. N. S.; Rai, D. K.; Yadav, J. S.

1989-03-01

The energies of various conformations of N-acetyl-β- D-glucosamine (NAG) and its 3-O- D-lactic acid derivative N-acetyl-β- D-muramic acid (NAM) have been calculated by geometry optimization using the molecular mechanics program MM2. The geometries of these systems have been analyzed in the light of ring torsion, bond lengths, bond angles and conformational states of side groups of the pyranosyl ring and compared with available experimental data of similar pyranose derivatives. The present study indicates the presence of hydrogen bonds to stabilize the side group conformations. Discrepancies with experimental data that are seen in a few cases are ascribed to the nature of the side groups and their geometry.

Investigating the nature of palladium chain-walking in the enantioselective redox-relay Heck reaction of alkenyl alcohols.

PubMed

Hilton, Margaret J; Xu, Li-Ping; Norrby, Per-Ola; Wu, Yun-Dong; Wiest, Olaf; Sigman, Matthew S

2014-12-19

The mechanism of the redox-relay Heck reaction was investigated using deuterium-labeled substrates. Results support a pathway through a low energy palladium-alkyl intermediate that immediately precedes product formation, ruling out a tautomerization mechanism. DFT calculations of the relevant transition structures at the M06/LAN2DZ+f/6-31+G* level of theory show that the former pathway is favored by 5.8 kcal/mol. Palladium chain-walking toward the alcohol, following successive β-hydride eliminations and migratory insertions, is also supported in this study. The stereochemistry of deuterium labels is determined, lending support that the catalyst remains bound to the substrate during the relay process and that both cis- and trans-alkenes form from β-hydride elimination.

Ames interactive molecular model building system - A 3-D computer modelling system applied to the study of the origin of life

NASA Technical Reports Server (NTRS)

Coeckelenbergh, Y.; Macelroy, R. D.; Rein, R.

1978-01-01

The investigation of specific interactions among biological molecules must take into consideration the stereochemistry of the structures. Thus, models of the molecules are essential for describing the spatial organization of potentially interacting groups, and estimations of conformation are required for a description of spatial organization. Both the function of visualizing molecules, and that of estimating conformation through calculations of energy, are part of the molecular modeling system described in the present paper. The potential uses of the system in investigating some aspects of the origin of life rest on the assumption that translation of conformation from genetic elements to catalytic elements would have been required for the development of the first replicating systems subject to the process of biological evolution.

Synthesis, characterization stereochemistry and anti-bacterial evaluation of certain N-acyl-c-3,t-3-dimethyl-r-2,c-6-diphenylpiperidin-4-ones

NASA Astrophysics Data System (ADS)

Ponnuswamy, S.; Kayalvizhi, R.; Jamesh, M.; Uma Maheswari, J.; Thenmozhi, M.; Ponnuswamy, M. N.

2016-09-01

A new series of N-acyl-c-3,t-3-dimethyl-r-2,c-6-diphenylpiperidin-4-ones 2-6 has been synthesized and characterized using IR, mass, 1H, 13C, DEPT and 2D (COSY and HSQC) NMR spectral techniques. The NMR spectral data indicate that the N-acylpiperidin-4-ones 2-6 prefer to exist in a distorted boat conformation B1 with coplanar orientation of N-C=O moiety. The stereodynamics of these systems have been studied by recording the dynamic 1H NMR spectra of compound 4, and the energy barrier for N-CO rotation is determined to be 52.75 kJ/mol. Furthermore the compounds 1-5 show significant antibacterial activity.

Choerosponins A and B, Two New Cytotoxic Bridged-Ring Ketones and the Determination of Their Absolute Configurations.

PubMed

Li, Chang-Wei; Han, Bing; Cai, Bing; Cui, Cheng-Bin

2017-03-27

Bioactivity-directed fractionation of antitumor compounds from the stem barks of Choerospondias axillaries (Roxb.) Burtt et Hill (Anacardiaceae) afforded two new cytotoxic bridged-ring ketones, choerosponins A ( 1 ) and B ( 2 ), and their structures were elucidated by spectroscopic methods; their stereochemistry was determined by NOE difference experiments, CD spectra and the modified Mosher's method. Compound 1 has a rare dioxatricyclo skeleton. Flow cytometry and SRB methods were employed to evaluate the antitumor activity of the two compounds against tsFT210, HCT-15, HeLa, A2780 and MCF-7 cell lines, and both of them showed strong cytotoxicity. MTT and paper disc methods were also used to evaluate their anti-hypoxia and antibacterial activities, and both of them showed no apparent activities.

Isobenzofuranones and Isochromenones from the Deep-Sea Derived Fungus Leptosphaeria sp. SCSIO 41005

PubMed Central

Luo, Xiaowei; Lin, Xiuping; Salendra, Limbadri; Pang, Xiaoyan; Dai, Yu; Yang, Bin; Liu, Juan; Wang, Junfeng; Liu, Yonghong

2017-01-01

Four new isobenzofuranones, leptosphaerins J–M (1–4), including an unusual naturally-occurring centrosymmetric dimer skeleton (1), and two new isochromenones, clearanols I–J (9–10), were obtained from a culture of a deep-sea sediment-derived fungus Leptosphaeria sp. SCSIO 41005, together with four known isobenzofuranones (5–8) and six known isochromenones (11–16). These structures were elucidated by extensive spectroscopic analyses, and absolute configurations were assigned on the basis of electronic circular dichroism and optical rotations data comparison. Additionally, the absolute configurations of the new compounds 1 and 9, together with the known one 7 with stereochemistry undetermined, were further confirmed by single crystal X-ray diffraction experiments. A plausible biosynthetic pathway of these isobenzofuranones and isochromenones was also proposed. PMID:28661451

Muscarinic subtypes profile modulation within a series of new antagonists, bridged bicyclic derivatives of 2,2-diphenyl-[1,3]-dioxolan-4-ylmethyl-dimethylamine.

PubMed

Piergentili, Alessandro; Gentili, Francesco; Ghelfi, Francesca; Marucci, Gabriella; Pigini, Maria; Quaglia, Wilma; Giannella, Mario

2003-09-01

A set of new muscarinic antagonists, bridged bicyclic derivatives of 2,2-diphenyl-[1,3]-dioxolan-4-ylmethyl-dimethylamine (1), was synthesized and tested to evaluate their affinity and selectivity for M(1), M(2), M(3) and M(4) receptor subtypes. The conformational constraint of 1 in a bicyclic structure, and the variation in distance and stereochemistry of the active functions allowed us to modulate the selectivity of interaction with the M(1)-M(3) receptor subtypes. The most interesting compound was (cis,trans)-2-(2,2-diphenylethyl)-5-methyl-tetrahydro-[1,3]dioxolo[4,5-c]pyrrole oxalate (6), which is equipotent with Pirenzepine on rabbit vas deferens (M(1)-putative) but shows a better selectivity profile.

Correcting ligands, metabolites, and pathways

PubMed Central

Ott, Martin A; Vriend, Gert

2006-01-01

Background A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metabolic network reconstruction, and systems biology. Most available databases, however, treat chemical structures more as illustrations than as a datafield in its own right. Lack of chemical accuracy impedes progress in the areas mentioned above. We present a database of metabolites called BioMeta that augments the existing pathway databases by explicitly assessing the validity, correctness, and completeness of chemical structure and reaction information. Description The main bulk of the data in BioMeta were obtained from the KEGG Ligand database. We developed a tool for chemical structure validation which assesses the chemical validity and stereochemical completeness of a molecule description. The validation tool was used to examine the compounds in BioMeta, showing that a relatively small number of compounds had an incorrect constitution (connectivity only, not considering stereochemistry) and that a considerable number (about one third) had incomplete or even incorrect stereochemistry. We made a large effort to correct the errors and to complete the structural descriptions. A total of 1468 structures were corrected and/or completed. We also established the reaction balance of the reactions in BioMeta and corrected 55% of the unbalanced (stoichiometrically incorrect) reactions in an automatic procedure. The BioMeta database was implemented in PostgreSQL and provided with a web-based interface. Conclusion We demonstrate that the validation of metabolite structures and reactions is a feasible and worthwhile undertaking, and that the validation results can be used to trigger corrections and improvements to BioMeta, our metabolite database. BioMeta provides some tools for rational drug design, reaction searches, and visualization. It is freely available at provided that the copyright notice of all original data is cited. The database will be useful for querying and browsing biochemical pathways, and to obtain reference information for identifying compounds. However, these applications require that the underlying data be correct, and that is the focus of BioMeta. PMID:17132165

Medicinal uses, phytochemistry and pharmacology of the genus Uncaria.

PubMed

Zhang, Qian; Zhao, Jiao Jiao; Xu, Jian; Feng, Feng; Qu, Wei

2015-09-15

The genus Uncaria belongs to the family Rubiaceae, which mainly distributed in tropical regions, such as Southeast Asia, Africa and Southeast America. Their leaves and hooks have long been thought to have healing powers and are already being tested as a treatment for asthma, cancer, cirrhosis, diabetes, hypertension, stroke and rheumatism. The present review aims to provide systematically reorganized information on the ethnopharmacology, phytochemistry and pharmacology of the genus Uncaria to support for further therapeutic potential of this genus. To better understanding this genus, information on the stereo-chemistry and structure-activity relationships in indole alkaloids is also represented. The literature study of this review is based on various databases search (SCIFinder, Science Direct, CNKI, Wiley online library, Spring Link, Web of Science, PubMed, Wanfang Data, Medalink, Google scholar, ACS, Tropicos, Council of Heads of Australasian Herbaria, The New York Botanical Garden, African Plants Database at Genera Botanical Garden, The Plant List and SEINet) and library search for Biological Abstract and some local books on ethnopharmacology. 19 species of the genus Uncaria are found to be important folk medicines in China, Malaysia, Phillippines, Africa and Southeast America, etc, and have been served for the treatment of asthma, rheumatism, hyperpyrexia, hypertension and headaches, etc. More than 200 compounds have been isolated from Uncaria, including indole alkaloids, triterpenes, flavonoids, phenols, phenylpropanoids, etc. As characteristic constituents, indole alkaloids have been considered as main efficacy component for hypertension, epilepsy, depressant, Parkinson's disease and Alzheimer's disease. In addition, pharmacokinetic and metabolism investigation reveal that the indole alkaloids are likely to be absorbed, metabolized and excreted at early time points. Moreover, the specific inhibition of CYP isozymes can regulate their hydroxylation metabolites at C-10 and C-11. Preliminary investigations on pharmacological properties of the Uncaria species have enlightened their efficacious remedy for hypertension, asthma, cancer, diabetes, rheumatism and neurodegenerative diseases. To ensure the safety and effectiveness in clinical application, research on bioactive compounds, pharmacological mechanisms and toxicity of the genus Uncaria as well as the stereo-chemistry and structure-activity relationships of indole alkaloids seem very important. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

ON THE RELATIONSHIPS OF SUBSTRATE ORIENTATION, HYDROGEN ABSTRACTION AND PRODUCT STEREOCHEMISTRY IN SINGLE AND DOUBLE DIOXYGENATIONS BY SOYBEAN LIPOXYGENASE-1 AND ITS ALA542GLY MUTANT*

PubMed Central

Coffa, Gianguido; Imber, Ann N.; Maguire, Brendan C.; Laxmikanthan, Gurunathan; Schneider, Claus; Gaffney, Betty J.; Brash, Alan R.

2005-01-01

Recent findings associate the control of stereochemistry in lipoxygenase (LOX) catalysis with a conserved active site alanine for S configuration hydroperoxide products, or a corresponding glycine for R stereoconfiguration. To further elucidate the mechanistic basis for this stereocontrol we compared the stereoselectivity of the initiating hydrogen abstraction in soybean LOX-1 and an Ala542Gly mutant that converts linoleic acid to both 13S and 9R configuration hydroperoxide products. Using 11R-3H- and 11S-3H-labeled linoleic acid substrates to examine the initial hydrogen abstraction, we found that all the primary hydroperoxide products were formed with an identical and highly stereoselective proS hydrogen abstraction from C-11 of the substrate (97–99% pro-S selective). This strongly suggests that 9R and 13S oxygenations occur with the same binding orientation of substrate in the active site, and as the equivalent 9R and 13S products were formed from a bulky ester derivative (1-palmitoyl-2-linoleoyl-phosphatidylcholine), one can infer that the orientation is tail-first. Both the EPR spectrum and the reaction kinetics were altered by the R product-inducing Ala-Gly mutation, indicating a substantial influence of this Ala-Gly substitution extending to the environment of the active site iron. To examine also the reversed orientation of substrate binding, we studied oxygenation of the 15S-hydroperoxide of arachidonic acid by the Ala542Gly mutant soybean LOX-1. In addition to the usual 5S,15S- and 8S,15S-dihydroperoxides, a new product was formed and identified by HPLC, UV, GC-MS and NMR as 9R , 1 5 S -dihydroperoxy-eicosa-5Z,7E,11Z,13E-tetraenoic acid, the R configuration “partner” of the normal 5S,15S product. This provides evidence that both tail-first and carboxylate end-first binding of substrate can be associated with S or R partnerships in product formation in the same active site. PMID:16157595

Biochemistry students' ideas about shape and charge in enzyme-substrate interactions.

PubMed

Linenberger, Kimberly J; Bretz, Stacey Lowery

2014-01-01

Biochemistry is a visual discipline that requires students to develop an understanding of numerous representations. However, there is very little known about what students actually understand about the representations that are used to communicate ideas in biochemistry. This study investigated biochemistry students' understanding of multiple representations of enzyme-substrate interactions through both student interviews (N = 25) and responses by a national sample (N = 707) to the Enzyme-Substrate Interactions Concept Inventory. This manuscript reports the findings regarding one category of misconceptions measured by the concept inventory, namely, students' understandings of shape and charge in the context of enzyme-substrate interactions. Students interpret molecular representations depicting such interactions by determining the complementarity between enzyme and substrate by focusing upon charge and hydrogen bonding, but with a disregard for stereochemistry. Copyright © 2014 by The International Union of Biochemistry and Molecular Biology.

Antiproliferative Diterpenes from a Malleastrum sp. from the Madagascar dry forest[1

PubMed Central

Liu, Yixi; Wiedle, C. Houston; Brodie, Peggy J.; Callmander, Martin W.; Rakotondrajaona, R.; Rakotobe, Etienne; Rasamison, Vincent E.

2015-01-01

An ethanol extract of leaves of the plant species Malleastrum sp. collected in northern Madagascar afforded the new clerodane diterpene 18-oxo-cleroda-3,13-dien-16,15-olide (1), together with the three known clerodane diterpenes 16,18-dihydroxykolavenic acid lactone (2), solidagolactone (3) and (−)-kolavenol (4), and the known labdane diterpene 3-oxo-ent-Iabda-8(17),13-dien-15,16-olide (5). Compounds 1, 3, and 4 showed moderate antiproliferative activities against the A2780 ovarian cancer cell line, with the IC50 values of 3.01 ± 0.8, 7.84 ± 0.2, and 17.9 ± 3 μM, respectively. The structure elucidations of all compounds were carried out based on analysis of NMR and mass spectroscopic data. The relative stereochemistry of compound 1 was determined by NOESY NMR spectrum. PMID:26594745

Self assembly of organic nanostructures and dielectrophoretic assembly of inorganic nanowires.

NASA Astrophysics Data System (ADS)

Dholakia, Geetha; Kuo, Steven; Allen, E. L.

2007-03-01

Self assembly techniques enable the organization of organic molecules into nanostructures. Currently engineering strategies for efficient assembly and routine integration of inorganic nanoscale objects into functional devices is very limited. AC Dielectrophoresis is an efficient technique to manipulate inorganic nanomaterials into higher dimensional structures. We used an alumina template based sol-gel synthesis method for the growth of various metal oxide nanowires with typical diameters of 100-150 nm, ranging in length from 3-10 μm. Here we report the dielectrophoretic assembly of TiO2 nanowires, an important material for photocatalysis and photovoltaics, onto interdigitated devices. Self assembly in organic nanostructures and its dependence on structure and stereochemistry of the molecule and dielectrophoretic field dependence in the assembly of inorganic nanowires will be compared and contrasted. Tunneling spectroscopy and DOS of these nanoscale systems will also be discussed.

Structures and biological activities of azaphilones produced by Penicillium sp. KCB11A109 from a ginseng field.

PubMed

Son, Sangkeun; Ko, Sung-Kyun; Kim, Jong Won; Lee, Jae Kyoung; Jang, Mina; Ryoo, In-Ja; Hwang, Gwi Ja; Kwon, Min Cheol; Shin, Kee-Sun; Futamura, Yushi; Hong, Young-Soo; Oh, Hyuncheol; Kim, Bo Yeon; Ueki, Masashi; Takahashi, Shunji; Osada, Hiroyuki; Jang, Jae-Hyuk; Ahn, Jong Seog

2016-02-01

Twelve metabolites, including five highly oxygenated azaphilones, geumsanols A-E, along with seven known analogues were isolated from Penicillium sp. KCB11A109, a fungus derived from a ginseng field. Their structures were assigned by spectroscopic means (NMR and MS), and stereochemistries were determined by extensive spectroscopic analyses ((1)H-(1)H coupling constants, NOESY, and HETLOC) and chemical derivatizations (modified Mosher's method and acetonide formation). The isolates were evaluated for their anticancer, antimicrobial, antimalarial activities, and phenotypic effects in zebrafish development. Of these compounds possessing no pyranoquinone core, only geumsanol E exhibited cytotoxic activities and toxic effects on zebrafish embryos, suggesting that a double bond at C-11 and C-12 is important for biological activity. Copyright © 2015 Elsevier Ltd. All rights reserved.

Modular Chemical Descriptor Language (MCDL): Stereochemical modules

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

Gakh, Andrei A; Burnett, Michael N; Trepalin, Sergei V.

2011-01-01

In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure Editor which is capable of drawing chemical structures from linear representations and generating MCDL descriptors from structures. In this paper we present MCDL modules and accompanying software that incorporate unique representation of molecular stereochemistry based on Cahn-Ingold-Prelog and Fischer ideas in constructing stereoisomer descriptors. The paper also contains additional discussions regarding canonical representation of stereochemical isomers, and brief algorithm descriptions of the open source LINDES, Java applet, and Open Babel MCDLmore » processing module software packages. Testing of the upgraded MCDL Java Chemical Structure Editor on compounds taken from several large and diverse chemical databases demonstrated satisfactory performance for storage and processing of stereochemical information in MCDL format.« less

A Dual-Catalysis Approach to Enantioselective [2+2] Photocycloadditions Using Visible Light

PubMed Central

Du, Juana; Skubi, Kazimer L.; Schultz, Danielle M.; Yoon, Tehshik P.

2015-01-01

In contrast to the wealth of catalytic systems that are available to control the stereochemistry of thermally promoted cycloadditions, few similarly effective methods exist for the stereocontrol of photochemical cycloadditions. A major unsolved challenge in the design of enantioselective catalytic photocycloaddition reactions has been the difficulty of controlling racemic background reactions that occur by direct photoexcitation of substrates while unbound to catalyst. Here we describe a strategy for eliminating the racemic background reaction in asymmetric [2+2] photocycloadditions of α,β-unsaturated ketones to the corresponding cyclobutanes by employing a dual-catalyst system consisting of a visible light-absorbing transition metal photocatalyst and a stereocontrolling Lewis acid co-catalyst. The independence of these two catalysts enables broader scope, greater stereochemical flexibility, and better efficiency than previously reported methods for enantioselective photochemical cycloadditions. PMID:24763585

An antibacterial ortho-quinone diterpenoid and its derivatives from Caryopteris mongolica.

PubMed

Saruul, Erdenebileg; Murata, Toshihiro; Selenge, Erdenechimeg; Sasaki, Kenroh; Yoshizaki, Fumihiko; Batkhuu, Javzan

2015-06-15

To identify antibacterial components in traditional Mongolian medicinal plant Caryopteris mongolica, an ortho-quinone abietane caryopteron A (1) and three its derivatives caryopteron B-D (2-4) were isolated from the roots of the plant together with three known abietanes demethylcryptojaponol (5), 6α-hydroxydemethyl cryptojaponol (6), and 14-deoxycoleon U (7). The chemical structures of these abietane derivatives were elucidated on the basis of spectroscopic data. Compounds 1-4 had C-13 methylcyclopropane substructures, and 2-4 had a hexanedioic anhydride ring C instead of ortho-quinone in 1. The stereochemistry of these compound was assumed from NOE spectra and ECD Cotton effects. Compounds 1 and 5-7 showed antibacterial activities against the Gram-positive bacteria Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, and Micrococcus luteus, being 1 the more potent. Copyright © 2015 Elsevier Ltd. All rights reserved.

Crystal structure of (2,4-di-tert-butyl-6-{[(6,6'-dimethyl-2'-oxido-1,1'-biphenyl-2-yl)imino]methyl}phenolato-κ(3) O,N,O')bis(propan-2-olato-κO)titanium(IV).

PubMed

Chen, Liang; Wang, Huiran; Deng, Xuebin

2014-09-01

In the mononuclear Ti(IV) title complex, [Ti(C29H33NO2)(C3H6O)2], the TiNO4 coordination polyhedron comprises an N-atom and two O-atom donors from the dianionic Schiff base ligand and two O-atom donors from monodentate isopropoxide anions. The stereochemistry is distorted trigonal-bipyramidal with the N-donor in an elongated axial site [Ti-N = 2.2540 (17) Å], the O-donors having normal Ti-O bond lengths [1.7937 (14) Å (axial)-1.8690 (14) Å]. In the crystal, C-H⋯π inter-actions link mol-ecules into centrosymmetric dimers.

Hydrozirconation of lithium alkynylselenolate anions. Generation and reactions of alpha-zirconated vinyl selenide intermediates

PubMed

Dabdoub; Begnini; Guerrero; Baroni

2000-01-14

Lithium alkynylselenolate anions react completely with 1.0 equiv of Cp(2)Zr(H)Cl in THF at room temperature to give exclusively the alpha-zirconated vinylselenolate intermediates 23-27, which by treatment with an alkyl halide afforded the alpha-zirconated vinyl alkylselenide intermediates 29-33. Reaction of 29-33 with butyltellurenyl bromide results in the formation of ketene telluro(seleno) acetals 35-39 with total control of the regio- and stereochemistry. The synthetic utility of the ketene telluro(seleno) acetals obtained here was demonstrated by reaction of 36 with butyllithium. This promotes the exclusive and stereospecific removal of the tellurium moiety and enables formation of the corresponding selenium-containing allylic alcohol of type 44, alpha-(alkylseleno)-alpha,beta-unsaturated aldehyde 45, ester 46, or carboxylic acid 47, after reaction with different types of electrophiles.

Activity-guided isolation of the chemical constituents of Muntingia calabura using a quinone reductase induction assay.

PubMed

Su, Bao-Ning; Jung Park, Eun; Vigo, Jose Schunke; Graham, James G; Cabieses, Fernando; Fong, Harry H S; Pezzuto, John M; Kinghorn, A Douglas

2003-06-01

Activity-guided fractionation of an EtOAc-soluble extract of the leaves of Muntingia calabura collected in Peru, using an in vitro quinone reductase induction assay with cultured Hepa 1c1c7 (mouse hepatoma) cells, resulted in the isolation of a flavanone with an unsubstituted B-ring, (2R,3R)-7-methoxy-3,5,8-trihydroxyflavanone (5), as well as 24 known compounds, which were mainly flavanones and flavones. The structure including absolute stereochemistry of compound 5 was determined by spectroscopic (HRMS, 1D and 2D NMR, and CD spectra) methods. Of the isolates obtained, in addition to 5, (2S)-5-hydroxy-7-methoxyflavanone, 2',4'-dihydroxychalcone, 4,2',4'-trihydroxychalcone, 7-hydroxyisoflavone and 7,3',4'-trimethoxyisoflavone were found to induce quinone reductase activity.

Six New Polyacetylenic Alcohols from the Marine Sponges Petrosia sp. and Halichondria sp.

PubMed

Gabriel, Adeyemi Francis; Li, Zhen; Kusuda, Ryouhei; Tanaka, Chiaki; Miyamoto, Tomofumi

2015-01-01

Six new polyacetylenic alcohols, termed strongylotriols A and B; pellynols J, K, and L; and isopellynol A, together with three known polyacetylenic alcohols, pellynols A, B, and C were isolated from the marine sponges Petrosia sp., and Halichondria sp. collected in Okinawa, Japan. Their planer structures were determined based on 2D-NMR and mass spectrometric analysis of the degraded products by RuCl3 oxidation. The absolute stereochemistry of isolates was examined by their Mosher's esters. The strongylotriols were found to be optically pure compounds, whereas the pellynols are diastereomeric mixtures at the C-6 position. Proliferation experiments using the HeLa and K562 cell lines suggested that the essential structural units for activity are the "hexa-2,4-diyn-1,6-diol" and "pent-1-en-4-yn-3-ol" on the termini.

Design and use of nanostructured single-site heterogeneous catalysts for the selective transformation of fine chemicals.

PubMed

Dal Santo, Vladimiro; Liguori, Francesca; Pirovano, Claudio; Guidotti, Matteo

2010-05-26

Nanostructured single-site heterogeneous catalysts possess the advantages of classical solid catalysts, in terms of easy recovery and recycling, together with a defined tailored chemical and steric environment around the catalytically active metal site. The use of inorganic oxide supports with selected shape and porosity at a nanometric level may have a relevant impact on the regio- and stereochemistry of the catalytic reaction. Analogously, by choosing the optimal preparation techniques to obtain spatially isolated and well-characterised active sites, it is possible to achieve performances that are comparable to (or, in the most favourable cases, better than) those obtained with homogeneous systems. Such catalysts are therefore particularly suitable for the transformation of highly-functionalised fine chemicals and some relevant examples where high chemo-, regio- and stereoselectivity are crucial will be described.

Microbial degradation of poly-b-esters: A mechanistic study, cellulose acetate biodegradability. Final report, 1 May 1990-31 July 1993

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

Gross, R.A.

1993-08-30

In this Final Report, work carried out under ARO grant C-DAAL03-G-0111 is described. The investigations performed include the following: (1) isolation, purification and characterization of a poly(3-hydroxybutyrate) depolymerase enzyme from Penicillium funiculosum, (2) determination that the depolymerase is a serine esterase, (3) study of the effect of polymer stereochemistry and crystalline order in a semi-crystalline polymer film substrate on enzyme specificity and activity, (3) isolation, purification and characterization of cellulose acetate degrading microorganisms and (4) determination of the biodegradability of cellulose acetate with degrees of substitution up to 2.5 under aerobic thermophilic conditions. Poly(3-hydroxybutyrate) biodegradation, Poly(3-hydroxybutyrate) depolymerase enzyme, Depolymerase frommore » Penicillium funiculosum, Cellulose acetate degrading microorganisms, Composting polymer biodegradable.« less

Allosteric transcriptional regulation via changes in the overall topology of the core promoter

DOE PAGES

Philips, Steven J.; Canalizo-Hernandez, Monica; Yildirim, Ilyas; ...

2015-08-21

Many transcriptional activators act at a distance from core promoter elements and work by recruiting RNA polymerase through protein-protein interactions. We show here how the prokaryotic regulatory protein CueR both represses and activates transcription by differentially modulating local DNA structure within the promoter. Structural studies reveal that the repressor state slightly bends the promoter DNA, precluding optimal RNA polymerase-promoter recognition. Upon binding a metal ion in the allosteric site, CueR switches into an activator conformation. It maintains all protein-DNA contacts but introduces torsional stresses that kink and undertwist the promoter, stabilizing an A-DNA-like conformation. Finally, these factors switch on andmore » off transcription by exerting dynamic control of DNA stereochemistry, reshaping the core promoter and making it a better or worse substrate for polymerase.« less

An Additive Definition of Molecular Complexity.

PubMed

Böttcher, Thomas

2016-03-28

A framework for molecular complexity is established that is based on information theory and consistent with chemical knowledge. The resulting complexity index Cm is derived from abstracting the information content of a molecule by the degrees of freedom in the microenvironments on a per-atom basis, allowing the molecular complexity to be calculated in a simple and additive way. This index allows the complexity of any molecule to be universally assessed and is sensitive to stereochemistry, heteroatoms, and symmetry. The performance of this complexity index is evaluated and compared against the current state of the art. Its additive character gives consistent values also for very large molecules and supports direct comparisons of chemical reactions. Finally, this approach may provide a useful tool for medicinal chemistry in drug design and lead selection, as demonstrated by correlating molecular complexities of antibiotics with compound-specific parameters.

Polyunsaturated C-Glycosidic 4-Hydroxy-2-pyrone Derivatives: Total Synthesis Shows that Putative Orevactaene Is Likely Identical with Epipyrone A.

PubMed

Preindl, Johannes; Schulthoff, Saskia; Wirtz, Conny; Lingnau, Julia; Fürstner, Alois

2017-06-19

Orevactaene and epipyrone A were previously thought to comprise the same polyunsaturated tail but notably different C-glycosylated 4-hydroxy-2-pyrone head groups. Total synthesis now shows that the signature bicyclic framework assigned to orevactaene is a chimera; the compound is almost certainly identical with epipyrone A, whose previously unknown stereochemistry has also been established during this study. Key to success was the ready formation of the bicyclic core of putative orevactaene by a sequence of two alkyne cycloisomerization reactions using tungsten and gold catalysis. Equally important was the flexibility in the assembly process gained by the use of heterobimetallic polyunsaturated modules whose termini could be selectively and consecutively addressed in a practical one-pot cross-coupling sequence. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Benzomorphan skeleton, a versatile scaffold for different targets: A comprehensive review.

PubMed

Turnaturi, Rita; Montenegro, Lucia; Marrazzo, Agostino; Parenti, Rosalba; Pasquinucci, Lorella; Parenti, Carmela

2018-06-07

Despite the fact that the benzomorphan skeleton has mainly been employed in medicinal chemistry for the development of opioid analgesics, it is a versatile structure. Its stereochemistry, as well as opportune modifications at the phenolic hydroxyl group and at the basic nitrogen, play a pivotal role addressing the benzomorphan-based compounds to a specific target. In this review, we describe the structure activity-relationships (SARs) of benzomorphan-based compounds acting at sigma 1 receptor (σ1R), sigma 2 receptor (σ2R), voltage-dependent sodium channel, N-Methyl-d-Aspartate (NMDA) receptor-channel complex and other targets. Collectively, the SARs data have highlighted that the benzomorphan nucleus could be regarded as a useful template for the synthesis of drug candidates for different targets. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Mono- and dinuclear bioxazoline-palladium complexes for the stereocontrolled synthesis of CO/styrene polyketones.

PubMed

Scarel, Alessandro; Durand, Jérôme; Franchi, Davide; Zangrando, Ennio; Mestroni, Giovanni; Carfagna, Carla; Mosca, Luca; Seraglia, Roberta; Consiglio, Giambattista; Milani, Barbara

2005-10-07

The coordination chemistry of the chiral bioxazoline ligand (4S,4'S)-2,2'-bis(4-isopropyl-4,5-dihydrooxazole) to Pd(II) provides evidence that the ligand bonding can occur either through chelation of one Pd(II) ion leading to a mononuclear species with the expected cis geometry, or by double bridging of two Pd(II) ions giving a dinuclear complex with trans geometry. The species in solution are identified by 1H NMR spectroscopy. Both the mononuclear and the dinuclear complexes promote the CO/styrene copolymerization, yielding the corresponding polyketone with a fully or a predominantly isotactic microstructure, depending on the reaction medium. The nature of the anion present in the palladium precatalysts affects the polyketone stereochemistry. MALDI-TOF analysis of the copolymers synthesized reveals the presence of p-hydroxyphenolic end-groups, thus confirming and explaining the role of 1,4-hydroquinone as a molecular weight regulator.

Alkyne–Aldehyde Reductive C–C Coupling through Ruthenium-Catalyzed Transfer Hydrogenation: Direct Regio- and Stereoselective Carbonyl Vinylation to Form Trisubstituted Allylic Alcohols in the Absence of Premetallated Reagents

PubMed Central

Leung, Joyce C.; Patman, Ryan L.; Sam, Brannon

2011-01-01

Nonsymmetric 1,2-disubstituted alkynes engage in reductive coupling to a variety of aldehydes under the conditions of ruthenium-catalyzed transfer hydrogenation by employing formic acid as the terminal reductant and delivering the products of carbonyl vinylation with good to excellent levels of regioselectivity and with complete control of olefin stereochemistry. As revealed in an assessment of the ruthenium counterion, iodide plays an essential role in directing the regioselectivity of C–C bond formation. Isotopic labeling studies corroborate reversible catalytic propargyl C–H oxidative addition in advance of the C–C coupling, and demonstrate that the C–C coupling products do not experience reversible dehydrogenation by way of enone intermediates. This transfer hydrogenation protocol enables carbonyl vinylation in the absence of stoichiometric metallic reagents. PMID:21953608

Lobatamide C: total synthesis, stereochemical assignment, preparation of simplified analogues, and V-ATPase inhibition studies.

PubMed

Shen, Ruichao; Lin, Cheng Ting; Bowman, Emma Jean; Bowman, Barry J; Porco, John A

2003-07-02

The total synthesis and stereochemical assignment of the potent antitumor macrolide lobatamide C, as well as synthesis of simplified lobatamide analogues, is reported. Cu(I)-mediated enamide formation methodology has been developed to prepare the highly unsaturated enamide side chain of the natural product and analogues. A key fragment coupling employs base-mediated esterification of a beta-hydroxy acid and a salicylate cyanomethyl ester. Three additional stereoisomers of lobatamide C have been prepared using related synthetic routes. The stereochemistry at C8, C11, and C15 of lobatamide C was assigned by comparison of stereoisomers and X-ray analysis of a crystalline derivative. Synthetic lobatamide C, stereoisomers, and simplified analogues have been evaluated for inhibition of bovine chromaffin granule membrane V-ATPase. The salicylate phenol, enamide NH, and ortho-substitution of the salicylate ester have been shown to be important for V-ATPase inhibitory activity.

Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system

PubMed Central

Desguin, Benoît; Goffin, Philippe; Viaene, Eric; Kleerebezem, Michiel; Martin-Diaconescu, Vlad; Maroney, Michael J; Declercq, Jean-Paul; Soumillion, Patrice; Hols, Pascal

2014-01-01

Racemases catalyze the inversion of stereochemistry in biological molecules, giving the organism the ability to use both isomers. Among them, lactate racemase remains unexplored due to its intrinsic instability and lack of molecular characterization. Here we determine the genetic basis of lactate racemization in Lactobacillus plantarum. We show that, unexpectedly, the racemase is a nickel-dependent enzyme with a novel α/β fold. In addition, we decipher the process leading to an active enzyme, which involves the activation of the apo-enzyme by a single nickel-containing maturation protein that requires preactivation by two other accessory proteins. Genomic investigations reveal the wide distribution of the lactate racemase system among prokaryotes, showing the high significance of both lactate enantiomers in carbon metabolism. The even broader distribution of the nickel-based maturation system suggests a function beyond activation of the lactate racemase and possibly linked with other undiscovered nickel-dependent enzymes. PMID:24710389

Isolation of rotational isomers and developments derived therefrom

PubMed Central

ŌKI, Michinori

2010-01-01

Isolation of rotational isomer models of ethane-type molecules is described. We could experimentally prove that, if rotational isomers whose molecular shape was chiral, the molecule could be optically active, even though it did not carry an asymmetric carbon atom. As an extension, other types of stereochemically fundamental and optically active molecules were isolated and their absolute stereochemistry was determined. One example is the model of meso-tartaric acid, for which optical inactivity had been attributed to internal compensation but is now explained as follows. On dissolution of meso-tartaric acid in a solvent, the molecule gives two kinds of conformers, one of which is a Ci molecule and the other is a C1 molecule. Although the latter is intrinsically optically active, the optical activity is cancelled by its enantiomer. The theory of internal compensation is recommended to be abandoned. As an extension to another area, some reactions of conformers are also discussed. PMID:21084771

Reentrant Structural and Optical Properties and Large Positive Thermal Expansion in Perovskite Formamidinium Lead Iodide.

PubMed

Fabini, Douglas H; Stoumpos, Constantinos C; Laurita, Geneva; Kaltzoglou, Andreas; Kontos, Athanassios G; Falaras, Polycarpos; Kanatzidis, Mercouri G; Seshadri, Ram

2016-12-05

The structure of the hybrid perovskite HC(NH 2 ) 2 PbI 3 (formamidinium lead iodide) reflects competing interactions associated with molecular motion, hydrogen bonding tendencies, thermally activated soft octahedral rotations, and the propensity for the Pb 2+ lone pair to express its stereochemistry. High-resolution synchrotron X-ray powder diffraction reveals a continuous transition from the cubic α-phase (Pm3‾ m, #221) to a tetragonal β-phase (P4/mbm, #127) at around 285 K, followed by a first-order transition to a tetragonal γ-phase (retaining P4/mbm, #127) at 140 K. An unusual reentrant pseudosymmetry in the β-to-γ phase transition is seen that is also reflected in the photoluminescence. Around room temperature, the coefficient of volumetric thermal expansion is among the largest for any extended crystalline solid. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

New arylalkanones from Horsfieldia macrobotrys, effective antidiabetic agents concomitantly inhibiting α-glucosidase and free radicals.

PubMed

Ramadhan, Rico; Phuwapraisirisan, Preecha

2015-10-15

In search of effective antidiabetic agents having therapeutic effect by inhibiting α-glucosidase and preventive effect by scavenging free radicals, Horsfieldia macrobotrys showed promising bioactivity required for the proposed criteria. Bioassay-guided isolation of the stem bark extract resulted in two new arylalkanones named horsfieldone A (1) and maingayone D (2), together with a new flavanone C-glucoside named 8-C-β-d-glucopyranosylpinocembrin (3). Their structures and stereochemistry were determined by spectroscopic techniques as well as Mosher's method. Of isolated compounds, maingayone D (2) was the most potent inhibitors against both α-glucosidases and free radicals. The presence of additional phenolic moieties in 2 clearly indicated their critical roles in inhibitory effects. Further investigation on mechanism underlying α-glucosidase inhibition indicated that maingayone D (2) could retard the enzyme function by both competitive and noncompetitive manners. Copyright © 2015 Elsevier Ltd. All rights reserved.

Synthesis, stereochemical, structural, and biological studies of a series of N‧-(2r,4c-diaryl-3-azabicyclo[3.3.1]nonan-9-ylidene)pyrazine-2-carbohydrazides

NASA Astrophysics Data System (ADS)

Mangalam, M.; Sebastian Antony Selvan, C.; Sankar, C.

2017-02-01

A new series of N‧-(2r,4c-diaryl-3-azabicyclo[3.3.1]nonan-9-ylidene)pyrazine-2-carbohydrazides (8-14) were synthesized by the corresponding 2r,4c-diaryl-3-azabicyclo[3.3.1]nonan-9-ones (1-7) reaction with pyrazine-2-carbohydrazide. The stereochemistry of the newly synthesized compounds were unambiguously assigned using FT-IR, 1H, 13C, and 2D (COSY, HSQC, HMBC, ROESY) nuclear magnetic resonance (NMR) spectral data. The chemical shifts suggest that all these compounds adopt twin-chair conformation with equatorial orientation of aryl substitutions in solution. Hydrazones were screened for their in vitro antitubercular activity against Mycobacterium tuberculosis H37Rv and antibacterial activity against a set of pathogenic bacteria. Most of the halogenated compounds showed promising antitubercular and antibacterial activities.

[The mass-spectrometry studies of the interaction of polyhexamethyleneguanidine with lipids].

PubMed

Lysytsia, A V; Rebriiev, A V

2014-01-01

In this work the integral components of the cytoplasmic membrane, lecithin and cholesterol were used for mass spectrometry analysis carried out on polyhexamethyleneguanidine (PHMG) mixtures with lipids. The study was performed by mass-spectrometry methods of the MALDI-TOF MS. Our results showed that despite the common use of PHGM polymer derivatives as disinfectants the persistent intermolecular complexes of PHMG oligomers with lipids were not formed. The binding of polycation PHMG with the membrane has been explained by the model proposed. According to this model PHGM can adhere to negatively charged plasma membrane of bacterial cell due to electrostatic interaction and the formation of loop-like structures. Similar stereochemistry mechanism makes the adsorption of the investigated polycation to membrane robust. The mechanism described together with additional destructive factors provides a reasonable explanation for the PHMG induced damage of bacterial cell plasma membrane and the biocide action of disinfectants prepared on the basis of the PHMG salts.

Synthesis and properties of dithymidine phosphate analogues containing 3'-thiothymidine.

PubMed Central

Cosstick, R; Vyle, J S

1990-01-01

Dithymidine-3'-S-phosphorothioate (d(TspT)) has been prepared from a 5'-O-monomethoxytritylthymidine-3'-S-phosphorothioamidite (7) by activation with 5-(p-nitrophenyl)tetrazole in the presence of 3'-O-acetylthymidine. The resulting dinucleoside phosphorothioite is readily oxidised to the corresponding 3'-S-phosphorothioate using either tetrabutylammonium (TBA) periodate or TBA oxone and has been deprotected under standard conditions to yield d(TspT). This dithymidine phosphate analogue is comparatively resistant to hydrolysis by nuclease P1, but the P-S bond is readily cleaved by aqueous solutions of either iodine or silver nitrate. Dithymidine-3'-S-phosphorodithioate (d[Tsp(s)T]) was prepared in an analogous fashion using sulphur to oxidise the intermediate dinucleoside phosphorothioite. Absolute stereochemistry has been assigned to the diastereoisomers of d[Tsp(s)T] by comparing their physical and chemical properties to those of the dinucleoside phosphorothioates. PMID:2315041

Specific Stereoisomeric Conformations Determine the Drug Potency of Cladosporin Scaffold against Malarial Parasite.

PubMed

Das, Pronay; Babbar, Palak; Malhotra, Nipun; Sharma, Manmohan; Jachak, Gorakhnath R; Gonnade, Rajesh G; Shanmugam, Dhanasekaran; Harlos, Karl; Yogavel, Manickam; Sharma, Amit; Reddy, D Srinivasa

2018-05-21

The dependence of drug potency on diastereomeric configurations is a key facet. Using a novel general divergent synthetic route for a three-chiral centre anti-malarial natural product cladosporin, we built its complete library of stereoisomers (cladologs) and assessed their inhibitory potential using parasite-, enzyme- and structure-based assays. We show that potency is manifest via tetrahyropyran ring conformations that are housed in the ribose binding pocket of parasite lysyl tRNA synthetase (KRS). Strikingly, drug potency between top and worst enantiomers varied 500-fold, and structures of KRS-cladolog complexes reveal that alterations at C3 and C10 are detrimental to drug potency where changes at C3 are sensed by rotameric flipping of Glutamate332. Given that scores of anti-malarial and anti-infective drugs contain chiral centers, this work provides a new foundation for focusing on inhibitor stereochemistry as a facet of anti-microbial drug development.

Structural Stereochemistry of Androstene Hormones Determines Interactions with Human Androgen, Estrogen, and Glucocorticoid Receptors

PubMed Central

Shaak, Thomas L.; Wijesinghe, Dayanjan S.; Chalfant, Charles E.; Diegelmann, Robert F.; Ward, Kevin R.; Loria, Roger M.

2013-01-01

DHEA, 17α-AED, 17β-AED, and 17β-AET exhibit strong biological activity that has been attributed to androgenic, estrogenic, or antiglucocorticoid activity in vivo and in vitro. This study compared DHEA, 17α-AED, 17β-AED, and 17β-AET for their ability to activate the human AR, ER, and GR and determine the relative androgenicity, estrogenicity, and glucocorticoid activity. The results show that, at the receptor level, these androstene hormones are weak AR and even weaker ER activators. Direct androstene hormone activation of the human AR, ERα, and ERβ may not be essential for their biological function. Similarly, these hormones indirectly activated the human GR, only in the presence of high dexamethasone concentrations. These results underscore the major difference between androstene hormone interactions with these nuclear receptors and their biological effects. PMID:24729874

Stepwise cycloaddition reaction of N-phenacylbenzothiazolium bromides and nitroalkenes for tetrahydro-, dihydro- and benzo[d]pyrrolo[2,1-b]thiazoles

NASA Astrophysics Data System (ADS)

Jin, Gong; Sun, Jing; Yang, Ren-Yin; Yan, Chao-Guo

2017-04-01

The triethylamine promoted stepwise 1,3-dipolar cycloaddition reaction of N-phenacylbenzothiazolium bromides with nitroalkenes in ethanol resulted in a mixture of two isomeric tetrahydrobenzo[d]pyrrolo[2,1-b]thiazoles with cis/trans/cis- and all-trans-configurations. More importantly, the corresponding dihydrobenzo[d]pyrrolo[2,1-b]thiazoles can be selectively prepared in refluxing ethanol and the benzo[d]pyrrolo[2,1-b]thiazoles can be obtained in satisfactory yields by sequential dehydrogenation with DDQ as oxidizer. On the other hand, the similar cycloaddition reaction of N-phenacylbenzothiazolium bromides with 1-methy-1-nitroalkenes in refluxing ethanol afforded benzo[d]pyrrolo[2,1-b]thiazoles with splitting out of nitro group. The stereochemistry of the spiro compounds was clearly elucidated on the basis of NMR spectra and sixteen single crystal structures.

Ultrasound-assisted green bromination of N-cinnamoyl amino acid amides - Structural characterization and antimicrobial evaluation

NASA Astrophysics Data System (ADS)

Stoykova, Boyka; Chochkova, Maya; Ivanova, Galya; Markova, Nadezhda; Enchev, Venelin; Tsvetkova, Iva; Najdenski, Hristo; Štícha, Martin; Milkova, Tsenka

2017-05-01

N-phenylpropenoyl amino acid amides have been brominated using two alternative sonochemically activated green chemistry procedures. The first synthetic procedure has involved an ultrasound assisted bromination in an aqueous medium using ionic liquid as a catalyst of the reaction, whereas in the second one an in situ formation of Br2 via oxidation of HBr by H2O2 has been used. For comparison, the conventional bromination procedure was also used. The newly brominated compounds were characterized by appropriate analytical techniques. A detailed NMR spectroscopic analysis and quantum chemical calculations using Density Functional Theory (DFT) methods have been used to define the stereochemistry of the products. The results confirmed the physicochemical identity and similar yields of the products obtained by the three synthetic procedures employed, and reveal the co-existence of two diastereoisomeric forms of the newly synthesized products. The antibacterial and antifungal activities of the dibrominated amides were evaluated.

Shape and symmetry of heptacoordinate transition-metal complexes: structural trends.

PubMed

Casanova, David; Alemany, Pere; Bofill, Josep M; Alvarez, Santiago

2003-03-17

The stereochemistries of heptacoordinate transition-metal complexes are analyzed by using continuous symmetry and shape measures of their coordination spheres. The distribution of heptacoordination through the transition-metal series is presented based on structural database searches including organometallic and Werner-type molecular complexes, metalloproteins, and extended solids. The most common polyhedron seems to be the pentagonal bipyramid, while different preferences are found for specific families of compounds, as in the complexes with three or four carbonyl or phosphine ligands, which prefer the capped octahedron or the capped trigonal prism rather than the pentagonal bipyramid. The symmetry maps for heptacoordination are presented and shown to be helpful for detecting stereochemical trends. The maximal symmetry interconversion pathways between the three most common polyhedra are defined in terms of symmetry constants and a large number of experimental structures are seen to fall along those paths.

Spin-orbit effects on the (119)Sn magnetic-shielding tensor in solids: a ZORA/DFT investigation.

PubMed

Alkan, Fahri; Holmes, Sean T; Iuliucci, Robbie J; Mueller, Karl T; Dybowski, Cecil

2016-07-28

Periodic-boundary and cluster calculations of the magnetic-shielding tensors of (119)Sn sites in various co-ordination and stereochemical environments are reported. The results indicate a significant difference between the predicted NMR chemical shifts for tin(ii) sites that exhibit stereochemically-active lone pairs and tin(iv) sites that do not have stereochemically-active lone pairs. The predicted magnetic shieldings determined either with the cluster model treated with the ZORA/Scalar Hamiltonian or with the GIPAW formalism are dependent on the oxidation state and the co-ordination geometry of the tin atom. The inclusion of relativistic effects at the spin-orbit level removes systematic differences in computed magnetic-shielding parameters between tin sites of differing stereochemistries, and brings computed NMR shielding parameters into significant agreement with experimentally-determined chemical-shift principal values. Slight improvement in agreement with experiment is noted in calculations using hybrid exchange-correlation functionals.

Stereochemistry of silicon in oxygen-containing compounds

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

Serezhkin, V. N., E-mail: Serezhkin@samsu.ru; Urusov, V. S.

2017-01-15

Specific stereochemical features of silicon in oxygen-containing compounds, including hybrid silicates with all oxygen atoms of SiO{sub n} groups ({sub n} = 4, 5, or 6) entering into the composition of organic anions or molecules, are described by characteristics of Voronoi—Dirichlet polyhedra. It is found that in rutile-like stishovite and post-stishovite phases with the structures similar to those of СаСl{sub 2}, α-PbO{sub 2}, or pyrite FeS{sub 2}, the volume of Voronoi—Dirichlet polyhedra of silicon and oxygen atoms decreases linearly with pressure increasing to 268 GPa. Based on these results, the possibility of formation of new post-stishovite phases is shown, namely,more » the fluorite-like structure (transition predicted at ~400 GPa) and a body-centered cubic lattice with statistical arrangement of silicon and oxygen atoms (~900 GPa).« less

Chirality-selected phase behaviour in ionic polypeptide complexes

DOE PAGES

Perry, Sarah L.; Leon, Lorraine; Hoffmann, Kyle Q.; ...

2015-01-14

In this study, polyelectrolyte complexes present new opportunities for self-assembled soft matter. Factors determining whether the phase of the complex is solid or liquid remain unclear. Ionic polypeptides enable examination of the effects of stereochemistry on complex formation. Here we demonstrate that chirality determines the state of polyelectrolyte complexes, formed from mixing dilute solutions of oppositely charged polypeptides, via a combination of electrostatic and hydrogen-bonding interactions. Fluid complexes occur when at least one of the polypeptides in the mixture is racemic, which disrupts backbone hydrogen-bonding networks. Pairs of purely chiral polypeptides, of any sense, form compact, fibrillar solids with amore » β-sheet structure. Analogous behaviour occurs in micelles formed from polypeptide block copolymers with polyethylene oxide, where assembly into aggregates with either solid or fluid cores, and eventually into ordered phases at high concentrations, is possible. Chirality is an exploitable tool for manipulating material properties in polyelectrolyte complexation.« less

Isolation and characterisation of an unexpected byproduct in the regioselective butane diacetal protection of α-methyl galactopyranoside.

PubMed

Fontenelle, Clément Q; Kuppala, Ramakrishna; Light, Mark; Linclau, Bruno

2018-01-02

The regioselective protection of both methyl galactopyranoside anomers at the 2 and 3-positions as the butane diacetal (BDA) is well known. Here we describe the formation of an unexpected byproduct, which mainly occurs when α-methyl galactopyranoside is reacted with 2,3-butanedione under BF 3 •OEt 2 catalysis. The structure of the byproduct, which did not arise from anomerisation to the β-anomer or from BDA formation at the galactopyranoside 3,4-positions, was elucidated by NMR and X-ray crystallographic analysis, and proved to be the expected BDA protected galactopyranoside, but in which the stereochemistry of both its BDA acetal centres are inverted. Interestingly, the conformation of the resulting six-membered BDA ring was distorted to a skew boat conformation in order to maintain anomeric stabilisation. Copyright © 2017. Published by Elsevier Ltd.

Phosphine-Catalyzed Doubly Stereoconvergent γ-Additions of Racemic Heterocycles to Racemic Allenoates: The Catalytic Enantioselective Synthesis of Protected α,α-Disubstituted α-Amino Acid Derivatives.

PubMed

Kalek, Marcin; Fu, Gregory C

2015-07-29

Methods have recently been developed for the phosphine-catalyzed asymmetric γ-addition of nucleophiles to readily available allenoates and alkynoates to generate useful α,β-unsaturated carbonyl compounds that bear a stereogenic center in either the γ or the δ position (but not both) with high stereoselectivity. The utility of this approach would be enhanced considerably if the stereochemistry at both termini of the new bond could be controlled effectively. In this report, we describe the achievement of this objective, specifically, that a chiral phosphepine can catalyze the stereoconvergent γ-addition of a racemic nucleophile to a racemic electrophile; through the choice of an appropriate heterocycle as the nucleophilic partner, this new method enables the synthesis of protected α,α-disubstituted α-amino acid derivatives in good yield, diastereoselectivity, and enantioselectivity.

Ring size of somatostatin analogues (ODT-8) modulates receptor selectivity and binding affinity

PubMed Central

Erchegyi, Judit; Grace, Christy Rani R.; Samant, Manoj; Cescato, Renzo; Piccand, Veronique; Riek, Roland; Reubi, Jean Claude; Rivier, Jean E.

2009-01-01

The synthesis, biological testing and NMR studies of several analogues of H-c[Cys3-Phe6-Phe7-dTrp8-Lys9-Thr10-Phe11-Cys14]-OH (ODT-8, a pan-somatostatin analogue) (1), have been performed to assess the effect of changing the stereochemistry and the number of the atoms in the disulfide bridge on binding affinity. Cysteine at positions 3 and/or 14 (SRIF numbering) were/was substituted with d-cysteine, Nor-cysteine, d-Nor-cysteine, Homo-cysteine and/or d-Homo-cysteine. The 3D structures of selected partially selective, bioactive analogues (3, 18, 19 and 21) were carried out in DMSO. Interestingly and not unexpectedly, the 3D structures of these analogues comprised the pharmacophore for which the analogues had the highest binding affinities (i.e., sst4 in all cases). PMID:18410084

Acid-catalyzed ring-opening reactions of a cyclopropanated 3-aza-2-oxabicyclo[2.2.1]hept-5-ene with alcohols.

PubMed

Tait, Katrina; Horvath, Alysia; Blanchard, Nicolas; Tam, William

2017-01-01

The acid-catalyzed ring-opening reactions of a cyclopropanated 3-aza-2-oxabicylic alkene using alcohol nucleophiles were investigated. Although this acid-catalyzed ring-opening reaction did not cleave the cyclopropane unit as planned, this represent the first examples of ring-openings of cyclopropanated 3-aza-2-oxabicyclo[2.2.1]alkenes that lead to the cleavage of the C-O bond instead of the N-O bond. Different acid catalysts were tested and it was found that pyridinium toluenesulfonate in methanol gave the best yields in the ring-opening reactions. The scope of the reaction was successfully expanded to include primary, secondary, and tertiary alcohol nucleophiles. Through X-ray crystallography, the stereochemistry of the product was determined which confirmed an S N 2-like mechanism to form the ring-opened product.

Synthesis, stereochemistry, crystal structure, docking study and biological evaluation of some new N-benzylpiperidin-4-ones

NASA Astrophysics Data System (ADS)

Ponnuswamy, S.; Kayalvizhi, R.; Sethuvasan, S.; Sugumar, P.; Ponnuswamy, M. N.

2018-03-01

Two new N-benzylpiperidin-4-ones 3 and 4 have been synthesized and characterized using IR, 1D and 2D NMR spectral studies. The NMR data of N-benzylpiperidin-4-ones 3 and 4 reveal that the compounds prefer to exist in chair conformation with equatorial orientation of the bulky substituents and the single crystal X-ray structure of compound 4 also reveals a similar conformation in solid state. Furthermore, the antimicrobial studies carried out for the compounds 1-4 indicate moderate activities with the selected strains. The antioxidant potency of 3 is superior whereas 4 exhibits moderate activity when compared to that of standard drug. The results of molecular docking studies with the AmpC β-lactamase enzyme indicate that compound 3 shows better docking score and binding energy than the co-crystal ligand.

Synthesis, structure and antidiabetic activity of chromium(III) complexes of metformin Schiff-bases

NASA Astrophysics Data System (ADS)

Mahmoud, M. A.; Zaitone, S. A.; Ammar, A. M.; Sallam, S. A.

2016-03-01

A series of Cr3+ complexes with Schiff-bases of metformin with each of salicylaldehyde (HL1); 2,3-dihydroxybenzaldehyde (H2L2); 2,4-dihydroxybenzaldehyde (H2L3); 2,5-dihydroxybenzaldehyde (H2L4); 3,4-dihydroxybenzaldehyde (H2L5) and 2-hydroxynaphthaldehyde (HL6) were synthesized by template reaction. The new compounds were characterized through elemental analysis, conductivity and magnetic moment measurements, IR, UV-Vis., NMR and mass spectroscopy. The complexes have octahedral structure with μ value of hexacoordinated chromium ion. TGA, DTG and DTA analysis confirm the proposed stereochemistry and a mechanism for thermal decomposition was proposed. Thermodynamic parameters are calculated for the second and third decomposition steps. [CrL4Cl(H2O)2].3H2O and [CrL5Cl(H2O)2].2½H2O were able to produce significant decreases in the blood glucose level.

Cardiolipin: a stereospecifically spin-labeled analogue and its specific enzymic hydrolysis.

PubMed Central

Cable, M B; Jacobus, J; Powell, G L

1978-01-01

The spin-labeled cardiolipin 1-(3-sn-phosphatidyl)-3-[1-acyl-2-(16-doxylstearoyl)glycero(3)phosphol]-sn-glycerol has been prepared. The stereoselective synthesis makes use of the monolysocardiolipin 1-(3-sn-phosphatidyl)-3-[1-acyl-2-lyso-sn-glycero(3)phospho]-sn-glycerol, available from the stereospecific hydrolysis of cardiolipin by phospholipase A2 (phosphatide 2-acylhydrolase, EC 3.1.1.4) of Trimeresurus flavoviridis. The results of treatment of the spin-labeled cardiolipin with the cardiolipin-specific phospholipase D (phosphatidylcholine phosphatidohydrolase, EC 3.1.4.4) (Hemophilus parainfluenzae) of known specificity and with phospholipase C (phosphatidylcholine cholinephosphohydrolase, EC 3.1.4.3) of Bacillus cereus are consistent with the assigned structure. The spin-labeled cardiolipin is further characterized and the unique features of this diastereomer are discussed in the context of the unusual stereochemistry of the natural phospholipid. PMID:274715

Synthesis of highly functionalized macrocycles by the peripheral functionalization of macrocyclic diimines.

PubMed

Sierra, Miguel A; Pellico, Daniel; Gómez-Gallego, Mar; Mancheño, María José; Torres, Rosario

2006-11-10

The easily available macrocyclic diimines 4-7 can be stereoselectively transformed to macrocyclic bis-beta-amino acids 13-17, macrocyclic bisazetidines 18-20, and macrocyclic bisamides 21 and 22 by means of the corresponding bis-beta-lactam scaffolds 8-12. These key intermediates are available through standard Staudinger reaction and obtained as the cis-cis diastereomers, exclusively. An interesting relation between the proximity of the reactive C=N bonds and the selectivity in the formation of the bis-beta-lactams 8-12 is observed. Thus, diimine 4 leads to low selectivities, producing a 1:1 mixture of cis-syn-cis and cis-anti-cis diastereomers, while diimines 5-7 having the diimine sites more separated lead almost exclusively to the cis-anti-cis diastereomers. The stereochemistry of all the products was unambiguously assigned by X-ray diffraction analysis of compounds cis-syn-cis 8 and cis-anti-cis 12-Co2CO6 complex.

Comparative structural analysis of cytidine, ethenocytidine and their protonated salts III. 1H, 13C and 15N NMR studies at natural isotope abundance.

PubMed Central

Kozerski, L; Sierzputowska-Gracz, H; Krzyzosiak, W; Bratek-Wiewiórowska, M; Jaskólski, M; Wiewiórowski, M

1984-01-01

The 1H, 13C, 15N NMR spectra of cytidine /Cyd/, ethenocytidine /epsilon Cyd/ and their hydrochlorides /Cyd X HC1/ and /epsilon Cyd X HC1/ have been analysed to compare structural differences observed in solution with those existing in the crystalline state. The effects of ethenobridging and protonation of the hertero-aromatic base on the intramolecular stereochemistry, intermolecular interactions and electronic structure of the whole molecule are discussed on the basis of the NMR studies in DMSO solutions. Particular interest is devoted to the discussion of the conformation of the ribose ring, the presence of the intramolecular C-5'-0...H-6-C hydrogen bond, unambiguous assignment of the site of protonation, the mechanism of the 5C-H deuterium exchange in Cyd X HC1, and the intermolecular interactions in solution. PMID:6701098

Biosynthetic studies on the botcinolide skeleton: new hydroxylated lactones from Botrytis cinerea.

PubMed

Reino, José L; Durán-Patrón, Rosa M; Daoubi, Mourad; Collado, Isidro G; Hernández-Galán, Rosario

2006-01-20

[reaction: see text] The biosynthetic origin of the botcinolide skeleton was investigated by means of feeding 13C- and 2H-labeled precursors to Botrytis cinerea. Three new compounds, two homobotcinolide derivatives, 3-O-acetylhomobotcinolide (5) and 8-methylhomobotcinolide (6), and a new 11-membered lactone (7), were isolated. Their structures were elucidated on the basis of spectroscopic data, including one-bond and long-range 1H-13C correlations. The relative stereochemistries were determined by combined analyses of NOE data and 1H-1H coupling constants. According to the results of feeding experiments with 13C- and 2H-labeled acetate and l-S-methylmethionine, 5 is an acetate-derived polyketide whose methyl groups originate from l-S-methylmethionine. This is a rare example of the incorporation of a methyl from methionine into a supposed C3 starter unit of the polyketide synthesis.

Allelopathic Polyketides from an Endolichenic Fungus Myxotrichum SP. by Using OSMAC Strategy.

PubMed

Yuan, Chao; Guo, Yu-Hua; Wang, Hai-Ying; Ma, Xiao-Jun; Jiang, Tao; Zhao, Jun-Ling; Zou, Zhong-Mei; Ding, Gang

2016-02-03

Three new polyketides myxotritones A-C (2-4), together with a new natural product 7,8-dihydro-7R,8S-dihydroxy-3,7-dimethyl-2-benzopyran-6-one (1) were obtained from the endolichenic fungus Myxotrichum sp. by using OMSAC (One Strain, Many Compounds) method. The planar structures of these new compounds were determined by NMR experiment and HRESIMS data, and the absolute configuration of 1 was established by X-ray diffraction, and the stereochemistry of the new compounds 2-4 were determined by same biosynthesis origin, and similar CD spectra with 1. Allelopathic test showed that compound 4 significantly retarded root elongation of Arabidopsis thaliana seed, indicating that this fungus might contribute to the defense of its host lichen. From the view of biosynthetic pathway, all four compounds 1-4 might be originated from Non-Reduced Polyketide synthase (NR-PKS).

Conformationally constrained opioid ligands: the Dmt-Aba and Dmt-Aia versus Dmt-Tic scaffold.

PubMed

Ballet, Steven; Feytens, Debby; Wachter, Rien De; Vlaeminck, Magali De; Marczak, Ewa D; Salvadori, Severo; Graaf, Chris de; Rognan, Didier; Negri, Lucia; Lattanzi, Roberta; Lazarus, Lawrence H; Tourwé, Dirk; Balboni, Gianfranco

2009-01-15

Replacement of the constrained phenylalanine analogue 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic) in the opioid Dmt-Tic-Gly-NH-Bn scaffold by the 4-amino-1,2,4,5-tetrahydro-indolo[2,3-c]azepin-3-one (Aia) and 4-amino-1,2,4,5-tetrahydro-2-benzazepin-3-one (Aba) scaffolds has led to the discovery of novel potent mu-selective agonists (Structures 5 and 12) as well as potent and selective delta-opioid receptor antagonists (Structures 9 and 15). Both stereochemistry and N-terminal N,N-dimethylation proved to be crucial factors for opioid receptor selectivity and functional bioactivity in the investigated small peptidomimetic templates. In addition to the in vitro pharmacological evaluation, automated docking models of Dmt-Tic and Dmt-Aba analogues were constructed in order to rationalize the observed structure-activity data.

Conformationally constrained opioid ligands: The Dmt-Aba and Dmt-Aia vs. Dmt-Tic scaffold

PubMed Central

Ballet, Steven; Feytens, Debby; De Wachter, Rien; De Vlaeminck, Magali; Marczak, Ewa D.; Salvadori, Severo; de Graaf, Chris; Rognan, Didier; Negri, Lucia; Lattanzi, Roberta; Lazarus, Lawrence H.; Tourwé, Dirk; Balboni, Gianfranco

2009-01-01

Replacement of the constrained phenylalanine analogue 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic) in the opioid Dmt-Tic-Gly-NH-Bn scaffold by the 4-amino-1,2,4,5-tetrahydro-indolo[2,3-c]azepin-3-one (Aia) and 4-amino-1,2,4,5-tetrahydro-2-benzazepin-3-one (Aba) scaffolds has led to the discovery of novel potent μ-selective agonists (Structures 5 and 12) as well as potent and selective δ-opioid receptor antagonists (Structures 9 and 15). Both stereochemistry and N-terminal N,N-dimethylation proved to be crucial factors for opioid receptor selectivity and functional bioactivity in the investigated small peptidomimetic templates. In addition to the in vitro pharmacological evaluation, automated docking models of Dmt-Tic and Dmt-Aba analogues were constructed in order to rationalize the observed structure-activity data. PMID:19062273

The metabolism of anabolic-androgenic steroids in the greyhound.

PubMed

McKinney, Andrew R; Cawley, Adam T; Young, E Bruce; Kerwick, Carmel M; Cunnington, Karen; Stewart, Rhiannon T; Ambrus, Joseph I; Willis, Anthony C; McLeod, Malcolm D

2013-04-01

Effective control of the use of anabolic-androgenic steroids (AASs) in animal sports is essential in order to ensure both animal welfare and integrity. In order to better police their use in Australian and New Zealand greyhound racing, thorough metabolic studies have been carried out on a range of registered human and veterinary AASs available in the region. Canine metabolic data are presented for the AASs boldenone, danazol, ethylestrenol, mesterolone, methandriol, nandrolone and norethandrolone. The principal Phase I metabolic processes observed were the reduction of A-ring unsaturations and/or 3-ketones with either 3α,5β- or 3β,5α-stereochemistry, the oxidation of secondary 17β-hydroxyl groups and 16α-hydroxylation. The Phase II β-glucuronylation of sterol metabolites was extensive. The presented data have enabled the effective analysis of AASs and their metabolites in competition greyhound urine samples.

X-Ray absorption spectroscopy quantitative analysis of biomimetic copper(II) complexes with tridentate nitrogen ligands mimicking the tris(imidazole) array of protein centres.

PubMed

Borghi, Elena; Casella, Luigi

2010-02-21

In this study copper(ii) complexes with the tridentate nitrogen ligand bis[2-(1-methylbenzimidazol-2-yl)ethyl]amine (2-BB) are considered as model compounds for the Cu-tris(imidazole) array found in several copper proteins. 2-BB chelates copper(ii) forming two six-membered rings and the complexes contain methanol, nitrite, azide and water as ancillary ligands; both the coordination numbers and stereochemistries differ in these complexes. Their key structural features were investigated by using full multiple-scattering theoretical analysis of the copper K-edge X-ray absorption spectrum with the MXAN code. We showed that using cluster sizes large enough to include all atoms of the ligand, the analysis of the XANES region can give both a structural model of the metal centre and map the structure of the 2-BB complexes. Complex [Cu(2-BB)(N(3))](+) provided a critical test through the comparison of the XANES simulation results with crystallographic data, thus permitting the extension of the method to the complex [Cu(2-BB)(H(2)O)(n)](+) (n = 1 or 2), for which crystallographic data are not available but is expected to bear a five-coordinated Cu(3N)(2O) core (n = 2). The structural data of [Cu(2-BB)(MeOH)(ClO(4))](+) and [Cu(2-BB)(NO(2))](+), both with a Cu(3N)(2O) core but with a different stereochemistry, were used as the starting parameters for two independent simulations of the XANES region of the [Cu(2-BB)(H(2)O)(2)](+) cation. The two structural models generated by simulation converge towards a structure for the aqua-cation with a lower coordination number. New calculations, where four-coordinated Cu(3N)(O) cores were considered as the starting structures, validated that the structure of the aqua-complex in the powder state has a copper(ii) centre with a four-coordinated Cu(3N)(O) core and a molecular formula [Cu(2-BB)(H(2)O)](ClO(4)).(H(2)O). A water solvation molecule, presumed to be disordered from the simulations with the two Cu(3N)(2O) cores, is present. The successful treatment of this Cu-2-BB complex system allows the extension of the method to other biomimetic compounds when a structural characterization is lacking.

Synthesis of methyl (13(2)R/S)-alkyl-pyropheophorbide a and a non-epimerized chlorophyll a mimic.

PubMed

Ogasawara, Shin; Tamiaki, Hitoshi

2015-10-15

The (13(2)R/S)-methoxycarbonyl group of methyl pheophorbides a/a' (chlorophyll a/a' derivatives) was converted to methyl, ethyl, propyl, and isopropyl groups through the C13(2)-alkylation under basic conditions followed by pyrolysis in 2,4,6-collidine with lithium iodide. All the resulting products, methyl 13(2)-alkyl-pyropheophorbides a, predominantly gave the (13(2)R)-stereoisomers with about one tenth of the (13(2)S)-epimers. Their stereochemistry was determined by 1D/2D NMR and their optical properties were characterized by visible absorption and circular dichroism spectroscopy. Methyl (13(2)R)-propyl-pyropheophorbide a was converted to (13(2)R)-propyl-pyrochlorophyll a by ester exchanging and magnesium chelating reactions. The synthetic chlorophyll a analogue showed non-epimerization at the 13(2)-position in pyridine-d5 at 40°C, while naturally occurring chlorophyll a was easily epimerized under the same conditions to give its epimeric mixture. Copyright © 2015 Elsevier Ltd. All rights reserved.

Bonding in phase change materials: concepts and misconceptions

NASA Astrophysics Data System (ADS)

Jones, R. O.

2018-04-01

Bonding concepts originating in chemistry are surveyed from a condensed matter perspective, beginning around 1850 with ‘valence’ and the word ‘bond’ itself. The analysis of chemical data in the 19th century resulted in astonishing progress in understanding the connectivity and stereochemistry of molecules, almost without input from physicists until the development of quantum mechanics in 1925 and afterwards. The valence bond method popularized by Pauling and the molecular orbital methods of Hund, Mulliken, Bloch, and Hückel play major roles in the subsequent development, as does the central part played by the kinetic energy in covalent bonding (Ruedenberg and others). ‘Metallic’ (free electron) and related approaches, including pseudopotential and density functional theories, have been remarkably successful in understanding structures and bonding in molecules and solids. We discuss these concepts in the context of phase change materials, which involve the rapid and reversible transition between amorphous and crystalline states, and note the confusion that some have caused, in particular ‘resonance’ and ‘resonant bonding’.

Supercritical fluid chromatography for GMP analysis in support of pharmaceutical development and manufacturing activities.

PubMed

Hicks, Michael B; Regalado, Erik L; Tan, Feng; Gong, Xiaoyi; Welch, Christopher J

2016-01-05

Supercritical fluid chromatography (SFC) has long been a preferred method for enantiopurity analysis in support of pharmaceutical discovery and development, but implementation of the technique in regulated GMP laboratories has been somewhat slow, owing to limitations in instrument sensitivity, reproducibility, accuracy and robustness. In recent years, commercialization of next generation analytical SFC instrumentation has addressed previous shortcomings, making the technique better suited for GMP analysis. In this study we investigate the use of modern SFC for enantiopurity analysis of several pharmaceutical intermediates and compare the results with the conventional HPLC approaches historically used for analysis in a GMP setting. The findings clearly illustrate that modern SFC now exhibits improved precision, reproducibility, accuracy and robustness; also providing superior resolution and peak capacity compared to HPLC. Based on these findings, the use of modern chiral SFC is recommended for GMP studies of stereochemistry in pharmaceutical development and manufacturing. Copyright © 2015 Elsevier B.V. All rights reserved.

Mycobacterium tuberculosis and cholinesterase inhibitors from Voacanga globosa.

PubMed

Macabeo, Allan Patrick G; Vidar, Warren S; Chen, Xinyu; Decker, Michael; Heilmann, Jörg; Wan, Baojie; Franzblau, Scott G; Galvez, Elano V; Aguinaldo, Ma Alicia M; Cordell, Geoffrey A

2011-07-01

Globospiramine (1), a new spirobisindole alkaloid possessing an Aspidosperma-Aspidosperma skeleton, together with deoxyvobtusine (2), deoxyvobtusine lactone (3), vobtusine lactone (4) and lupeol (5), were isolated and identified from Voacanga globosa through a bioassay-guided purification. The gross structure and absolute stereochemistry of 1 were established by circular dichroism spectroscopy, HR-MS and unambiguous NMR spectroscopic experiments. In addition, a new biogenetic pathway for the formation of the spiro-Aspidosperma-Aspidosperma skeleton is proposed. Alkaloid 1 showed potent antituberculosis activity against Mycobacterium tuberculosis H(37)Rv as evidenced in microplate Alamar blue assay (MIC = 4 μg/mL) and low-oxygen recovery assay (LORA (MIC = 5.2 μg/mL). The bisindole alkaloids also exhibited promising activity against acetylcholinesterase and, especially butyrylcholinesterase, with deoxyvobtusine (2) (IC(50) = 6.2 μM) as the most strongly inhibiting compound. This study extends the variety of alkaloid structural platforms which exhibit antimycobacterial and anticholinesterase activity. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Automated building of organometallic complexes from 3D fragments.

PubMed

Foscato, Marco; Venkatraman, Vishwesh; Occhipinti, Giovanni; Alsberg, Bjørn K; Jensen, Vidar R

2014-07-28

A method for the automated construction of three-dimensional (3D) molecular models of organometallic species in design studies is described. Molecular structure fragments derived from crystallographic structures and accurate molecular-level calculations are used as 3D building blocks in the construction of multiple molecular models of analogous compounds. The method allows for precise control of stereochemistry and geometrical features that may otherwise be very challenging, or even impossible, to achieve with commonly available generators of 3D chemical structures. The new method was tested in the construction of three sets of active or metastable organometallic species of catalytic reactions in the homogeneous phase. The performance of the method was compared with those of commonly available methods for automated generation of 3D models, demonstrating higher accuracy of the prepared 3D models in general, and, in particular, a much wider range with respect to the kind of chemical structures that can be built automatically, with capabilities far beyond standard organic and main-group chemistry.

Metabolic profiling and systematic identification of flavonoids and isoflavonoids in roots and cell suspension cultures of Medicago truncatula using HPLC-UV-ESI-MS and GC-MS.

PubMed

Farag, Mohamed A; Huhman, David V; Lei, Zhentian; Sumner, Lloyd W

2007-02-01

An integrated approach utilizing HPLC-UV-ESI-MS and GC-MS was used for the large-scale and systematic identification of polyphenols in Medicago truncatula root and cell culture. Under optimized conditions, we were able to simultaneously quantify and identify 35 polyphenols including 26 isoflavones, 3 flavones, 2 flavanones, 2 aurones and a chalcone. All identifications were based upon UV spectra, mass spectral characteristics of protonated molecules, tandem mass spectral data, mass measurements obtained using a quadrupole time-of-flight mass spectrometer (QtofMS), and confirmed through the co-characterization of authentic compounds. In specific instances where the stereochemistry of sugar conjugates was uncertain, subsequent enzymatic hydrolysis of the conjugate followed by GC-MS was used to assign the sugar stereochemical configuration. Comparative metabolic profiling of Medicago truncatula root and cell cultures was then performed and revealed significant differences in the isoflavonoid composition of these two tissues.

Design and synthesis of a tetradentate '3-amine-1-carboxylate' ligand to mimic the metal binding environment at the non-heme iron(II) oxidase active site.

PubMed

Dungan, Victoria J; Ortin, Yannick; Mueller-Bunz, Helge; Rutledge, Peter J

2010-04-07

Non-heme iron(II) oxidases (NHIOs) catalyse a diverse array of oxidative chemistry in Nature. As part of ongoing efforts to realize biomimetic, iron-mediated C-H activation, we report the synthesis of a new 'three-amine-one-carboxylate' ligand designed to complex with iron(II) and mimic the NHIO active site. The tetradentate ligand has been prepared as a single enantiomer in nine synthetic steps from N-Cbz-L-alanine, pyridine-2,6-dimethanol and diphenylamine, using Seebach oxazolidinone chemistry to control the stereochemistry. X-Ray crystal structures are reported for two important intermediates, along with variable temperature NMR experiments to probe the hindered interconversion of conformational isomers of several key intermediates, 2,6-disubstituted pyridine derivatives. The target ligand and an N-Cbz-protected precursor were each then complexed with iron(II) and tested for their ability to promote alkene dihydroxylation, using hydrogen peroxide as the oxidant.

Three new cytotoxic aryltetralin lignans from Sinopodophyllum emodi.

PubMed

Sun, Yan-Jun; Li, Zhan-Lin; Chen, Hong; Liu, Xiao-Qiu; Zhou, Wei; Hua, Hui-Ming

2011-06-15

Three new aryltetralin lignans, 4-acetyl-4-demethyl-podophyllotoxin (1) and sinolignans A, B (2-3), and two new natural products (4-5), were isolated from the roots and rhizomes of Sinopodophyllum emodi together with twelve known lignans (6-17). Their structures and stereochemistry were elucidated on the basis of spectroscopic evidence, and circular dichroism (CD) method. The cytotoxic activities of all isolated compounds were evaluated against HeLa and KB cell lines. Compared with etoposide, compounds 1, 6-9, and 13 showed more potent cytotoxicities against two tumor cell lines. On the basis of IC(50) values, deoxypodophyllotoxin (7) was about 579 and 1123 times more toxic than etoposide in HeLa and KB cell lines, respectively. The preliminary SAR study indicated that an oxygenated group at C-7' might decrease cytotoxicity against two cell lines, which was different from most previous studies. However, this needs to be systematically verified by extensive pharmacological experiments. Copyright © 2011 Elsevier Ltd. All rights reserved.

A bimetallic aluminum(salen) complex for the synthesis of 1,3-oxathiolane-2-thiones and 1,3-dithiolane-2-thiones.

PubMed

Clegg, William; Harrington, Ross W; North, Michael; Villuendas, Pedro

2010-09-17

The combined use of the bimetallic aluminum(salen) complex [Al(salen)](2)O and tetrabutylammonium bromide (or tributylamine) is found to catalyze the reaction between epoxides and carbon disulfide. In most cases, at 50 °C, the reaction produces 1,3-oxathiolane-2-thiones, while at 90 °C, 1,3-dithiolane-2-thiones are the main product. The structure and stereochemistry of three of the 1,3-dithiolane-2-thiones is unambiguously determined by X-ray crystallographic analysis, and this is used to correct errors in the literature concerning the synthesis of cyclic di- and trithiocarbonates. The kinetics of 1,3-oxathiolane-2-thione synthesis are determined, and the resulting rate equation, along with a stereochemical analysis of the reaction and catalyst modification studies, is used to determine a mechanism for the synthesis of 1,3-oxathiolane-2-thiones which contrasts with the mechanism previously determined for cyclic carbonate synthesis using the same bimetallic aluminum(salen) complex.

MDN-0170, a New Napyradiomycin from Streptomyces sp. Strain CA-271078

PubMed Central

Lacret, Rodney; Pérez-Victoria, Ignacio; Oves-Costales, Daniel; de la Cruz, Mercedes; Domingo, Elizabeth; Martín, Jesús; Díaz, Caridad; Vicente, Francisca; Genilloud, Olga; Reyes, Fernando

2016-01-01

A new napyradiomycin, MDN-0170 (1), was isolated from the culture broth of the marine-derived actinomycete strain CA-271078, together with three known related compounds identified as 4-dehydro-4a-dechloronapyradiomycin A1 (2), napyradiomycin A1 (3) and 3-chloro-6,8-dihydroxy-8-α-lapachone (4). The structure of the new compound was determined using a combination of spectroscopic techniques, including 1D and 2D NMR and electrospray-time of flight mass spectrometry (ESI-TOF MS). The relative configuration of compound 1, which contains two independent stereoclusters, has been established by molecular modelling in combination with nOe and coupling constant analyses. Biosynthetic arguments also allowed us to propose its absolute stereochemistry. The antimicrobial properties of the compounds isolated were evaluated against methicillin-resistant Staphylococcus aureus (MRSA), Escherichia coli, Aspergillus fumigatus, and Candida albicans. The potent bioactivity previously reported for compounds 2 and 3 against methicillin-sensitive S. aureus has been extended to methicillin-resistant strains in this report. PMID:27763545

Application of Biocatalysis to on-DNA Carbohydrate Library Synthesis.

PubMed

Thomas, Baptiste; Lu, Xiaojie; Birmingham, William R; Huang, Kun; Both, Peter; Reyes Martinez, Juana Elizabeth; Young, Robert J; Davie, Christopher P; Flitsch, Sabine L

2017-05-04

DNA-encoded libraries are increasingly used for the discovery of bioactive lead compounds in high-throughput screening programs against specific biological targets. Although a number of libraries are now available, they cover limited chemical space due to bias in ease of synthesis and the lack of chemical reactions that are compatible with DNA tagging. For example, compound libraries rarely contain complex biomolecules such as carbohydrates with high levels of functionality, stereochemistry, and hydrophilicity. By using biocatalysis in combination with chemical methods, we aimed to significantly expand chemical space and generate generic libraries with potentially better biocompatibility. For DNA-encoded libraries, biocatalysis is particularly advantageous, as it is highly selective and can be performed in aqueous environments, which is an essential feature for this split-and-mix library technology. In this work, we demonstrated the application of biocatalysis for the on-DNA synthesis of carbohydrate-based libraries by using enzymatic oxidation and glycosylation in combination with traditional organic chemistry. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Divergent prebiotic synthesis of pyrimidine and 8-oxo-purine ribonucleotides

NASA Astrophysics Data System (ADS)

Stairs, Shaun; Nikmal, Arif; Bučar, Dejan-Krešimir; Zheng, Shao-Liang; Szostak, Jack W.; Powner, Matthew W.

2017-05-01

Understanding prebiotic nucleotide synthesis is a long standing challenge thought to be essential to elucidating the origins of life on Earth. Recently, remarkable progress has been made, but to date all proposed syntheses account separately for the pyrimidine and purine ribonucleotides; no divergent synthesis from common precursors has been proposed. Moreover, the prebiotic syntheses of pyrimidine and purine nucleotides that have been demonstrated operate under mutually incompatible conditions. Here, we tackle this mutual incompatibility by recognizing that the 8-oxo-purines share an underlying generational parity with the pyrimidine nucleotides. We present a divergent synthesis of pyrimidine and 8-oxo-purine nucleotides starting from a common prebiotic precursor that yields the β-ribo-stereochemistry found in the sugar phosphate backbone of biological nucleic acids. The generational relationship between pyrimidine and 8-oxo-purine nucleotides suggests that 8-oxo-purine ribonucleotides may have played a key role in primordial nucleic acids prior to the emergence of the canonical nucleotides of biology.

C-nor-9,11-secoestranes as modified estrogens and fertility regulation.

PubMed

Lal, K; Sharma, I; Agarwal, A K; Agnihotri, A; Ray, S

1988-06-01

The synthesis of C-nor-9,11-secoestradiol (4) has been achieved from 17 beta-acetoxy-11-chloro-3-methoxy-C-nor-9,11-secoestra-1,3,5(10)-tr ien-9-one (1) through a sequence of reactions without affecting the stereochemistry of estradiol-17 beta. Removal of the 9-keto function of 1 by hydrogenolysis and its subsequent treatment with Na/NH3 gives C-nor-9,11-secoestradiol 3-(methyl ether) (3), which has been demethylated under alkaline conditions to furnish C-nor-9,11-secoestradiol (4). Pyridinium chlorochromate oxidation of 3 gives the corresponding 17-ketone 6. Jones' oxidation of 4 to the ketone 5 and reaction of 5 and 6 with lithium acetylide gives corresponding 17 alpha-ethynyl derivatives 7 and 8. Relative binding affinity to estradiol-17 beta receptors and uterotropic, antiuterotrophic, and antiimplantation activities of compounds 3-8 have been studied. The effect of conformational flexibility on ligand-receptor interaction of these compounds is discussed.

Crystal Structure of an LSD-Bound Human Serotonin Receptor

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

Wacker, Daniel; Wang, Sheng; McCorvy, John D.

The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT2B. The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD’s key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT2BR and 5-HT2AR—a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD’s slow binding kinetics may be due to a “lid” formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatlymore » accelerates LSD’s binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD’s actions at human serotonin receptors.« less

Design of a new peptidomimetic agonist for the melanocortin receptors based on the solution structure of the peptide ligand, Ac-Nle-cyclo[Asp-Pro-DPhe-Arg-Trp-Lys]-NH(2).

PubMed

Fotsch, Christopher; Smith, Duncan M; Adams, Jeffrey A; Cheetham, Janet; Croghan, Michael; Doherty, Elizabeth M; Hale, Clarence; Jarosinski, Mark A; Kelly, Michael G; Norman, Mark H; Tamayo, Nuria A; Xi, Ning; Baumgartner, James W

2003-07-21

The solution structure of a potent melanocortin receptor agonist, Ac-Nle-cyclo[Asp-Pro-DPhe-Arg-Trp-Lys]-NH(2) (1) was calculated using distance restraints determined from 1H NMR spectroscopy. Eight of the lowest energy conformations from this study were used to identify non-peptide cores that mimic the spatial arrangement of the critical tripeptide region, DPhe-Arg-Trp, found in 1. From these studies, compound 2a, containing the cis-cyclohexyl core, was identified as a functional agonist of the melanocortin-4 receptor (MC4R) with an IC(50) and EC(50) below 10 nM. Compound 2a also showed 36- and 7-fold selectivity over MC3R and MC1R, respectively, in the binding assays. Subtle changes in cyclohexane stereochemistry and removal of functional groups led to analogues with lower affinity for the MC receptors.

Membrane-Targeting DCAP Analogues with Broad-Spectrum Antibiotic Activity against Pathogenic Bacteria

PubMed Central

2015-01-01

We performed a structure–activity relationship study of 2-((3-(3,6-dichloro-9H-carbazol-9-yl)-2-hydroxypropyl)amino)-2-(hydroxymethyl)propane-1,3-diol (DCAP), which is an antibacterial agent that disrupts the membrane potential and permeability of bacteria. The stereochemistry of DCAP had no effect on the biological activity of DCAP. The aromaticity and electronegativity of the chlorine-substituted carbazole was required for activity, suggesting that its planar and dipolar characteristics orient DCAP in membranes. Increasing the hydrophobicity of the tail region of DCAP enhanced its antibiotic activity. Two DCAP analogues displayed promising antibacterial activity against the BSL-3 pathogens Bacillus anthracis and Francisella tularensis. Codosing DCAP analogues with ampicillin or kanamycin increased their potency. These studies demonstrate that DCAP and its analogues may be a promising scaffold for developing chemotherapeutic agents that bind to bacterial membranes and kill strains of slow-growing or dormant bacteria that cause persistent infections. PMID:25941556

Crystal Structure of an LSD-Bound Human Serotonin Receptor.

PubMed

Wacker, Daniel; Wang, Sheng; McCorvy, John D; Betz, Robin M; Venkatakrishnan, A J; Levit, Anat; Lansu, Katherine; Schools, Zachary L; Che, Tao; Nichols, David E; Shoichet, Brian K; Dror, Ron O; Roth, Bryan L

2017-01-26

The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT 2B . The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD's key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT 2B R and 5-HT 2A R-a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD's slow binding kinetics may be due to a "lid" formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatly accelerates LSD's binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD's actions at human serotonin receptors. PAPERCLIP. Copyright © 2017 Elsevier Inc. All rights reserved.

Cytotoxic macrolides from a new species of the deep-water marine sponge Leiodermatium.

PubMed

Sandler, Joel S; Colin, Patrick L; Kelly, Michelle; Fenical, William

2006-09-15

Chemical investigation of a new species of the deep-water marine sponge Leiodermatium, collected by manned submersible at a depth of 740 feet in Palau, resulted in the isolation of two cytotoxic macrolides, leiodolides A (1) and B (2). The leiodolides represent the first members of a new class of 19-membered ring macrolides, incorporating several unique functional groups including a conjugated oxazole ring, a bromine substituent, and an alpha-hydroxy-alpha-methyl carboxylic acid side-chain terminus. The structures of these new metabolites were established by spectroscopic analysis, chemical modification, and degradation. The relative and absolute stereochemistries at most chiral centers were assigned on detailed interpretation of spectroscopic data, coupled with chemical degradation and application of the modified Mosher ester method. Leiodolide A showed significant cytotoxicity (average GI(50) = 2.0 microM) in the National Cancer Institute's 60 cell line panel with enhanced activity against HL-60 leukemia and OVCAR-3 ovarian cancer cell lines.

Preferential adsorption of polycarboxylate superplasticizers on cement and silica fume in ultra-high performance concrete (UHPC)

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

Schroefl, Ch.; Gruber, M.; Plank, J., E-mail: sekretariat@bauchemie.ch.tum.de

2012-11-15

UHPC is fluidized particularly well when a blend of MPEG- and APEG-type PCEs is applied. Here, the mechanism for this behavior was investigated. Testing individual cement and micro silica pastes revealed that the MPEG-PCE disperses cement better than silica whereas the APEG-PCE fluidizes silica particularly well. This behavior is explained by preferential adsorption of APEG-PCE on silica while MPEG-PCEs exhibit a more balanced affinity to both cement and silica. Adsorption data obtained from individual cement and micro silica pastes were compared with those found for the fully formulated UHPC containing a cement/silica blend. In the UHPC formulation, both PCEs stillmore » exhibit preferential and selective adsorption similar as was observed for individual cement and silica pastes. Preferential adsorption of PCEs is explained by their different stereochemistry whereby the carboxylate groups have to match with the steric position of calcium ions/atoms situated at the surfaces of cement hydrates or silica.« less

Enhanced reactivity in dioxirane C-H oxidations via strain release: a computational and experimental study.

PubMed

Zou, Lufeng; Paton, Robert S; Eschenmoser, Albert; Newhouse, Timothy R; Baran, Phil S; Houk, K N

2013-04-19

The site selectivities and stereoselectivities of C-H oxidations of substituted cyclohexanes and trans-decalins by dimethyldioxirane (DMDO) were investigated computationally with quantum mechanical density functional theory (DFT). The multiconfiguration CASPT2 method was employed on model systems to establish the preferred mechanism and transition state geometry. The reaction pathway involving a rebound step is established to account for the retention of stereochemistry. The oxidation of sclareolide with dioxirane reagents is reported, including the oxidation by the in situ generated tBu-TFDO, a new dioxirane that better discriminates between C-H bonds on the basis of steric effects. The release of 1,3-diaxial strain in the transition state contributes to the site selectivity and enhanced equatorial C-H bond reactivity for tertiary C-H bonds, a result of the lowering of distortion energy. In addition to this strain release factor, steric and inductive effects contribute to the rates of C-H oxidation by dioxiranes.

Assigning the stereochemistry of syn and anti β-trimethylsiloxy-α-trimethylsilyl alkanoic acid silyl esters using GIAO 1H NMR chemical shift calculations

NASA Astrophysics Data System (ADS)

Hadj Mohamed, Slim; Trabelsi, Mahmoud; Champagne, Benoît

2017-08-01

The stereostructure of β-trimethylsiloxy-α-trimethylsilyl alkanoic acid silyl esters synthesized by Bellassoued et al. [J. Org. Chem. 2001, 66, 5054-5057] using Mukaiyama aldol reaction has been reassigned using density functional theory NMR 1H chemical shifts calculations. It is now concluded that the major diastereoisomer is syn and the minor is anti. Within this assignment, for all silyl esters, δHa(anti) > δHa(syn), δHb(anti) < δHb(syn), and 3JHa-Hb (anti) > 3JHa-Hb (syn). Since the experimental assignment was based on the stereostructure (E/Z) of the cinnamic acid obtained by elimination of trimethylsilyl 3-phenyl-3-(trimethylsiloxy)-2-(trimethylsilyl)propanoate in the presence of TiCl4 and on the assumption that this elimination is anti stereospecific in acidic medium, one arrives at the conclusion that the elimination of syn and anti β-trimethylsiloxy-α-trimethylsilyl alkanoic acid silyl esters is not anti stereospecific.

Amphidinolide B: Total Synthesis, Structural Investigation and Biological Evaluation

PubMed Central

Lu, Liang; Zhang, Wei; Nam, Sangkil; Horne, David A.; Jove, Richard

2013-01-01

The total synthesis of amphidinolide B1 and the proposed structure of amphidinolide B2 has been accomplished. Key aspects of this work include the development of a practical, non-transition metal mediated method for the construction of the C13-C15 diene, the identification of α-chelation and dipole minimization models for diastereoselective methyl ketone aldol reactions, the discovery of a spontaneous Horner-Wadsworth-Emmons macrocyclization strategy and the development of a novel late stage method for construction of an allylic epoxide moiety. The originally proposed structure for amphidinolide B2 and diastereomers thereof display potent anti-tumor activities with IC50 values ranging from 3.3 nM to 94.5 nM against human solid and blood tumor cells. Of the different stereoisomers, the proposed structure of amphidinolide B2 is over 12-fold more potent than the C8,9-epimer and C18-epimer in human DU145 prostate cancer cells. These data suggest that the epoxide stereochemistry is a significant factor for anticancer activity. PMID:23406192

Automated design evolution of stereochemically randomized protein foldamers

NASA Astrophysics Data System (ADS)

Ranbhor, Ranjit; Kumar, Anil; Patel, Kirti; Ramakrishnan, Vibin; Durani, Susheel

2018-05-01

Diversification of chain stereochemistry opens up the possibilities of an ‘in principle’ increase in the design space of proteins. This huge increase in the sequence and consequent structural variation is aimed at the generation of smart materials. To diversify protein structure stereochemically, we introduced L- and D-α-amino acids as the design alphabet. With a sequence design algorithm, we explored the usage of specific variables such as chirality and the sequence of this alphabet in independent steps. With molecular dynamics, we folded stereochemically diverse homopolypeptides and evaluated their ‘fitness’ for possible design as protein-like foldamers. We propose a fitness function to prune the most optimal fold among 1000 structures simulated with an automated repetitive simulated annealing molecular dynamics (AR-SAMD) approach. The highly scored poly-leucine fold with sequence lengths of 24 and 30 amino acids were later sequence-optimized using a Dead End Elimination cum Monte Carlo based optimization tool. This paper demonstrates a novel approach for the de novo design of protein-like foldamers.

Bonding in phase change materials: concepts and misconceptions.

PubMed

Jones, R O

2018-04-18

Bonding concepts originating in chemistry are surveyed from a condensed matter perspective, beginning around 1850 with 'valence' and the word 'bond' itself. The analysis of chemical data in the 19th century resulted in astonishing progress in understanding the connectivity and stereochemistry of molecules, almost without input from physicists until the development of quantum mechanics in 1925 and afterwards. The valence bond method popularized by Pauling and the molecular orbital methods of Hund, Mulliken, Bloch, and Hückel play major roles in the subsequent development, as does the central part played by the kinetic energy in covalent bonding (Ruedenberg and others). 'Metallic' (free electron) and related approaches, including pseudopotential and density functional theories, have been remarkably successful in understanding structures and bonding in molecules and solids. We discuss these concepts in the context of phase change materials, which involve the rapid and reversible transition between amorphous and crystalline states, and note the confusion that some have caused, in particular 'resonance' and 'resonant bonding'.

Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis.

PubMed

Zarychta, Bartosz; Lyubimov, Artem; Ahmed, Maqsood; Munshi, Parthapratim; Guillot, Benoît; Vrielink, Alice; Jelsch, Christian

2015-04-01

Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein-cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O···H-N hydrogen bonds was analyzed with respect to the different secondary-structure elements.

Rhodium-catalysed asymmetric allylic arylation of racemic halides with arylboronic acids

NASA Astrophysics Data System (ADS)

Sidera, Mireia; Fletcher, Stephen P.

2015-11-01

Csp2-Csp2 cross-coupling reactions between arylboronic acid and aryl halides are widely used in both academia and industry and are strategically important in the development of new agrochemicals and pharmaceuticals. Csp2-Csp3 cross-coupling reactions have been developed, but enantioselective variations are rare and simply retaining the stereochemistry is a problem. Here we report a highly enantioselective Csp2-Csp3 bond-forming method that couples arylboronic acids to racemic allyl chlorides. Both enantiomers of a cyclic chloride are converted into a single enantiomer of product via a dynamic kinetic asymmetric transformation. This Rh-catalysed method uses readily available and inexpensive building blocks and is mild and broadly applicable. For electron-deficient, electron-rich or ortho-substituted boronic acids better results are obtained with racemic allyl bromides. Oxygen substitution in the allyl halide is tolerated and the products can be functionalized to provide diverse building blocks. The approach fills a significant gap in the methods for catalytic asymmetric synthesis.

Inhibitory activity and mechanism of inhibition of the N-[[(4-benzoylamino)phenyl]sulfonyl]amino acid aldose reductase inhibitors.

PubMed

DeRuiter, J; Mayfield, C A

1990-11-15

A series of substituted N-[[(4-benzoylamino)phenyl]sulfonyl]amino acids (BAPS-amino acids) were synthesized by established methods, and the stereochemistry of the products was confirmed by HPLC analysis after chiral derivatization. When tested against aldose reductase (alditol:NADP+ oxidoreductase; EC 1.1.1.21; ALR2) isolated from rat lens, all of the BAPS-amino acids were determined to be significantly more inhibitory than the corresponding N-(phenylsulfonyl)amino acids. Structure-inhibition and enzyme kinetic analyses suggest that the BAPS-amino acids inhibit ALR2 by a mechanism similar to the N-(phenylsulfonyl)amino acids. However, multiple inhibition analyses indicate that the increased inhibitory activity of the BAPS-amino acids is a result of interaction with multiple sites present on ALR2. Enzyme specificity studies with several of the BAPS-amino acids demonstrated that these compounds do not produce significant inhibition of other nucleotide-requiring enzymes including aldehyde reductase (alcohol: NADP+ oxidoreductase; EC 1.1.1.2; ALR1).

Stereochemistry Balances Cell Permeability and Solubility in the Naturally Derived Phepropeptin Cyclic Peptides.

PubMed

Schwochert, Joshua; Lao, Yongtong; Pye, Cameron R; Naylor, Matthew R; Desai, Prashant V; Gonzalez Valcarcel, Isabel C; Barrett, Jaclyn A; Sawada, Geri; Blanco, Maria-Jesus; Lokey, R Scott

2016-08-11

Cyclic peptide (CP) natural products provide useful model systems for mapping "beyond-Rule-of-5" (bRo5) space. We identified the phepropeptins as natural product CPs with potential cell permeability. Synthesis of the phepropeptins and epimeric analogues revealed much more rapid cellular permeability for the natural stereochemical pattern. Despite being more cell permeable, the natural compounds exhibited similar aqueous solubility as the corresponding epimers, a phenomenon explained by solvent-dependent conformational flexibility among the natural compounds. When analyzing the polarity of the solution structures we found that neither the number of hydrogen bonds nor the total polar surface area accurately represents the solvation energies of the high and low dielectric conformations. This work adds to a growing number of natural CPs whose solvent-dependent conformational behavior allows for a balance between aqueous solubility and cell permeability, highlighting structural flexibility as an important consideration in the design of molecules in bRo5 chemical space.

Asymmetric total synthesis of onoseriolide, bolivianine, and isobolivianine.

PubMed

Du, Biao; Yuan, Changchun; Yu, Tianzi; Yang, Li; Yang, Yang; Liu, Bo; Qin, Song

2014-02-24

In this article, we describe our efforts on the total synthesis of bolivianine (1) and isobolivianine (2), involving the synthesis of onoseriolide (3). The first generation synthesis of bolivianine was completed in 21 steps by following a chiral resolution strategy. Based on the potential biogenetic relationship between bolivianine (1), onoseriolide (3), and β-(E)-ocimene (8), the second generation synthesis of bolivianine was biomimetically achieved from commercially available (+)-verbenone in 14 steps. The improved total synthesis features an unprecedented palladium-catalyzed intramolecular cyclopropanation through an allylic metal carbene, for the construction of the ABC tricyclic system, and a Diels-Alder/intramolecular hetero-Diels-Alder (DA/IMHDA) cascade for installation of the EFG tricyclic skeleton with the correct stereochemistry. Transformation from bolivianine to isobolivianine was facilitated in the presence of acid. The biosynthetic mechanism and the excellent regio- and endo selectivities in the cascade are well supported by theoretical chemistry based on the DFT calculations. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Determination of the Molecular Structures of Ferric Enterobactin and Ferric Enantioenterobactin Using Racemic Crystallography.

PubMed

Johnstone, Timothy C; Nolan, Elizabeth M

2017-10-25

Enterobactin is a secondary metabolite produced by Enterobacteriaceae for acquiring iron, an essential metal nutrient. The biosynthesis and utilization of enterobactin permits many Gram-negative bacteria to thrive in environments where low soluble iron concentrations would otherwise preclude survival. Despite extensive work carried out on this celebrated molecule since its discovery over 40 years ago, the ferric enterobactin complex has eluded crystallographic structural characterization. We report the successful growth of single crystals containing ferric enterobactin using racemic crystallization, a method that involves cocrystallization of a chiral molecule with its mirror image. The structures of ferric enterobactin and ferric enantioenterobactin obtained in this work provide a definitive assignment of the stereochemistry at the metal center and reveal secondary coordination sphere interactions. The structures were employed in computational investigations of the interactions of these complexes with two enterobactin-binding proteins, which illuminate the influence of metal-centered chirality on these interactions. This work highlights the utility of small-molecule racemic crystallography for obtaining elusive structures of coordination complexes.

Syncarpamide, a new antiplasmodial (+)-norepinephrine derivative from Zanthoxylum syncarpum.

PubMed

Ross, Samir A; Sultana, Gazi N N; Burandt, Charles L; ElSohly, Mahmoud A; Marais, Jannie P J; Ferreira, Daneel

2004-01-01

A new (+)-norepinephrine derivative, syncarpamide (1), along with a known coumarin, (+)-S-marmesin (2), and one known alkaloid, decarine (3), have been isolated from the stem of Zanthoxylum syncarpum. The structure of compound 1 was elucidated on the basis of 1D and 2D NMR, MS, IR, optical rotation, and CD analyses. Its absolute stereochemistry was elucidated by synthesis of its enantiomer and subsequent comparison of CD data. Characterizations of compounds 2 and 3 were based on spectral analysis and comparison with reported data. Compounds 1 and 3 showed antiplasmodial activity, with IC(50) values of 2.04 and 1.44 microM against Plasmodium falciparum D(6) clone and 3.06 and 0.88 microM against P. falciparum W(2) clone, respectively. Compound 3 showed cytotoxicity at 56.42 microM, whereas compound 1 was not cytotoxic at 10.42 microM. Compound 1 was tested for hypotensive activity, but no activity was observed. Compound 2 showed no antiplasmodial or antimicrobial activities.

The origin and fate of 4-methyl steroid hydrocarbons. I. Diagenesis of 4-methyl sterenes

NASA Astrophysics Data System (ADS)

Wolff, George A.; Lamb, Neil A.; Maxwell, James R.

1986-03-01

Treatment of 4-methylcholest-4-ene under mild acid conditions at low temperatures gives chemical evidence for certain features seen in the distributions of sedimentary 4-methyl steroid hydrocarbons, and further indicates that many low temperature diagenetic reactions of steroids are explicable in terms of acid catalysed rearrangements. Specifically, the results provide: (i) Indirect evidence that the 4-ene skeleton is a key intermediate in the dehydration of 4-methyl stanols in sediments. (ii) An explanation for the distribution of 4-methyl sterenes and A-nor sterenes in the lacustrine Messel shale (Eocene). (iii) An explanation for the presence of 4β-methyl steranes in relatively immature sedimentary rocks, despite the precursor stanols having the 4α-methyl configuration. With increasing maturity in the Paris Basin shales (Lower Toarcian), the less stable 4β-methyl steranes decrease gradually in abundance relative to their 4α-methyl counterparts, at a rate fairly similar to the change in pristane stereochemistry.

Potential anthelmintics: polyphenols from the tea plant Camellia sinensis L. are lethally toxic to Caenorhabditis elegans.

PubMed

Mukai, Daisuke; Matsuda, Noriko; Yoshioka, Yu; Sato, Masashi; Yamasaki, Toru

2008-04-01

A novel gallate of tannin, (-)-epigallocatechin-(2 beta-->O-->7',4 beta-->8')-epicatechin-3'-O-gallate (8), together with (-)-epicatechin-3-O-gallate (4), (-)-epigallocatechin (5), (-)-epigallocatechin-3-O-gallate (6), and (+)-gallocatechin-(4 alpha-->8')-epigallocatechin (7), were isolated from the tea plant Camellia sinensis (L.) O. Kuntze var. sinensis (cv., Yabukita). The structure of 8, including stereochemistry, was elucidated by spectroscopic methods and hydrolysis. The compounds, along with commercially available pyrogallol (1), (+)-catechin (2), and (-)-epicatechin (3), were examined for toxicity towards egg-bearing adults of Caenorhabditis elegans. The anthelmintic mebendazole (9) was used as a positive control. Neither 2 nor 3 were toxic but the other compounds were toxic in the descending order 8, 7 approximately 6, 9, 4, 5, 1. The LC(50) (96 h) values of 8 and 9 were evaluated as 49 and 334 micromol L(-1), respectively. These data show that many green tea polyphenols may be potential anthelmintics.

Structure and mechanism of human DNA polymerase [eta

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

Biertümpfel, Christian; Zhao, Ye; Kondo, Yuji

2010-11-03

The variant form of the human syndrome xeroderma pigmentosum (XPV) is caused by a deficiency in DNA polymerase {eta} (Pol{eta}), a DNA polymerase that enables replication through ultraviolet-induced pyrimidine dimers. Here we report high-resolution crystal structures of human Pol{eta} at four consecutive steps during DNA synthesis through cis-syn cyclobutane thymine dimers. Pol{eta} acts like a 'molecular splint' to stabilize damaged DNA in a normal B-form conformation. An enlarged active site accommodates the thymine dimer with excellent stereochemistry for two-metal ion catalysis. Two residues conserved among Pol{eta} orthologues form specific hydrogen bonds with the lesion and the incoming nucleotide to assistmore » translesion synthesis. On the basis of the structures, eight Pol{eta} missense mutations causing XPV can be rationalized as undermining the molecular splint or perturbing the active-site alignment. The structures also provide an insight into the role of Pol{eta} in replicating through D loop and DNA fragile sites.« less

Crystal structure of di-μ-chlorido-bis-(chlorido-{N1,N1-diethyl-N4-[(pyridin-2-yl-κN)methyl-idene]benzene-1,4-di-amine-κN4}mercury(II)).

PubMed

Faizi, Md Serajul Haque; Dege, Necmi; Goleva, Kateryna

2017-06-01

The title dinuclear mercury(II) complex, [Hg 2 Cl 4 (C 16 H 19 N 3 ) 2 ], synthesized from the pyridine-derived Schiff base ( E )- N 1 , N 1 -diethyl- N 4 -[(pyridin-2-yl)methyl-idene]benzene-1,4-di-amine (DPMBD), has inversion symmetry. The five-coordinated Hg II atoms have distorted square-pyramidal stereochemistry comprising two N-atom donors from bidentate chelate BPMBD ligands and three Cl-atom donors, two bridging and one monodentate. The dihedral angle between the benzene and the pyridine rings in the BPMBD ligand is 7.55 (4)°. In the crystal, the dinuclear mol-ecules are linked by weak C-H⋯Cl hydrogen bonds, forming zigzag ribbons lying parallel to [001]. Also present in the structure are π-π inter-actions between benzene and pyridine rings [minimum ring-centroid separation = 3.698 (8) Å].

Synthesis of β-Nicotinamide Riboside Using an Efficient Two-Step Methodology.

PubMed

Zhang, Ning; Sauve, Anthony A

2017-12-24

A two-step chemical method for the synthesis of β-nicotinamide riboside (NR) is described. NR has achieved wide use as an NAD + precursor (vitamin B3) and can significantly increase central metabolite NAD + concentrations in mammalian cells. β-NR can be prepared with an efficient two-step procedure. The synthesis is initiated via coupling of commercially available 1,2,3,5-tetra-O-acetyl-β-D-ribofuranose with ethyl nicotinate in the presence of trimethylsilyl trifluoromethanesulfonate (TMSOTf). 1 H NMR showed that the product was formed with complete stereoselectivity to produce only the β-isomer in high yield (>90% versus starting sugar). The clean stereochemical result suggests that the coupling proceeds via a cationic cis-1,2-acyloxonium-sugar intermediate, which controls addition by nucleophiles to generate predominantly β-stereochemistry. The subsequent deprotection of esters in methanolic ammonia generates the desired product in 85% overall yield versus sugar. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Preferences of the peripheral olfactory system of Western Flower Thrips, Frankliniella occidentalis towards stereoisomers of common plant volatiles.

PubMed

Abdullah, Zayed S; Butt, Tariq M

Stereochemistry plays a significant role in structure-activity relationships of messenger chemicals. The ability to distinguish between enantiomers and geometric isomers, however, may be limited to certain stereoisomeric substances, depending on the receiver. In this study, we assessed the preference of the peripheral olfactometry system of Western Flower Thrips, F. occidentalis towards ubiquitously expressed host compounds, with a goal of establishing whether particular stereoisomers enhance host odour recognition. We demonstrate that the peripheral olfactory system of a highly polyphagous thysanopteran insect has evolved to become highly sensitive to a type of green leaf volatile, which is highly ubiquitous in the plant kingdom. We show that there is a significantly greater antennal response to the cis isomer, more so than the isomerisation by-product trans -3-hexen-1-ol. We demonstrate that the antennae of a highly polyphagous insect are capable of detecting common plant secondary metabolites in both enantiomeric forms.

Toblerols: Cyclopropanol-Containing Polyketide Modulators of Antibiosis in Methylobacteria.

PubMed

Ueoka, Reiko; Bortfeld-Miller, Miriam; Morinaka, Brandon I; Vorholt, Julia A; Piel, Jörn

2018-01-22

Trans-AT polyketide synthases (PKSs) are a family of biosynthetically versatile modular type I PKSs that generate bioactive polyketides of impressive structural diversity. In this study, we detected, in the genome of several bacteria a cryptic, architecturally unusual trans-AT PKS gene cluster which eluded automated PKS prediction. Genomic mining of one of these strains, the model methylotroph Methylobacterium extorquens AM1, revealed unique epoxide- and cyclopropanol-containing polyketides named toblerols. Relative and absolute stereochemistry were determined by NMR experiments, chemical derivatization, and the comparison of CD data between the derivatized natural product and a synthesized model compound. Biosynthetic data suggest that the cyclopropanol moiety is generated by carbon-carbon shortening of a more extended precursor. Surprisingly, a knock-out strain impaired in polyketide production showed strong inhibitory activity against other methylobacteria in contrast to the wild-type producer. The activity was inhibited by complementation with toblerols, thus suggesting that these compounds modulate an as-yet unknown methylobacterial antibiotic. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The 2.3 {angstrom} crystal structure of cholera toxin B subunit pentamer: Choleragenoid

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

Zhang, Rong-Guang; Westbrook, M.L.; Maulik, P.R.

1996-02-01

Cholera toxin, a heterohexameric AB{sub 5} enterotoxin released by Vibrio cholera, induces a profuse secretory diarrhea in susceptible hosts. Choleragenoid, the B subunit pentamer of cholera toxin, directs the enzymatic A subunit to its target by binding to GM{sub 1} gangliosides exposed on the luminal surface of intestinal epithelial cells. We have solved the crystal structure of choleragenoid at 2.3 {Angstrom} resolution by combining single isomorphous replacement with non-crystallographic symmetry averaging. The structure of the B subunits, and their pentameric arrangement, closely resembles that reported for the intact holotoxin (choleragen), the heat-labile enterotoxin from E. coli, and for a choleragenoid-GM{submore » 1} pentasaccharide complex. In the absence of the A subunit the central cavity of the B pentamer is a highly solvated channel. The binding of the A subunit or the receptor pentasaccharide to choleragenoid has only a modest effect on the local stereochemistry and does not perceptibly alter the subunit interface.« less

Development of miracle medicines from sialic acids

PubMed Central

OGURA, Haruo

2011-01-01

Sialic acids are electronegatively charged C9-sugars and are considered to play important roles in higher animals and some microorganisms. Denoting their significance, understanding and exploiting the complexity of the sialic acids has been referred to as the “the third language of life”. In essence, “sialic acid derivatives possess a harmonious shape and good balance between two opposing hydrophilic and hydrophobic parts, meaning that they should display various kinds of potentially unique and possibly conflicting physiological activities (glycolipoids)”. Consequently, there are good omens that unprecedented ‘miracle’ medicines could be developed from sialic acid derivatives. In this review, the first problem, the preparation of sialic acids, is covered, the synthesis of sialic acid derivatives and confirmation of their structures obviously being of critical significance. In addition we needed to confirm their precise stereochemistry and a hydrolysis method has been developed for confirmation of the anomeric position. Several of the compounds have already demonstrated interesting bioactivity. PMID:21670567

cis,cis,cis-(Acetato-κ(2) O,O')bis-[1,2-bis-(diphenyl-phosphan-yl)ethane-κ(2) P,P']ruthenium(II) 0.75-trifluoro-methane-sulfonate 0.25-chloride.

PubMed

Figueira, João; Rodrigues, João; Valkonen, Arto

2013-04-01

In the title Ru(II) carboxyl-ate compound, [Ru(C2H3O2)(C26H24P2)2](CF3O3S)0.75Cl0.25, the distorted tris-bidentate octa-hedral stereochemistry about the Ru(II) atom in the complex cation comprises four P-atom donors from two 1,2-bis-(diphenyl-phosphan-yl)ethane ligands [Ru-P = 2.2881 (13)-2.3791 (13) Å] and two O-atom donors from the acetate ligand [Ru-O = 2.191 (3) and 2.202 (3) Å]. The disordered counter-anions are located on the same site in the structure in a 3:1 ratio, the expanded formula comprising four complex cations, three trifluoro-methane-sulfonate anions and one chloride anion, with two such formula units in the unit cell.

Oxaphosphinanes: new therapeutic perspectives for glioblastoma.

PubMed

Clarion, Ludovic; Jacquard, Carine; Sainte-Catherine, Odile; Loiseau, Séverine; Filippini, Damien; Hirlemann, Marie-Hélène; Volle, Jean-Noël; Virieux, David; Lecouvey, Marc; Pirat, Jean-Luc; Bakalara, Norbert

2012-03-08

This paper reports the design and the synthesis of a new family of compounds, the phostines, belonging to the [1,2]oxaphosphinane family. Twenty-six compounds have been screened for their antiproliferative activity against a large panel of NCI cancer cell lines. Because of its easy synthesis and low EC(50) value (500 nM against the C6 rat glioma cell line), compound 3.1a was selected for further biological study. Moreover, the specific biological effect of 3.1a on the glioblastoma phylogenetic cluster from the NCI is dependent on its stereochemistry. Within that cluster, 3.1a has a higher antiproliferative activity than Temozolomide and is more potent than paclitaxel for the SF295 and SNB75 cell lines. In constrast with paclitaxel and vincristine, 3.1a is devoid of astrocyte toxicity. The original activity spectrum of 3.1a on the NCI cancer cell line panel allows the development of this family for use in association with existing drugs, opening new therapeutic perspectives.

Synthesis, spectroscopic characterization and biological activities of N4O2 Schiff base ligand and its metal complexes of Co(II), Ni(II), Cu(II) and Zn(II)

NASA Astrophysics Data System (ADS)

Al-Resayes, Saud I.; Shakir, Mohammad; Abbasi, Ambreen; Amin, Kr. Mohammad Yusuf; Lateef, Abdul

The Schiff base ligand, bis(indoline-2-one)triethylenetetramine (L) obtained from condensation of triethylenetetramine and isatin was used to synthesize the complexes of type, [ML]Cl2 [M = Co(II), Ni(II), Cu(II) and Zn(II)]. L was characterized on the basis of the results of elemental analysis, FT-IR, 1H and 13C NMR, mass spectroscopic studies. The stoichiometry, bonding and stereochemistries of complexes were ascertained on the basis of results of elemental analysis, magnetic susceptibility values, molar conductance and various spectroscopic studies. EPR, UV-vis and magnetic moments revealed an octahedral geometry for complexes. L and its Cu(II) and Zn(II) complexes were screened for their antibacterial activity. Analgesic activity of Cu(II) and Zn(II) complexes was also tested in rats by tail flick method. Both complexes were found to possess good antibacterial and moderate analgesic activity.

Stereochemistry and function of oxaloacetate keto-enol tautomerase

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

Creighton, D.J.; Johnson, J.D.; Lambert, M.R.

1986-05-01

Oxaloacetate keto-enol tautomerase, partially purified from porcine kidney, catalyzes the conversions of enol- to keto-oxaloacetate by a mechanism in which solvent protons end up equally distributed between the two prochiral positions at C3 of keto-oxaloacetate. This conclusion is based upon the observation that when enzyme catalyzed ketonization is conducted in /sup 3/H/sub 2/O in the presence of excess malate dehydrogenase and NADH, only 50% of the /sup 3/H in the isolated (2S)-(3-/sup 3/H)malate is labilized to solvent upon treatment with fumarase. Either the tautomerase operates on the basis of a highly unusual stereomechanistic principle or tautomerase activity is not anmore » evolved property of the enzyme protein. As a result of an attempt to clarify the physiological importance of oxaloacetate tautomerase activity, keto-oxaloacetate was demonstrated to be directly transported across the inner membrane of rat liver mitochrondria, on the basis of the results of kinetic and isotope-trapping experiments.« less

Iridoid glycosides from Gardeniae Fructus for treatment of ankle sprain.

PubMed

Chen, Quan Cheng; Zhang, Wei Yun; Youn, Uijoung; Kim, Hongjin; Lee, IkSoo; Jung, Hyun-Ju; Na, MinKyun; Min, Byung-Sun; Bae, KiHwan

2009-04-01

The iridoid glycosides, genipin 1-O-beta-D-isomaltoside (1) and genipin 1,10-di-O-beta-D-glucopyranoside (2), together with six known iridoid glycosides, genipin 1-O-beta-D-gentiobioside (3), geniposide (4), scandoside methyl ester (5), deacetylasperulosidic acid methyl ester (6), 6-O-methyldeacetylasperulosidic acid methyl ester (7), and gardenoside (8) were isolated from an EtOH extract of Gardeniae Fructus. The structures and relative stereochemistries of the metabolites were elucidated on the basis of 1D- and 2D-NMR spectroscopic techniques, high-resolution mass spectrometry, and chemical evidence. Geniposide (4), one of the main compounds of Gardeniae Fructus, was tested for treatment of ankle sprain using an ankle sprain model in rats. From the second to fifth day, the geniposide (4) (100mg/ml) treated group exhibited significant differences (p<0.01) with approximately 21-34% reduction in swelling ratio compared with those of the vehicle treated control group. This indicated the potential effect of geniposide (4) for the treatment of disorders such as ankle sprain.

Structure-Activity Relationships of 6- and 8-Gingerol Analogs as Anti-Biofilm Agents.

PubMed

Choi, Hyunsuk; Ham, So-Young; Cha, Eunji; Shin, Yujin; Kim, Han-Shin; Bang, Jeong Kyu; Son, Sang-Hyun; Park, Hee-Deung; Byun, Youngjoo

2017-12-14

Pseudomonas aeruginosa is a causative agent of chronic infections in immunocompromised patients. Disruption of quorum sensing circuits is an attractive strategy for treating diseases associated with P. aeruginosa infection. In this study, we designed and synthesized a series of gingerol analogs targeting LasR, a master regulator of quorum sensing networks in P. aeruginosa. Structure-activity relationship studies showed that a hydrogen-bonding interaction in the head section, stereochemistry and rotational rigidity in the middle section, and optimal alkyl chain length in the tail section are important factors for the enhancement of LasR-binding affinity and for the inhibition of biofilm formation. The most potent compound 41, an analog of (R)-8-gingerol with restricted rotation, showed stronger LasR-binding affinity and inhibition of biofilm formation than the known LasR antagonist (S)-6-gingerol. This new LasR antagonist can be used as an early lead compound for the development of anti-biofilm agents to treat P. aeruginosa infections.

δ-Deuterium Isotope Effects as Probes for Transition-State Structures of Isoprenoid Substrates

PubMed Central

2015-01-01

The biosynthetic pathways to isoprenoid compounds involve transfer of the prenyl moiety in allylic diphosphates to electron-rich (nucleophilic) acceptors. The acceptors can be many types of nucleophiles, while the allylic diphosphates only differ in the number of isoprene units and stereochemistry of the double bonds in the hydrocarbon moieties. Because of the wide range of nucleophilicities of naturally occurring acceptors, the mechanism for prenyltransfer reactions may be dissociative or associative with early to late transition states. We have measured δ-secondary kinetic isotope effects operating through four bonds for substitution reactions with dimethylallyl derivatives bearing deuterated methyl groups at the distal (C3) carbon atom in the double bond under dissociative and associative conditions. Computational studies with density functional theory indicate that the magnitudes of the isotope effects correlate with the extent of bond formation between the allylic moiety and the electron-rich acceptor in the transition state for alkylation and provide insights into the structures of the transition states for associative and dissociative alkylation reactions. PMID:24665882

Design, Synthesis, Biological Evaluation, and X-ray Studies of HIV-1 Protease Inhibitors with Modified P2′ Ligands of Darunavir

PubMed Central

Fyvie, W. Sean; Brindisi, Margherita; Steffey, Melinda; Agniswamy, Johnson; Wang, Yuan-Fang; Aoki, Manabu; Amano, Masayuki; Weber, Irene T.; Mitsuya, Hiroaki

2018-01-01

The structure-based design, synthesis, and biological evaluation of a series of nonpeptidic HIV-1 protease inhibitors with rationally designed P2′ ligands are described. The inhibitors are designed to enhance backbone binding interactions, particularly at the S2′ subsite. Synthesis of inhibitors was carried out efficiently. The stereochemistry of alcohol functionalities of the P2′ ligands was set by asymmetric reduction of the corresponding ketone using (R,R)- or (S,S)-Noyori catalysts. A number of inhibitors displayed very potent enzyme inhibitory and antiviral activity. Inhibitors 3g and 3h showed enzyme Ki values of 27.9 and 49.7 pM and antiviral activity of 6.2 and 3.9 nM, respectively. These inhibitors also remained quite potent against darunavir-resistant HIV-1 variants. An X-ray structure of inhibitor 3g in complex with HIV-1 protease revealed key interactions in the S2′ subsite. PMID:29110408

Flexible synthesis of poison-frog alkaloids of the 5,8-disubstituted indolizidine-class. II: Synthesis of (-)-209B, (-)-231C, (-)-233D, (-)-235B", (-)-221I, and an epimer of 193E and pharmacological effects at neuronal nicotinic acetylcholine receptors.

PubMed

Kobayashi, Soushi; Toyooka, Naoki; Zhou, Dejun; Tsuneki, Hiroshi; Wada, Tsutomu; Sasaoka, Toshiyasu; Sakai, Hideki; Nemoto, Hideo; Garraffo, H Martin; Spande, Thomas F; Daly, John W

2007-01-01

The 5,8-disubstituted indolizidines constitute the largest class of poison-frog alkaloids. Some alkaloids have been shown to act as noncompetitive blockers at nicotinic acetylcholine receptors but the proposed structures and the biological activities of most of the 5,8-disubstituted indolizidines have not been determined because of limited supplies of the natural products. We have therefore conducted experiments to confirm proposed structures and determine biological activities using synthetic compounds. Recently, we reported that one of this class of alkaloids, (-)-235B', acts as a noncompetitive antagonist for α4β2 nicotinic receptors, and its sensitivity is comparable to that of the classical competitive antagonist for this receptor, dihydro-β-erythroidine. The enantioselective syntheses of (-)-209B, (-)-231C, (-)-233D, (-)-235B", (-)-221I, and what proved to be an epimer of natural 193E, starting from common chiral lactams have been achieved. When we performed electrophysiological recordings to examine the effects of the synthetic alkaloids on two major subtypes of nicotinic receptors (α4β2 and α7) expressed in Xenopus laevis oocytes, (-)-231C effectively blocked α4β2 receptor responses (IC(50 )value, 1.5 μM) with a 7.0-fold higher potency than for blockade of α7 receptor responses. In contrast, synthetic (-)-221I and (-)-epi-193E were more potent in blocking α7 receptor responses (IC(50 )value, 4.4 μM and 9.1 μM, respectively) than α4β2 receptor responses (5.3-fold and 2.0-fold, respectively). We achieved the total synthesis of (-)-209B, (-)-231C, (-)-233D, (-)-235B", (-)-221I, and an epimer of 193E starting from common chiral lactams, and the absolute stereochemistry of natural (-)-233D was determined. Furthermore, the relative stereochemistry of (-)-231C and (-)-221I was also determined. The present asymmetric synthesis of the proposed structure for 193E revealed that the C-8 configuration of natural 193E should be revised. The selectivity for α4β2 and α7 nicotinic receptors differed markedly for the 5,8-disubstituted indolizidines tested, and thus it appears that the nature of the side chains in these indolizidines is crucial with regard to subtype-selectivity.

Synthesis of cis- and trans-α-l-[4.3.0]bicyclo-DNA monomers for antisense technology: methods for the diastereoselective formation of bicyclic nucleosides.

PubMed

Hanessian, Stephen; Schroeder, Benjamin R; Merner, Bradley L; Chen, Bin; Swayze, Eric E; Seth, Punit P

2013-09-20

Two α-L-ribo-configured bicyclic nucleic acid modifications, represented by analogues 12 and 13, which are epimeric at C3' and C5' have been synthesized using a carbohydrate-based approach to build the bicyclic core structure. An intramolecular L-proline-mediated aldol reaction was employed to generate the cis-configured ring junction of analogue 12 and represents a rare application of this venerable organocatalytic reaction to a carbohydrate system. In the case of analogue 13, where a trans-ring junction was desired, an intermolecular diastereoselective Grignard reaction followed by ring-closing metathesis was used. In order to set the desired stereochemistry at the C5' positions of both nucleoside targets, a study of diastereoselective Lewis acid mediated allylation reactions on a common bicyclic aldehyde precursor was carried out. Analogue 12 was incorporated in oligonucleotide sequences, and thermal denaturation experiments indicate that it is destabilizing when paired with complementary DNA and RNA. However, this construct shows a significant improvement in nuclease stability relative to a DNA oligonucleotide.

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase.

PubMed

Nascimento, Érica C M; Oliva, Mónica; Andrés, Juan

2018-05-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

The truth about false unicorn (Chamaelirium luteum): total synthesis of 23R,24S-chiograsterol B defines the structure and stereochemistry of the major saponins from this medicinal herb.

PubMed

Matovic, Nicholas J; Stuthe, Julia M U; Challinor, Victoria L; Bernhardt, Paul V; Lehmann, Reginald P; Kitching, William; De Voss, James J

2011-06-27

Chamaelirium luteum is used in traditional medicine systems and commercial botanical dietary supplements for the treatment of female reproductive health problems. Despite the wide use of this herb, only very limited phytochemical characterisation is available. Our investigation of C. luteum roots led to the isolation of two new steroidal saponins 1 and 2 that contain an unusual aglycone 3. The absolute configurations of these molecules were unable to be determined spectroscopically and thus the total synthesis of 3 was undertaken and achieved in 16 steps and 1.6 % overall yield from pregnenolone. The key step in the synthesis was the stereoselective installation of the side chain at C-17 and C-20, which employed anion-accelerated oxy-Cope methodology. The relative configuration of aglycone 3 was determined by X-ray crystallography of an advanced synthetic intermediate. The absolute configuration was based upon that of the pregnenolone-derived steroidal skeleton and determined to be 23R,24S. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure and cytotoxic activity of sesquiterpene glycoside esters from Calendula officinalis L.: Studies on the conformation of viridiflorol.

PubMed

D'Ambrosio, Michele; Ciocarlan, Alexandru; Colombo, Elisa; Guerriero, Antonio; Pizza, Cosimo; Sangiovanni, Enrico; Dell'Agli, Mario

2015-09-01

Topic applications of Calendula officinalis L. lipophilic extracts are used in phytotherapy to relieve skin inflammatory conditions whereas infusions are used as a remedy for gastric complaints. Such a different usage might be explained by some cytotoxicity of lipophilic extracts at gastric level but little is known about this. Therefore, we screened the CH2Cl2 extract from the flowers of C. officinalis by MTT and LDH assays in human epithelial gastric cells AGS. This bioassay-oriented approach led to the isolation of several sesquiterpene glycosides which were structurally characterized by spectroscopic measurements, chemical reactions and MM calculations. The conformational preferences of viridiflorol fucoside were established and a previously assigned stereochemistry was revised. The compounds 1a, 2a and 3f showed comparably high cytotoxicity in the MTT assays, whereas the effect on LDH release was lower. Our study provides new insights on the composition of C. officinalis extracts of medium polarity and identifies the main compounds that could be responsible for cytotoxic effects at gastric level. Copyright © 2015 Elsevier Ltd. All rights reserved.

Design and synthesis of biotin analogues reversibly binding with streptavidin.

PubMed

Yamamoto, Tomohiro; Aoki, Kiyoshi; Sugiyama, Akira; Doi, Hirofumi; Kodama, Tatsuhiko; Shimizu, Yohei; Kanai, Motomu

2015-04-01

Two new biotin analogues, biotin carbonate 5 and biotin carbamate 6, have been synthesized. These molecules were designed to reversibly bind with streptavidin by replacing the hydrogen-bond donor NH group(s) of biotin's cyclic urea moiety with oxygen. Biotin carbonate 5 was synthesized from L-arabinose (7), which furnishes the desired stereochemistry at the 3,4-cis-dihydroxy groups, in 11% overall yield (over 10 steps). Synthesis of biotin carbamate 6 was accomplished from L-cysteine-derived chiral aldehyde 33 in 11% overall yield (over 7 steps). Surface plasmon resonance analysis of water-soluble biotin carbonate analogue 46 and biotin carbamate analogue 47 revealed that KD values of these compounds for binding to streptavidin were 6.7×10(-6)  M and 1.7×10(-10)  M, respectively. These values were remarkably greater than that of biotin (KD =10(-15)  M), and thus indicate the importance of the nitrogen atoms for the strong binding between biotin and streptavidin. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

New pseudopterosin and seco-pseudopterosin diterpene glycosides from two Colombian isolates of Pseudopterogorgia elisabethae and their diverse biological activities.

PubMed

Rodríguez, Ileana I; Shi, Yan-Ping; García, Oscar J; Rodríguez, Abimael D; Mayer, Alejandro M S; Sánchez, Juan A; Ortega-Barria, Eduardo; González, José

2004-10-01

As part of an ongoing program to explore the chemical constituents of Caribbean marine invertebrates, a family of 13 new diterpene glycosides, pseudopterosins P-Z (1-11) and seco-pseudopterosins H (12) and I (13), have been isolated from the organic extracts of two collections of the sea whip Pseudopterogorgia elisabethae procured near the Colombian Southwestern Caribbean Sea. The structures of compounds 1-13, including absolute stereochemistry, have been proposed on the basis of comprehensive spectral analyses, chemical transformations, specific rotation, and TLC chromatographic analyses. Pseudopterosin Q (2) inhibited thromboxane B2 (TXB2) (IC50 = 4.7 microM) and superoxide anion (O2-) (IC50 = 11.2 microM) generation from E. coli lipopolysaccharide (LPS) activated rat neonatal microglia in vitro. In contrast, pseudopterosins P (1), U (6), V (7), W (8), and X (9) as well as seco-pseudopterosins H (12) and I (13) demonstrated minimal effects on both TXB2 and O2- release. In addition, some of the new compounds displayed strong antituberculosis, antiviral, antimalarial, and anticancer activity.

Metal cluster chemistry: Structure and stereochemistry in the polynuclear rhodium hydrides HnRhn[P(OR)3]2n

PubMed Central

Brown, R. K.; Williams, J. M.; Fredrich, M. F.; Day, V. W.; Sivak, A. J.; Muetterties, E. L.

1979-01-01

Crystallographic analyses of x-ray and neutron diffraction data have provided a definitive structural representation of {HRh[P(O-i-C3H7)3]2}2 and {HRh[P(OCH3)3]2}3. These polynuclear hydrides are generated from square planar H2Rh[P(OR)3]2 units by edge (hydrogen atom) sharing and by vertex (hydrogen atom) sharing to form the dimeric and trimeric structures, respectively. The square-planar units are held together through four-center and three-center two-electron Rh—H—Rh bonds in the dimer and trimer, respectively. The dimer and trimer molecules each add one molecule of hydrogen to form H[(i-C3H7O)3P]2RhH3Rh [P(O-i-C3H7)3]2 and H5Rh3[P(OCH3)3]6, respectively. NMR spectral information has served to define the stereochemical features of these polyhydrides. The significance of this chemistry in the metal cluster-metal surface analogy is described. PMID:16592645

Conformer Hunting: An Open-Ended Computational Chemistry Exercise That Expresses Real-World Complexity and Student Forethought

NASA Astrophysics Data System (ADS)

Lipkowitz, Kenny B.; Robertson, Daniel

2000-02-01

A computational chemistry project suitable for both graduate and undergraduate classes has been developed, tested, and implemented successfully over the course of 10 years. In this project we ask students the following simple question: "Which conformer searching strategy in Spartan is the best?" To answer this question the students need to develop a working definition of what "best" means within the context of the project, design their own experiments that can address that question most suitably, carry out the calculations to derive a compelling answer, and then write their results in the form of a research paper. In addition to teaching students about potential energy surfaces, molecular modeling techniques, and stereochemistry, the pedagogical advantages of this computational chemistry exercise compared to others published in this Journal are that it (i) requires a significant amount of student forethought in addition to afterthought by forcing students to design their own experiments, (ii) demonstrates real-world levels of complexity by using molecules having multiple rotatable bonds, (iii) allows for student creativity that is missing in most other published exercises, (iv) focuses on writing in the curriculum.

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase

NASA Astrophysics Data System (ADS)

Nascimento, Érica C. M.; Oliva, Mónica; Andrés, Juan

2018-03-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

A new irregular monoterpene acetate along with eight known compounds with antifungal potential from the aerial parts of Artemisia incisa Pamp (Asteraceae).

PubMed

Rashid, Mamoon Ur; Alamzeb, Muhammad; Ali, Saqib; Shah, Zafar Ali; Naz, Ishrat; Khan, Ashfaq Ahmad; Semaan, Dima; Khan, Mohammad Rafiullah

2017-02-01

A new compound named as santolinylol-3-acetate (4-(2-hydroxypropan-2-yl)-2-methylhexa-1,5-dien-3-yl acetate) (3), along with seven known compounds; linoleic acid (1), benzoic acid (2), santolinylol (4), ethyl-(E)-p-hydroxy cinnamate (5), scopoletin (6), esculetin (7) isofraxidin (8) and eupatorin (9), were isolated from the aerial parts (ethanolic extract) of endangered species: Artemisia incisa Pamp (Asteraceae). The compounds' structures were determined through modern spectroscopic techniques, and comparison of data (physicochemical constants) with the literature. The relative stereochemistry of santolinylol-3-acetate (3) was determined by comparing its data of NOESY, and specific rotation with its diol analogue; santolinylol (4), isolated from the same plant; A. incisa. The results of the antifungal activity showed that coumarins are as whole less active compounds. Compounds 3 (25 and 300 μg/mL), and 4 (12.5 and 300 μg/mL), showed good activities against Candida albicans, and Aspergillus flavus, respectively, which justifies A. incisa as a traditional medicine for curing the said fungal infections.

Copper-catalysed enantioselective stereodivergent synthesis of amino alcohols.

PubMed

Shi, Shi-Liang; Wong, Zackary L; Buchwald, Stephen L

2016-04-21

The chirality, or 'handedness', of a biologically active molecule can alter its physiological properties. Thus it is routine procedure in the drug discovery and development process to prepare and fully characterize all possible stereoisomers of a drug candidate for biological evaluation. Despite many advances in asymmetric synthesis, developing general and practical strategies for obtaining all possible stereoisomers of an organic compound that has multiple contiguous stereocentres remains a challenge. Here, we report a stereodivergent copper-based approach for the expeditious construction of amino alcohols with high levels of chemo-, regio-, diastereo- and enantioselectivity. Specifically, we synthesized these amino-alcohol products using sequential, copper-hydride-catalysed hydrosilylation and hydroamination of readily available enals and enones. This strategy provides a route to all possible stereoisomers of the amino-alcohol products, which contain up to three contiguous stereocentres. We leveraged catalyst control and stereospecificity simultaneously to attain exceptional control of the product stereochemistry. Beyond the immediate utility of this protocol, our strategy could inspire the development of methods that provide complete sets of stereoisomers for other valuable synthetic targets.

Ion Mobility Separation of Isomeric Carbohydrate Precursor Ions and Acquisition of their Independent Tandem Mass Spectra

PubMed Central

Zhu, Maolei; Bendiak, Brad; Clowers, Brian; Hill, Herbert H.

2010-01-01

The rapid separation of isomeric precursor ions of oligosaccharides prior to their analysis by MSn was demonstrated using an ambient pressure ion mobility spectrometer (IMS) interfaced with a quadrupole ion trap. Separations were not limited to specific types of isomers; representative isomers differing solely in the stereochemistry of sugars, in their anomeric configurations, and in their overall branching patterns and linkage positions could be resolved in the millisecond time frame. Physical separation of precursor ions permitted independent mass spectra of individual oligosaccharide isomers to be acquired to at least MS3, the number of stages of dissociation limited only practically by the abundance of specific product ions. IMS-MSn analysis was particularly valuable in the evaluation of isomeric oligosaccharides that yielded identical sets of product ions in MS/MS experiments, revealing pairs of isomers that would otherwise not be known to be present in a mixture if evaluated solely by MS dissociation methods alone. A practical example of IMS-MSn analysis of a set of isomers included within a single HPLC fraction of oligosaccharides released from bovine submaxillary mucin is described. PMID:19562326

Anti-inflammatory sesquiterpene lactones from the flower of Vernonia cinerea.

PubMed

Youn, Ui Joung; Park, Eun-Jung; Kondratyuk, Tamara P; Simmons, Charles J; Borris, Robert P; Tanamatayarat, Patcharawan; Wongwiwatthananukit, Supakit; Toyama, Onoomar; Songsak, Thanapat; Pezzuto, John M; Chang, Leng Chee

2012-09-01

Bioassay-guided fractionation of the hexane extract from the flowers of Vernonia cinerea (Asteraceae) led to the isolation of a new sesquiterpene lactone, 8α-hydroxyhirsutinolide (2), and a new naturally occurring derivative, 8α-hydroxyl-1-O-methylhirsutinolide (3), along with seven known compounds (1 and 4-9). The structures of the new compounds were determined by 1D and 2D NMR experiments and by comparison with the structure of compound 1, whose relative stereochemistry was determined by X-ray analysis. The isolated compounds were evaluated for their cancer chemopreventive potential based on their ability to inhibit nitric oxide (NO) production and tumor necrosis factor alpha (TNF-α)-induced NF-κB activity. Compounds 1, 2, 4, 5, and 9 inhibited TNF-α-induced NF-κB activity with IC(50) values of 3.1, 1.9, 0.6, 5.2, and 1.6 μM, respectively; compounds 4 and 6-9 exhibited significant NO inhibitory activity with IC(50) values of 2.0, 1.5, 1.2, 2.7, and 2.4 μM, respectively. Published by Elsevier Ltd.

Bioorganic Chemistry. A Natural Reunion of the Physical and Life Sciences

PubMed Central

Poulter, C. Dale

2009-01-01

Organic substances were conceived as those found in living organisms. Although the definition was soon broadened to include all carbon-containing compounds, naturally occurring molecules have always held a special fascination for organic chemists. From these beginnings, molecules from nature were indespensible tools as generations of organic chemists developed new techniques for determining structures, analyzed the mechanisms of reactions, explored the effects conformation and stereochemistry on reactions, and found challenging new targets to synthesize. Only recently have organic chemists harnessed the powerful techniques of organic chemistry to study the functions of organic molecules in their biological hosts, the enzymes that synthesize molecules and the complex processes that occur in a cell. In this Perspective, I present a personal account my entrée into bioorganic chemistry as a physical organic chemist and subsequent work to understand the chemical mechanisms of enzyme-catalyzed reactions, to develop techniques to identify and assign hydrogen bonds in tRNAs through NMR studies with isotopically labeled molecules, and to study how structure determines function in biosynthetic enzymes with proteins obtained by genetic engineering. PMID:19323569

Synthetic nat- or ent-steroids in as few as five chemical steps from epichlorohydrin

NASA Astrophysics Data System (ADS)

Kim, Wan Shin; Du, Kang; Eastman, Alan; Hughes, Russell P.; Micalizio, Glenn C.

2018-01-01

Today, more than 100 Food and Drug Administration-approved steroidal agents are prescribed daily for indications including heart failure, inflammation, pain and cancer. While triumphs in organic chemistry have enabled the establishment and sustained growth of the steroid pharmaceutical industry, the production of highly functionalized synthetic steroids of varying substitution and stereochemistry remains challenging, despite the numerous reports of elegant strategies for their de novo synthesis. Here, we describe an advance in chemical synthesis that has established an enantiospecific means to access novel steroids with unprecedented facility and flexibility through the sequential use of two powerful ring-forming reactions: a modern metallacycle-mediated annulative cross-coupling and a new acid-catalysed vinylcyclopropane rearrangement cascade. In addition to accessing synthetic steroids of either enantiomeric series, these steroidal products have been selectively functionalized within each of the four carbocyclic rings, a synthetic ent-steroid has been prepared on a multigram scale, the enantiomer of a selective oestrogen has been synthesized, and a novel ent-steroid with growth inhibitory properties in three cancer cell lines has been discovered.

Radiolabeled cycloSaligenyl Monophosphates of 5-Iodo-2′-deoxyuridine, 5-Iodo-3′-fluoro-2′, 3′-dideoxyuridine, and 3′-Fluorothymidine for Molecular Radiotherapy of Cancer: Synthesis and Biological Evaluation

PubMed Central

Kortylewicz, Zbigniew P.; Kimura, Yu; Inoue, Kotaro; Mack, Elizabeth; Baranowska-Kortylewicz, Janina

2012-01-01

Targeted molecular radiotherapy opens unprecedented opportunities to eradicate cancer cells with minimal irradiation of normal tissues. Described in this study are radioactive cycloSaligenyl monophosphates designed to deliver lethal doses of radiation to cancer cells. These compounds can be radiolabeled with SPECT- and PET-compatible radionuclides as well as radionuclides suitable for Auger electron therapies. This characteristic provides an avenue for the personalized and comprehensive treatment strategy that comprises diagnostic imaging to identify sites of disease, followed by the targeted molecular radiotherapy based on the imaging results. The developed radiosynthetic methods produce no-carrier-added products with high radiochemical yield and purity. The interaction of these compounds with their target, butyrylcholinesterase, depends on the stereochemistry around the P atom. IC50 values are in the nM range. In vitro studies indicate that radiation doses delivered to the cell nucleus are sufficient to kill cells of several difficult to treat malignancies including glioblastoma, and ovarian and colorectal cancers. PMID:22339166

Rapid phenolic O-glycosylation of small molecules and complex unprotected peptides in aqueous solvent

NASA Astrophysics Data System (ADS)

Wadzinski, Tyler J.; Steinauer, Angela; Hie, Liana; Pelletier, Guillaume; Schepartz, Alanna; Miller, Scott J.

2018-06-01

Glycosylated natural products and synthetic glycopeptides represent a significant and growing source of biochemical probes and therapeutic agents. However, methods that enable the aqueous glycosylation of endogenous amino acid functionality in peptides without the use of protecting groups are scarce. Here, we report a transformation that facilitates the efficient aqueous O-glycosylation of phenolic functionality in a wide range of small molecules, unprotected tyrosine, and tyrosine residues embedded within a range of complex, fully unprotected peptides. The transformation, which uses glycosyl fluoride donors and is promoted by Ca(OH)2, proceeds rapidly at room temperature in water, with good yields and selective formation of unique anomeric products depending on the stereochemistry of the glycosyl donor. High functional group tolerance is observed, and the phenol glycosylation occurs selectively in the presence of virtually all side chains of the proteinogenic amino acids with the singular exception of Cys. This method offers a highly selective, efficient, and operationally simple approach for the protecting-group-free synthesis of O-aryl glycosides and Tyr-O-glycosylated peptides in water.

From inanimate matter to living systems

NASA Technical Reports Server (NTRS)

Fox, S. W.

1980-01-01

Since the early part of this century, the Genesis account of the origin and evolution of life has been explained as an extrapolation of astronomical and geochemical processes. The essence of the answer to date is a protoreproductive protocell of much biochemical and cytophysical competance. The processes of its origin, molecular ordering, and its functions are described. A crucial understanding is that of the nonrandomness of evolutionary processes at all stages (with perhaps a minor statistical component). In this way, evolution conflicts with statistical randomness; the latter is a favorite assumption of both scientific and creationistic critics of the proteinoid theory. The principle contribution of the proteinoid theory to the understanding of general biology is to particularize the view that evolutionary direction is rooted in the shapes of molecules, in stereochemistry. After molecules of the right kind first assembled to protocells, life in its various stages of evolution was an inevitable consequence. It is molecules that continue to assemble as part of living process and, in the role of enzymes, continue to direct life cycle of the cell.

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase

NASA Astrophysics Data System (ADS)

Nascimento, Érica C. M.; Oliva, Mónica; Andrés, Juan

2018-05-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

An enantiomer-based virtual screening approach: Discovery of chiral organophosphates as acetyl cholinesterase inhibitors.

PubMed

Zhang, Aiqian; Mu, Yunsong; Wu, Fengchang

2017-04-01

Chiral organophosphates (OPs) have been used widely around the world, very little is known about binding mechanisms with biological macromolecules. An in-depth understanding of the stereo selectivity of human AChE and discovering bioactive enantiomers of OPs can decrease health risks of these chiral chemicals. In the present study, a flexible molecular docking approach was conducted to investigate different binding modes of twelve phosphorus enantiomers. A pharmacophore model was then developed on basis of the bioactive conformations of these compounds. After virtual screening, twenty-four potential bioactive compounds were found, of which three compounds (Ethyl p-nitrophenyl phenylphosphonate (EPN), 1-naphthaleneacetic anhydride and N,4-dimethyl-N-phenyl-benzenesulfonamide) were tested by use of different in vitro assays. S-isomer of EPN was also found to exhibit greater inhibitory activity towards human AChE than the corresponding R-isomer. These findings affirm that stereochemistry plays a crucial role in virtual screening, and provide a new insight into designing safer organ phosphorus pesticides on human health. Copyright © 2017 Elsevier Inc. All rights reserved.

Novel polyacetylene derivatives and their inhibitory activities on acetylcholinesterase obtained from Panax ginseng roots.

PubMed

Murata, Kazuya; Iida, Daiki; Ueno, Yoshihiro; Samukawa, Keiichi; Ishizaka, Toshihiko; Kotake, Takeshi; Matsuda, Hideaki

2017-01-01

In our research program to identify cholinesterase and β-secretase inhibitors, we investigated Ginseng (root of Panax ginseng), a crude drug described as a multifunctional drug in the ancient Chinese herbal book Shennong Ben Cao Jing. Results from hexane and methanol extracts showed moderate inhibitory activities. This suggests that ginseng roots may be effective for the prevention of and therapy for dementia. We then focused on hexane extracts of raw ginseng root and dried ginseng root since the determination of hexane extract constituents has not been studied extensively. Activity-guided fractionation and purification led to the isolation of 4 polyacetylene compounds; homopanaxynol, homopanaxydol, (9Z)-heptadeca-1, 9-diene-4,6-diyn-3-one, and (8E)-octadeca-1,8-diene-4,6-diyn-3,10-diol. The chemical structures of these compounds, including stereochemistry, were determined. This is the first study to identify the structure of homopanaxynol and homopanaxydol. Moreover, the modes of action of some compounds were characterized as competitive inhibitors. This study showed, for the first time, that polyacetylene compounds possess acetylcholinesterase inhibitory activities.

Central-to-axial chirality transfer revealed by liquid crystals: a combined experimental and computational approach for the determination of absolute configuration of carboxylic acids with an α chirality centre.

PubMed

Ferrarini, Alberta; Ferroni, Fiammetta; Pieraccini, Silvia; Rosini, Carlo; Superchi, Stefano; Spada, Gian Piero

2011-10-01

The conversion into 6,7-dihydro-5H-dibenz[c,e]azepine (DAZ) N-protected amides is a viable route for the determination of the absolute configuration of chiral 2-substituted carboxylic acids. The biphenyl moiety of DAZ, besides being a probe of chirality for the electronic circular dichroism (ECD) spectroscopy, makes these systems suitable for configuration assignment by exploiting the chirality amplification which occurs in nematic liquid crystals. To assess the reliability of the liquid crystal method in detecting the absolute stereochemistry of chiral amides bound to a biphenyl group, we measured the helical twisting power of a series of DAZ-N-protected amides and compared these data with the results obtained from ECD measurements. We will show that the liquid crystal method, corroborated by HTP predictions, is trustworthy with our biphenyl derivatives, even when ECD spectra are ambiguous for the presence of aryl moieties displaying strong UV absorptions in the same range of the biphenyl chromophore. © 2011 Wiley-Liss, Inc.

Transmission of chirality through space and across length scales

NASA Astrophysics Data System (ADS)

Morrow, Sarah M.; Bissette, Andrew J.; Fletcher, Stephen P.

2017-05-01

Chirality is a fundamental property and vital to chemistry, biology, physics and materials science. The ability to use asymmetry to operate molecular-level machines or macroscopically functional devices, or to give novel properties to materials, may address key challenges at the heart of the physical sciences. However, how chirality at one length scale can be translated to asymmetry at a different scale is largely not well understood. In this Review, we discuss systems where chiral information is translated across length scales and through space. A variety of synthetic systems involve the transmission of chiral information between the molecular-, meso- and macroscales. We show how fundamental stereochemical principles may be used to design and understand nanoscale chiral phenomena and highlight important recent advances relevant to nanotechnology. The survey reveals that while the study of stereochemistry on the nanoscale is a rich and dynamic area, our understanding of how to control and harness it and dial-up specific properties is still in its infancy. The long-term goal of controlling nanoscale chirality promises to be an exciting journey, revealing insight into biological mechanisms and providing new technologies based on dynamic physical properties.

Synthesis, Formulation, and Adjuvanticity of Monodesmosidic Saponins with Olenanolic Acid, Hederagenin and Gypsogenin Aglycones, and some C‐28 Ester Derivatives†

PubMed Central

Greatrex, Ben W.; Daines, Alison M.; Hook, Sarah; Lenz, Dirk H.; McBurney, Warren; Rades, Thomas

2015-01-01

Abstract In an attempt to discover a new synthetic vaccine adjuvant, the glycosylation of hederagenin, gypsogenin, and oleanolic acid acceptors with di‐ and trisaccharide donors to generate a range of mimics of natural product QS‐21 was carried out. The saponins were formulated with phosphatidylcholine and cholesterol, and the structures analyzed by transmission electron microscopy. 3‐O‐(Manp(1→3)Glcp)hederagenin was found to produce numerous ring‐like micelles when formulated, while C‐28 choline ester derivatives preferred self‐assembly and did not interact with the liposomes. When alone and in the presence of cholesterol and phospholipid, the choline ester derivatives produced nanocrystalline rods or helical micelles. The effects of modifying sugar stereochemistry and the aglycone on the immunostimulatory effects of the saponins was then evaluated using the activation markers MHC class II and CD86 in murine bone marrow dendritic cells. The most active saponin, 3‐O‐(Manp(1→3)Glcp)hederagenin, was stimulatory at high concentrations in cell culture, but this did not translate to strong responses in vivo. PMID:27308200

Stereochemistry of complexes with double and triple metal-ligand bonds: a continuous shape measures analysis.

PubMed

Alvarez, Santiago; Menjón, Babil; Falceto, Andrés; Casanova, David; Alemany, Pere

2014-11-17

To each coordination polyhedron we can associate a normalized coordination polyhedron that retains the angular orientation of the central atom-ligand bonds but has all the vertices at the same distance from the center. The use of shape measures of these normalized coordination polyhedra provides a simple and efficient way of discriminating angular and bond distance distortions from an ideal polyhedron. In this paper we explore the applications of such an approach to analyses of several stereochemical problems. Among others, we discuss how to discern the off-center displacement of the metal from metal-ligand bond shortening distortions in families of square planar biscarbene and octahedral dioxo complexes. The normalized polyhedron approach is also shown to be very useful to understand stereochemical trends with the help of shape maps, minimal distortion pathways, and ligand association/dissociation pathways, illustrated by the Berry and anti Berry distortions of triple-bonded [X≡ML4] complexes, the square pyramidal geometries of Mo coordination polyhedra in oxido-reductases, the coordination geometries of actinyl complexes, and the tetrahedricity of heavy atom-substituted carbon centers.

iMODS: internal coordinates normal mode analysis server.

PubMed

López-Blanco, José Ramón; Aliaga, José I; Quintana-Ortí, Enrique S; Chacón, Pablo

2014-07-01

Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends its applicability while implicitly maintaining stereochemistry. Vibrational analysis, motion animations and morphing trajectories can be easily carried out at different resolution scales almost interactively. The server is versatile; non-specialists can rapidly characterize potential conformational changes, whereas advanced users can customize the model resolution with multiple coarse-grained atomic representations and elastic network potentials. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. The generated all-heavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies. The server is free and open to all users with no login requirement at http://imods.chaconlab.org. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Strigone, isolation and identification as a natural strigolactone from Houttuynia cordata.

PubMed

Kisugi, Takaya; Xie, Xiaonan; Kim, Hyun Il; Yoneyama, Kaori; Sado, Aika; Akiyama, Kohki; Hayashi, Hideo; Uchida, Kenichi; Yokota, Takao; Nomura, Takahito; Yoneyama, Koichi

2013-03-01

(+)-Strigone was described earlier in a paper on isolation of strigol and then recently examined for hyphal branching activity in arbuscular mycorrhizal fungi as a strigolactone. Herein, it was isolated from root exudates of Houttuynia cordata, and its structure was confirmed by direct comparison with synthetic standards in LC-MS/MS, GC-MS, and (1)H and (13)C NMR analyses. The stereochemistry of strigone was determined by comparing the CD spectra and RR(t) in chiral LC-MS/MS with those of synthetic (+)-strigone and (-)-strigone. Four stereoisomers of strigone exhibited clearly different levels of stimulation activity on the seeds of three root parasitic plants, Orobanche minor, Phelipanche ramosa, and Striga hermonthica. (+)-Strigone was a highly potent germination stimulant on S. hermonthica and also on P. ramosa, but less active than ent-2'-epi-strigone on O. minor. In addition to strigone, H. cordata was found to produce strigol, sorgomol, and 5-deoxystrigol, indicating that this plant produces mainly strigol-type strigolactones derived from 5-deoxystrigol. Copyright © 2012 Elsevier Ltd. All rights reserved.

Discovery of Potent and Selective Dipeptidyl Peptidase IV Inhibitors Derived from [beta]-Aminoamides Bearing Subsituted Triazolopiperazines

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

Kim, Dooseop; Kowalchick, Jennifer E.; Brockunier, Linda L.

2008-06-30

A series of {beta}-aminoamides bearing triazolopiperazines have been discovered as potent, selective, and orally active dipeptidyl peptidase IV (DPP-4) inhibitors by extensive structure-activity relationship (SAR) studies around the triazolopiperazine moiety. Among these, compound 34b with excellent in vitro potency (IC{sub 50} = 4.3 nM) against DPP-4, high selectivity over other enzymes, and good pharmacokinetic profiles exhibited pronounced in vivo efficacy in an oral glucose tolerance test (OGTT) in lean mice. On the basis of these properties, compound 34b has been profiled in detail. Further refinement of the triazolopiperazines resulted in the discovery of a series of extremely potent compounds withmore » subnanomolar activity against DPP-4 (42b-49b), that is, 4-fluorobenzyl-substituted compound 46b, which is notable for its superior potency (IC{sub 50} = 0.18 nM). X-ray crystal structure determination of compounds 34b and 46b in complex with DPP-4 enzyme revealed that (R)-stereochemistry at the 8-position of triazolopiperazines is strongly preferred over (S) with respect to DPP-4 inhibition.« less

Endoperoxide polyketides from a Chinese Plakortis simplex: further evidence of the impact of stereochemistry on antimalarial activity of simple 1,2-dioxanes.

PubMed

Chianese, Giuseppina; Persico, Marco; Yang, Fan; Lin, Hou-Wen; Guo, Yue-Wei; Basilico, Nicoletta; Parapini, Silvia; Taramelli, Donatella; Taglialatela-Scafati, Orazio; Fattorusso, Caterina

2014-09-01

Chemical investigation of the organic extract obtained from the sponge Plakortis simplex collected in the South China Sea afforded five new polyketide endoperoxides (2 and 4-7), along with two known analogues (1 and 3). The stereostructures of these metabolites have been deduced on the basis of spectroscopic analysis and chemical conversion. The isolated endoperoxide derivatives have been tested for their in vitro antimalarial activity against Plasmodium falciparum strains, showing IC50 values in the low micromolar range. The structure-activity relationships were analyzed by means of a detailed computational investigation and rationalized in the light of the mechanism of action proposed for this class of simple antimalarials. The relative orientation of the atoms involved in the putative radical generation and transfer reaction was demonstrated to have a great impact on the antimalarial activity. The resulting 3D pharmacophoric model can be a useful guide to design simple and effective antimalarial lead compounds belonging to the class of 1,2-dioxanes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Immunogenicity of Membrane-bound HIV-1 gp41 Membrane-proximal External Region (MPER) Segments Is Dominated by Residue Accessibility and Modulated by Stereochemistry*

PubMed Central

Kim, Mikyung; Song, Likai; Moon, James; Sun, Zhen-Yu J.; Bershteyn, Anna; Hanson, Melissa; Cain, Derek; Goka, Selasie; Kelsoe, Garnett; Wagner, Gerhard; Irvine, Darrell; Reinherz, Ellis L.

2013-01-01

Structural characterization of epitope-paratope pairs has contributed to the understanding of antigenicity. By contrast, few structural studies relate to immunogenicity, the process of antigen-induced immune responses in vivo. Using a lipid-arrayed membrane-proximal external region (MPER) of HIV-1 glycoprotein 41 as a model antigen, we investigated the influence of physicochemical properties on immunogenicity in relation to structural modifications of MPER/liposome vaccines. Anchoring the MPER to the membrane via an alkyl tail or transmembrane domain retained the MPER on liposomes in vivo, while preserving MPER secondary structure. However, structural modifications that affected MPER membrane orientation and antigenic residue accessibility strongly impacted induced antibody responses. The solvent-exposed MPER tryptophan residue (Trp-680) was immunodominant, focusing immune responses, despite sequence variability elsewhere. Nonetheless, immunogenicity could be readily manipulated using site-directed mutagenesis or structural constraints to modulate amino acid surface display. These studies provide fundamental insights for immunogen design aimed at targeting B cell antibody responses. PMID:24047898

Cyclic RGD peptidomimetics containing 4- and 5-amino-cyclopropane pipecolic acid (CPA) templates as dual αVβ3 and α5β1 integrin ligands.

PubMed

Sernissi, Lorenzo; Trabocchi, Andrea; Scarpi, Dina; Bianchini, Francesca; Occhiato, Ernesto G

2016-02-15

4-Amino- and 5-amino-cyclopropane pipecolic acids (CPAs) with cis relative stereochemistry between the carboxylic and amino groups were used as templates to prepare cyclic peptidomimetics containing the RGD sequence as possible integrin binders. The peptidomimetic c(RGD8) built on the 5-amino-CPA displayed an inhibition activity (IC50=2.4nM) toward the αvβ3 integrin receptor (expressed in M21 human melanoma cell line) comparable to that of the most potent antagonists reported so far and it was ten times more active than the corresponding antagonist c(RGD7) derived from the isomeric 4-amino-CPA. Both compounds were also nanomolar ligands of the α5β1 integrin (expressed in human erythroleukemia cell line K562). These results suggest that the CPA-derived templates are suitable for the preparation of dual αvβ3 and α5β1 ligands to suppress integrin-mediated events as well as for targeted drug delivery in cancer therapy. Copyright © 2015 Elsevier Ltd. All rights reserved.

Molecular Basis for the Recognition of Higher Fullerenes into Ureidopyrimidinone-Cyclotriveratrylene Self-Assembled Capsules.

PubMed

Huerta, Elisa; Serapian, Stefano Artin; Santos, Eva; Cequier, Enrique; Bo, Carles; de Mendoza, Javier

2016-09-12

Fullerenes C60 , C70 , and C84 may be readily encaged within a hydrogen-bonded dimeric capsule, based on two concave cyclotriveratrylene (CTV) scaffolds, each containing three self-complementary 2-ureido-4-[1H]-pyrimidinone (UPy) subunits. NMR spectroscopy and circular dichroism studies, complemented by dispersion-corrected DFT calculations, are reported with the aim of characterizing such capsule-fullerene complexes both structurally and energetically. Six fullerenes are considered: in agreement with experiments, calculations find that encapsulation is most favorable for C84 (on a par with C90 ), and follows the trend C60

Absolute configuration in 4-alkyl- and 4-aryl-3,4-dihydro-2(1H)-pyrimidones: a combined theoretical and experimental investigation.

PubMed

Uray, G; Verdino, P; Belaj, F; Kappe, C O; Fabian, W M

2001-10-05

Structural features (orientation of the carboxyl group, ring puckering), electronic absorption, and circular dichroism spectra of 4-alkyl- and 4-aryl-dihydropyrimidones 1-5 are calculated by semiempirical (AM1, INDO/S), ab initio (HF/6-31G, CIS/6-31G, RPA/6-31G), and density functional theory (B3LYP/6-31G) methods. These calculations allow an assignment of the absolute configuration by comparison of simulated and experimental CD spectra. Although the ab initio methods greatly overestimate electronic transition energies, the general appearance of the experimental CD spectra is quite nicely reproduced by these calculations. Thus, comparison of experimental with calculated CD spectra is a reliable tool for the assignment of the absolute configuration. For 4-methyl derivatives 1, the first enantiopure DHPM examples with no additional aromatic substituent, the stereochemistry at C4 provided by the theoretical results is confirmed by X-ray structure determination of the diastereomeric salt 6. Additional support is the consistent HPLC elution order found for all investigated DHPMs on a cellulose-derived chiral stationary phase.

In silico toxicity prediction by support vector machine and SMILES representation-based string kernel.

PubMed

Cao, D-S; Zhao, J-C; Yang, Y-N; Zhao, C-X; Yan, J; Liu, S; Hu, Q-N; Xu, Q-S; Liang, Y-Z

2012-01-01

There is a great need to assess the harmful effects or toxicities of chemicals to which man is exposed. In the present paper, the simplified molecular input line entry specification (SMILES) representation-based string kernel, together with the state-of-the-art support vector machine (SVM) algorithm, were used to classify the toxicity of chemicals from the US Environmental Protection Agency Distributed Structure-Searchable Toxicity (DSSTox) database network. In this method, the molecular structure can be directly encoded by a series of SMILES substrings that represent the presence of some chemical elements and different kinds of chemical bonds (double, triple and stereochemistry) in the molecules. Thus, SMILES string kernel can accurately and directly measure the similarities of molecules by a series of local information hidden in the molecules. Two model validation approaches, five-fold cross-validation and independent validation set, were used for assessing the predictive capability of our developed models. The results obtained indicate that SVM based on the SMILES string kernel can be regarded as a very promising and alternative modelling approach for potential toxicity prediction of chemicals.

Simulation of carbohydrates, from molecular docking to dynamics in water.

PubMed

Sapay, Nicolas; Nurisso, Alessandra; Imberty, Anne

2013-01-01

Modeling of carbohydrates is particularly challenging because of the variety of structures resulting for the high number of monosaccharides and possible linkages and also because of their intrinsic flexibility. The development of carbohydrate parameters for molecular modeling is still an active field. Nowadays, main carbohydrates force fields are GLYCAM06, CHARMM36, and GROMOS 45A4. GLYCAM06 includes the largest choice of compounds and is compatible with the AMBER force fields and associated. Furthermore, AMBER includes tools for the implementation of new parameters. When looking at protein-carbohydrate interaction, the choice of the starting structure is of importance. Such complex can be sometimes obtained from the Protein Data Bank-although the stereochemistry of sugars may require some corrections. When no experimental data is available, molecular docking simulation is generally used to the obtain protein-carbohydrate complex coordinates. As molecular docking parameters are not specifically dedicated to carbohydrates, inaccuracies should be expected, especially for the docking of polysaccharides. This issue can be addressed at least partially by combining molecular docking with molecular dynamics simulation in water.

Coupling and Reactions of 5-Hydroxyconiferyl Alcohol in Lignin Formation.

PubMed

Elder, Thomas; Berstis, Laura; Beckham, Gregg T; Crowley, Michael F

2016-06-15

The catechol alcohols, caffeyl and 5-hydroxyconiferyl alcohol, may be incorporated into lignin either naturally or through genetic manipulation. Due to the presence of o-OH groups, these compounds form benzodioxanes, a departure from the interunit connections found in lignins derived from the cinnamyl alcohols. In nature, lignins composed of caffeyl and 5-hydroxyconiferyl alcohol are linear homopolymers and, as such, may have properties that make them amenable for use in value-added products, such as lignin-based carbon fibers. In the current work, results from density functional theory calculations for the reactions of 5-hydroxyconiferyl alcohol, taking stereochemistry into account, are reported. Dehydrogenation and quinone methide formation are found to be thermodynamically favored for 5-hydroxyconiferyl alcohol, over coniferyl alcohol. The comparative energetics of the rearomatization reactions suggest that the formation of the benzodioxane linkage is under kinetic control. Ring-opening reactions of the benzodioxane groups show that the bond dissociation enthalpy of the α-O cleavage reaction is lower than that of the β-O reaction. The catechol lignins represent a novel form of the polymer that may offer new opportunities for bioproducts and genetic targets.

Regio- and Stereoselective Aliphatic-Aromatic Cross-Benzoin Reaction: Enzymatic Divergent Catalysis.

PubMed

Beigi, Maryam; Gauchenova, Ekaterina; Walter, Lydia; Waltzer, Simon; Bonina, Fabrizio; Stillger, Thomas; Rother, Dörte; Pohl, Martina; Müller, Michael

2016-09-19

The catalytic asymmetric synthesis of chiral 2-hydroxy ketones by using different thiamine diphosphate dependent enzymes, namely benzaldehyde lyase from Pseudomonas fluorescens (PfBAL), a variant of benzoylformate decarboxylase from Pseudomonas putida (PpBFD-L461A), branched-chain 2-keto acid decarboxylase from Lactococcus lactis (LlKdcA) and a variant of pyruvate decarboxylase from Acetobacter pasteurianus (ApPDC-E469G), was studied. Starting with the same set of substrates, substituted benzaldehydes in combination with different aliphatic aldehydes, PfBAL and PpBFD-L461A selectively deliver the (R)- and (S)-2-hydroxy-propiophenone derivatives, respectively. The (R)- and (S)-phenylacetylcarbinol (1-hydroxy-1-phenylacetone) derivatives are accessible in a similar way using LlKdcA and ApPDC-E469G, respectively. In many cases excellent stereochemical purities (>98 % enantiomeric excess) could be achieved. Hence, the regio- and stereochemistry of the product in the asymmetric aliphatic-aromatic cross-benzoin reaction can be controlled solely by choice of the appropriate enzyme or enzyme variant. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Overview of refinement procedures within REFMAC5: utilizing data from different sources.

PubMed

Kovalevskiy, Oleg; Nicholls, Robert A; Long, Fei; Carlon, Azzurra; Murshudov, Garib N

2018-03-01

Refinement is a process that involves bringing into agreement the structural model, available prior knowledge and experimental data. To achieve this, the refinement procedure optimizes a posterior conditional probability distribution of model parameters, including atomic coordinates, atomic displacement parameters (B factors), scale factors, parameters of the solvent model and twin fractions in the case of twinned crystals, given observed data such as observed amplitudes or intensities of structure factors. A library of chemical restraints is typically used to ensure consistency between the model and the prior knowledge of stereochemistry. If the observation-to-parameter ratio is small, for example when diffraction data only extend to low resolution, the Bayesian framework implemented in REFMAC5 uses external restraints to inject additional information extracted from structures of homologous proteins, prior knowledge about secondary-structure formation and even data obtained using different experimental methods, for example NMR. The refinement procedure also generates the `best' weighted electron-density maps, which are useful for further model (re)building. Here, the refinement of macromolecular structures using REFMAC5 and related tools distributed as part of the CCP4 suite is discussed.

Fungal growth inhibitory properties of new phytosphingolipid analogues.

PubMed

Mormeneo, D; Manresa, A; Casas, J; Llebaria, A; Delgado, A

2008-04-01

To study the growth inhibitory properties of a series of phytosphingosine (PHS) and phytoceramide (PHC) analogues. A panel of two yeast (Candida albicans and Saccharomyces cerevisiae) and six moulds (Aspergillus repens, Aspergillus niger, Penicillium chrysogenum, Cladosporium cladosporioides, Arthroderma uncinatum and Penicillium funiculosum) has been used in this study. A series of new PHS and PHC analogues differing at the sphingoid backbone and the functional group at C1 position were synthesized. Among PHS analogues, 1-azido derivative 1c, bearing the natural D-ribo stereochemistry, showed a promising growth inhibitory profile. Among PHC analogues, compound 12, with a bulky N-pivaloyl group and a Z double bond at C3 position of the sphingoid chain, was the most active growth inhibitor. Minimal inhibitory concentration values were in the range of 23-48 micromol l(-1) for 1c and 44-87 micromol l(-1) for 12. Only scattered data on the antifungal activity of phytosphingolipids have been reported in the literature. This is the first time that a series of analogues of this kind are tested and compared to discern their structural requirements for antifungal activity.

Synthesis, characterization, stereochemistry and biological investigation of certain N-dichloroacetyl-bis(2-chlorophenyl)piperidin-4-ones

NASA Astrophysics Data System (ADS)

Kayalvizhi, R.; Ponnuswamy, S.; Gomathi, K.; Ezhilarasi, K. S.; Usha, G.

2018-02-01

A new series of N-dichloroacetyl-bis(2-chlorophenyl)piperidin-4-ones 4-6 has been synthesized and characterized using IR, 1H, 13C, DEPT and 2D (COSY and HSQC) NMR spectral techniques. The NMR spectral data indicate that the N-acylpiperidin-4-ones 4-6 prefer to exist in an equilibrium between the twist boat conformations with coplanar orientation of Nsbnd Cdbnd O moiety. Furthermore, the antibacterial and antifungal studies have been carried out for compounds 1-6 and the results show that they possess significant activity towards the bacterial organisms Staphylococcus aureus and Salmoneela paratyphi and better activity against the remaining bacterial organisms. All the compounds 1-6 possess moderate antifungal activity. The compounds 4-6 have been docked with the structure of MRSA and the results demonstrate that the compounds 4-6 have similar docking score and glide energy when compared to each other and thus having equal binding affinity. The antioxidant studies show greater activity for compound 4 and poor activity for compounds 5 &6 when compared to the standard drug.

Practical Stereochemistry.

PubMed

Kellogg, Richard M

2017-04-18

The relationship between fundamental and applied is often uneasy, particularly in modern political climates. A familiar political view, aimed negatively at the scientific community, is that the former is a waste of money whereas the latter gives value for investment. The answer that fundamental is required as the basis for practical suffers from the fact that the timelines between fundamental and practical are often long and the routes contorted and unexpected. This has been my experience. In this Account, examples are given from the research in which I have been involved wherein quite fundamental considerations have led to various applications. The longer the time, the clearer and broader the relationship. Fundamental can and does lead to application. They need and depend on each other. I have seen this both from the side of academia and from small companies. In the course of the past 40 plus years, I have been involved in various aspects of stereochemistry and, in particular, chirality. It has been rewarding to see that several of the developments, most originally grounded in fundamental research considerations, have been used in the chemical community and given new dimensions and often practical applications by others. In this Account, a path-not planned deliberately by me-from orbital symmetry and Woodward-Hoffmann rules through crown ethers to conformational analysis to diastereomeric resolutions to deracemizations powered by Ostwald ripening and the Gibbs-Thomson effect to nucleation to helicenes is described. In order of discussion, the orbital symmetry aspects have via an unusual and unpredicted path has resulted in, among other things, a synthesis of hindered alkenes useful for the production of molecular motors. The crown ether aspects led to discovery of the utility of cesium salts particularly for racemization sensitive nucleophilic substitutions. Work on diastereomeric resolutions has concentrated on the mechanistic as well as practical/commercial aspects of the use of multiple resolving agents (Dutch resolution). During this work the complex relationship between nucleation and chirality in diastereomeric resolutions began to reveal itself. In general, nucleation, especially with involvement of chirality, is a topical challenge that has attracted the attention of many groups. The contribution of this knowledge to the development of attrition driven deracemizations of racemizable conglomerates is described. This remarkable technology allows, without intervention of chiral aids, conversion of certain racemates in quantitative yield and absolute enantiomeric excess to a single enantiomer. From a practical standpoint, this methodology has been used for the production in enantiomerically pure form of commercially interesting compounds like naproxen and clopidogrel (Plavix). Finally an STM investigation of the nucleation behavior of a helicene, prepared via a remarkably short and efficient route, on a metal surface is described.

Prediction of Stereochemistry using Q2MM

PubMed Central

2016-01-01

Conspectus The standard method of screening ligands for selectivity in asymmetric, transition metal-catalyzed reactions requires experimental testing of hundreds of ligands from ligand libraries. This “trial and error” process is costly in terms of time as well as resources and, in general, is scientifically and intellectually unsatisfying as it reveals little about the underlying mechanism behind the selectivity. The accurate computational prediction of stereoselectivity in enantioselective catalysis requires adequate conformational sampling of the selectivity-determining transition state but has to be fast enough to compete with experimental screening techniques to be useful for the synthetic chemist. Although electronic structure calculations are accurate and general, they are too slow to allow for sampling or fast screening of ligand libraries. The combined requirements can be fulfilled by using appropriately fitted transition state force fields (TSFFs) that represent the transition state as a minimum and allow fast conformational sampling using Monte Carlo. Quantum-guided molecular mechanics (Q2MM) is an automated force field parametrization method that generates accurate, reaction-specific TSFFs by fitting the functional form of an arbitrary force field using only electronic structure calculations by minimization of an objective function. A key feature that distinguishes the Q2MM method from many other automated parametrization procedures is the use of the Hessian matrix in addition to geometric parameters and relative energies. This alleviates the known problems of overfitting of TSFFs. After validation of the TSFF by comparison to electronic structure results for a test set and available experimental data, the stereoselectivity of a reaction can be calculated by summation over the Boltzman-averaged relative energies of the conformations leading to the different stereoisomers. The Q2MM method has been applied successfully to perform virtual ligand screens on a range of transition metal-catalyzed reactions that are important from both an industrial and an academic perspective. In this Account, we provide an overview of the continued improvement of the prediction of stereochemistry using Q2MM-derived TSFFs using four examples from different stages of development: (i) Pd-catalyzed allylation, (ii) OsO4-catalyzed asymmetric dihydroxylation (AD) of alkenes, (iii) Rh-catalyzed hydrogenation of enamides, and (iv) Ru-catalyzed hydrogenation of ketones. In the current form, correlation coefficients of 0.8–0.9 between calculated and experimental ee values are typical for a wide range of substrate–ligand combinations, and suitable ligands can be predicted for a given substrate with ∼80% accuracy. Although the generation of a TSFF requires an initial effort and will therefore be most useful for widely used reactions that require frequent screening campaigns, the method allows for a rapid virtual screen of large ligand libraries to focus experimental efforts on the most promising substrate–ligand combinations. PMID:27064579

Examining the Chirality, Conformation and Selective Kinase Inhibition of 3-((3R,4R)-4-methyl-3-(methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)-3-oxopropanenitrile (CP-690,550)

PubMed Central

Jiang, Jian-kang; Ghoreschi, Kamran; Deflorian, Francesca; Chen, Zhi; Perreira, Melissa; Pesu, Marko; Smith, Jeremy; Nguyen, Dac-Trung; Liu, Eric H.; Leister, William; Costanzi, Stefano; O’Shea, John J.; Thomas, Craig J.

2009-01-01

Here, we examine the significance that stereochemistry plays within the clinically relevant Janus Kinase 3 (Jak3) inhibitor CP-690,550. A synthesis of all four enantiopure stereoisomers of the drug was carried out and an examination of each compound revealed that only the enantiopure 3R, 4R isomer was capable of blocking Stat5 phosphorylation (Jak3 dependent). Each compound was profiled across a panel of over 350 kinases which revealed a high level of selectivity for the Jak family kinases for these related compounds. Each stereoisomer retained a degree of binding to Jak3 and Jak2 and the 3R, 4S and 3S, 4R stereoisomers were further revealed to have binding affinity for selected members of the STE7 and STE20 subfamily of kinases. Finally, an appraisal of the minimum energy conformation of each stereoisomer and molecular docking at Jak3 was performed in an effort to better understand each compounds selectivity and potency profiles. PMID:19053756

Synthesis and characterization of sulfolane-based amino alcohols: A combined experimental and computational study

NASA Astrophysics Data System (ADS)

Palchykov, Vitalii A.; Zarovnaya, Iryna S.; Tretiakov, Serhii V.; Reshetnyak, Alyona V.; Omelchenko, Iryna V.; Shishkin, Oleg V.; Okovytyy, Sergiy I.

2018-04-01

Aminolysis of 3,4-epoxysulfolane in aqueous media leads to a very complex mixture of products with unresolved stereochemistry. Herein, we report a detailed theoretical and experimental mechanistic investigation of this reaction along with extensive spectroscopic characterization of the resulting amino alcohols, using 1D and 2D NMR techniques (1H, 13C, NOE, NOESY, COSY, HSQC, HMBC) as well as XRD analysis. In addition to simple amines such as ammonia and benzylamine, our study also employed the more sterically hindered endo-bicyclo[2.2.1]hept-5-en-2-ylmethanamine. The mechanism of the aminolysis of 3,4-epoxysulfolane by aqueous ammonia was studied in more detail using quantum chemical calculations at the M06-2X/6-31++G** level of theory. The computational results led us to conclude that the most probable way of initial epoxide transformation is base-catalyzed rearrangement to a corresponding allylic alcohol. Subsequent formation of vicinal amino alcohols and diols proceeds via addition of ammonia or hydroxy-anions to activated double Cdbnd C bond with some preference of a cis-attack. Detailed analytical data obtained in the course of our work will be useful for the stereochemical identification of new sulfolane derivatives.

Preparation and Anti-Tumour Activity of Some Arylbismuth(III) Oxine Complexes

PubMed Central

Smith, Katharine A.; Deacon, Glen B.; Jackson, W. Roy; Tiekink, Edward R. T.; Rainone, Silvina; Webster, Lorraine K.

1998-01-01

New arylbismuth(lll) oxinates, PhBi(MeOx)2, (p-MeC6H4)Bi(Ox)2, (p-MeC6H4)Bi(MeOx)2, (p-ClC6H4)Bi(Ox)2, and (p-ClC6H4)Bi(MeOx)2 (Ox− = quinolin-8-olate and MeOx−=2-methylquinolin-8-olate) have been prepared by reaction of the appropriate diarylbismuth chlorides with Na(Ox) or Na(MeOx) in the presence of 15-crown-5. An X-ray crystallographic study has shown PhBi(MeOx)2 to be a five coordinate monomer with distorted square pyramidal stereochemistry. Chelating MeOx ligands have a cisoid arrangement in the square plane and the phenyl group is apical. The lattice is stabilised by significant π-π interactions between centrosymmetric molecules. A range of these complexes has been shown to have high in vitro biological activity (comparable with or better than cisplatin) against L1210 leukaemia, the corresponding cisplatin resistant line, and a human ovarian cell line, SKOV-3. However, initial in vivo testing against a solid mouse plasmacytoma (PC6) and P388 leukaemia has not revealed significant activity. PMID:18475861

Constituents of Musa x paradisiaca cultivar with the potential to induce the phase II enzyme, quinone reductase.

PubMed

Jang, Dae Sik; Park, Eun Jung; Hawthorne, Michael E; Vigo, Jose Schunke; Graham, James G; Cabieses, Fernando; Santarsiero, Bernard D; Mesecar, Andrew D; Fong, Harry H S; Mehta, Rajendra G; Pezzuto, John M; Kinghorn, A Douglas

2002-10-23

A new bicyclic diarylheptanoid, rel-(3S,4aR,10bR)-8-hydroxy-3-(4-hydroxyphenyl)-9-methoxy-4a,5,6,10b-tetrahydro-3H-naphtho[2,1-b]pyran (1), as well as four known compounds, 1,2-dihydro-1,2,3-trihydroxy-9-(4-methoxyphenyl)phenalene (2), hydroxyanigorufone (3), 2-(4-hydroxyphenyl)naphthalic anhydride (4), and 1,7-bis(4-hydroxyphenyl)hepta-4(E),6(E)-dien-3-one (5), were isolated from an ethyl acetate-soluble fraction of the methanol extract of the fruits of Musa x paradisiaca cultivar, using a bioassay based on the induction of quinone reductase (QR) in cultured Hepa1c1c7 mouse hepatoma cells to monitor chromatographic fractionation. The structure and relative stereochemistry of compound 1 were elucidated unambiguously by one- and two-dimensional NMR experiments ((1)H NMR, (13)C NMR, DEPT, COSY, HMQC, HMBC, and NOESY) and single-crystal X-ray diffraction analysis. Isolates 1-5 were evaluated for their potential cancer chemopreventive properties utilizing an in vitro assay to determine quinone reductase induction and a mouse mammary organ culture assay.

Rapid high-resolution four-dimensional NMR spectroscopy using the filter diagonalization method and its advantages for detailed structural elucidation of oligosaccharides.

PubMed

Armstrong, Geoffrey S; Mandelshtam, Vladimir A; Shaka, A J; Bendiak, Brad

2005-03-01

Four-dimensional nuclear magnetic resonance spectroscopy with high resolution of signals in the indirect dimensions is reported as an implementation of the filter diagonalization method (FDM). Using an oligosaccharide derivatized with 13C-labeled acetyl isotags, a four-dimensional constant-time pulse sequence was tailored for conjoint use with the FDM. Results demonstrate that high resolution in all dimensions can be achieved using a relatively short experimental time period (19 h), even though the spectrum is highly congested in the direct and all three indirect dimensions. The combined use of isotags, constant-time pulse sequences, and FDM permits rapid isolation of sugar ring proton spin systems in multiple dimensions and enables all endocyclic J-couplings to be simply measured, the key goal to assigning sugar stereochemistry and anomeric configuration. A general method for rapid, unambiguous elucidation of spin systems in oligosaccharides has been a long-sought goal of carbohydrate NMR, and isotags combined with the FDM now enable this to be easily performed. Additional general advantages of the FDM program for generating high-resolution 2D slices in any dimension from a 4D spectrum are emphasized.

Identification and characterization of two bisabolene synthases from linear glandular trichomes of sunflower (Helianthus annuus L., Asteraceae).

PubMed

Aschenbrenner, Anna-Katharina; Kwon, Moonhyuk; Conrad, Jürgen; Ro, Dae-Kyun; Spring, Otmar

2016-04-01

Sunflower is known to produce a variety of bisabolene-type sesquiterpenes and accumulates these substances in trichomes of leaves, stems and flowering parts. A bioinformatics approach was used to identify the enzyme responsible for the initial step in the biosynthesis of these compounds from its precursor farnesyl pyrophosphate. Based on sequence similarity with a known bisabolene synthases from Arabidopsis thaliana AtTPS12, candidate genes of Helianthus were searched in EST-database and used to design specific primers. PCR experiments identified two candidates in the RNA pool of linear glandular trichomes of sunflower. Their sequences contained the typical motifs of sesquiterpene synthases and their expression in yeast functionally characterized them as bisabolene synthases. Spectroscopic analysis identified the stereochemistry of the product of both enzymes as (Z)-γ-bisabolene. The origin of the two sunflower bisabolene synthase genes from the transcripts of linear trichomes indicates that they may be involved in the synthesis of sesquiterpenes produced in these trichomes. Comparison of the amino acid sequences of the sunflower bisabolene synthases showed high similarity with sesquiterpene synthases from other Asteracean species and indicated putative evolutionary origin from a β-farnesene synthase. Copyright © 2016 Elsevier Ltd. All rights reserved.

Formation of periodic γ-turns in α/β-hybrid peptides: DFT and NMR experimental evidence.

PubMed

Chandrasekhar, Srivari; Rao, Kakita Veera Mohana; Seenaiah, Mallikanti; Naresh, Police; Devi, Ambure Sharada; Jagadeesh, Bharatam

2014-02-01

Hybrid peptidic oligomers comprising natural and unnatural amino acid residues that can exhibit biomolecular folding and hydrogen-bonding mimicry have attracted considerable interest in recent years. While a variety of hybrid peptidic helices have been reported in the literature, other secondary structural patterns such as γ-turns and ribbons have not been well explored so far. The present work reports the design of novel periodic γ-turns in the oligomers of 1:1 natural-α/unnatural trans-β-norborenene (TNAA) amino acid residues. Through DFT, NMR, and MD studies, it is convincingly shown that, in the mixed conformational pool, the heterogeneous backbone of the hybrid peptides preferentially adopt periodic 8-membered (pseudo γ-turn)/7-membered (inverse γ-turn) hydrogen bonds in both polar and non-polar solvent media. It is observed that the stereochemistry and local conformational preference of the β-amino acid building blocks have a profound influence on accessing the specific secondary fold. These findings may be of significant relevance for the development of molecular scaffolds that facilitate desired positioning of functional side-chains. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Truncation studies of alpha-melanotropin peptides identify tripeptide analogues exhibiting prolonged agonist bioactivity.

PubMed

Haskell-Luevano, C; Sawyer, T K; Hendrata, S; North, C; Panahinia, L; Stum, M; Staples, D J; Castrucci, A M; Hadley, M F; Hruby, V J

1996-01-01

Truncation studies of alpha-melanotropin peptides identify tripeptide analogues exhibiting prolonged agonist bioactivity: PEPTIDES 17(6) 995-1002, 1996.-Systematic analysis of fragment derivatives of the superpotent alpha-MSH analogue. Ac-Ser.Tyr-Ser-Nle4-Glu- His-DPhe7-Arg-Trp-Gly-Lys-Pro-Val-NH2(NDP-MSH), led to the discovery of tripeptide agonists possessing prolonged bioactivity in the frog skin assay. Of particular significance to this discovery was Ac-DPhe-Arg-DTrp-NH2, which was the most potent tripeptide in this series exhibiting sustained melanotropic activity. Different pharmacophore models appear to exist that are dependent on the substructure and stereochemistry of the MSH(6-9) "active site." The tripeptides Ac-DPhe-Arg-Trp-NH2, Ac-DPhe-Arg-DTrp-NH2, and Ac-DPhe-DArg-Trp-NH2 stereo-chemical combinations require only Phe7-Xaa8-Trp9, whereas Ac-DPhe-DArg-DTrp-NH2, Ac-Phe-Arg-DTrp-NH2, and Ac-Phe-Arg-Trp-NH2 additionally require His4 for minimal biological activity. Ac-DPhe-Arg-DTrp-NH2 represents a novel prototype lead for the development of MSH-based peptidomimetic agonists.

Rapid purification and plasticization of D-glutamate-containing poly-γ-glutamate from Japanese fermented soybean food natto.

PubMed

Ashiuchi, Makoto; Oike, Shota; Hakuba, Hirofumi; Shibatani, Shigeo; Oka, Nogiho; Wakamatsu, Taisuke

2015-12-10

Poly-γ-glutamate (PGA) is a major component of mucilage derived from natto, a Japanese fermented food made from soybeans, and PGAs obtained under laboratory's conditions contain numerous d-glutamyl residues. Natto foods are thus promising as a source for nutritionally safe d-amino acids present in intact and digested polymers, although there is little information on the stereochemistry of PGA isolated directly from natto. Here, we describe the development of a new process for rapid purification of PGA using alum and determined the D-glutamate content of natto PGA by chiral high-performance liquid chromatographic analysis. Further, using hexadecylpyridinium cation (HDP(+)), which is a compound of toothpaste, we chemically transformed natto PGA into a new thermoplastic material, called DL-PGAIC. (1)H nuclear magnetic resonance and calorimetric measurements indicate that DL-PGAIC is a stoichiometric complex of natto PGA and HDP(+) with glass transition points of -16.8 °C and -3.1 °C. Then, DL-PGAIC began decomposing at 210°C, suggesting thermal stability suitable for use as a supramolecular soft plastic. Copyright © 2015 Elsevier B.V. All rights reserved.

pKa cycling of the general acid/base in glycoside hydrolase families 33 and 34.

PubMed

Yu, Haibo; Griffiths, Thomas M

2014-03-28

Glycoside hydrolase families 33 and 34 catalyse the hydrolysis of terminal sialic acid residues from sialyl oligosaccharides and glycoconjugates with a net retention of the stereochemistry at the anomeric centre. It is generally believed that the conserved aspartic acid in the active site functions as a general acid to protonate the hydroxyl group of the departing aglycone during glycosylation, and then as a general base to facilitate the nucleophilic attack of the water molecule on the intermediate state during the deglycosylation reaction. The dual role of the general acid/base places specific demands upon its protonation state, and thus pKa values. However, it is not fully understood how this catalytic residue can achieve such pKa cycling during catalysis. We present both MM and combined QM/MM simulations to characterise the pKa values of the proposed catalytic general acid/base in the glycoside hydrolase families 33 and 34. Collectively, our study suggests that the binding of anionic substrates and the local solvation properties along with the neutralisation of the nearby glutamic acid upon glycosylation modulate the electrostatic environment around the general acid/base to achieve its proper protonation states.

Synthesis, Properties and Stereochemistry of 2-Halo-1,2λ⁵-oxaphosphetanes.

PubMed

Kolodiazhna, Anastasy O; Kolodiazhnyi, Oleg I

2016-10-17

Results of research into four-membered 2-halo-1,2λ⁵-oxaphosphetane phosphorus(V)-heterocycles are presented. The preparation of 2-halo-1,2λ⁵-oxaphosphetanes by reaction of P- haloylides with carbonyl compounds is described. The mechanism of asynchronous [2+2]-сycloaddition of ylides to aldehydes was proposed on the base of low-temperature NMR investigations. 2-Halo-1,2λ⁵-oxaphosphetanes were isolated as individual compounds and their structures were confirmed by ¹Н-, 13 C-, 19 F- and 31 Р-NMR spectra. These compounds are convenient reagents for preparing of various organic and organophosphorus compounds hardly available by other methods. Chemical and physical properties of the 2-halo-1,2λ⁵-oxaphosphetanes are reviewed. The 2-chloro-1,2λ⁵-oxaphosphetanes, rearrange with formation of 2-chloroalkyl-phosphonates or convert into trans -phosphorylated alkenes depending on the substituents at the α-carbon atom. Prospective synthetic applications of 2-halo-1,2λ⁵-oxaphosphetanes are analyzed. The 2-halo-1,2λ⁵-oxaphosphetanes may be easily converted to various alkenylphosphonates: allyl- or vinylphosphonates, phosphorus ketenes, thioketenes, ketenimines.

Determination of the chirality of the saturated pyrrole in sulfmyoglobin using the nuclear Overhauser effect.

PubMed

Parker, W O; Chatfield, M J; La Mar, G N

1989-02-21

The interproton nuclear Overhauser effect (NOE) and paramagnetic dipolar relaxation rates for hyperfine-shifted resonances in the proton NMR spectra of sperm whale met-cyano sulfmyoglobin have led to the location and assignment of the proton signals of the heme pocket residue isoleucine 99 (FG5) in two sulfmyoglobin isomers. Dipolar relaxation rates of these protein signals indicate a highly conserved geometry of the heme pocket upon sulfmyoglobin formation, while the similar upfield direction of dipolar shifts for this residue to that observed in native sperm whale myoglobin reflects largely retained magnetic properties. Dipolar connectivity of this protein residue to the substituents of the reacted heme pyrrole ring B defines the stereochemistry of the puckered thiolene ring found in one isomer, with the 3-CH3 tilted out of the heme plane proximally. The chirality of the saturated carbons of pyrrole ring B in both the initial sulfmyoglobin product and the terminal alkaline product is consistent with a mechanism of formation in which an atom of sulfur is incorporated distally to form an episulfide across ring B, followed by reaction of the vinyl group to yield the thiolene ring that retains the C3 chirality.

Microwave-assisted synthesis of novel purine nucleosides as selective cholinesterase inhibitors.

PubMed

Schwarz, S; Csuk, R; Rauter, A P

2014-04-21

Alzheimer's disease (AD), the most common form of senile dementia, is characterized by high butyrylcholinesterase (BChE) levels in the brain in later AD stages, for which no treatment is available. Pursuing our studies on selective BChE inhibitors, that may contribute to understand the role of this enzyme in disease progression, we present now microwave-assisted synthesis and anticholinesterase activity of a new nucleoside series embodying 6-chloropurine or 2-acetamido-6-chloropurine linked to D-glucosyl, D-galactosyl and D-mannosyl residues. It was designed to assess the contribution of sugar stereochemistry, purine structure and linkage to the sugar for cholinesterase inhibition efficiency and selectivity. Compounds were subjected to Ellman's assay and their inhibition constants determined. The α-anomers were the most active compounds, while selectivity for BChE or acetylcholinesterase (AChE) inhibition could be tuned by the purine base, by the glycosyl moiety and by N(7)-ligation. Some of the nucleosides were far more potent than the drug galantamine, and the most promising competitive and selective BChE inhibitor, the N(7)-linked 2-acetamido-α-D-mannosylpurine, showed a Ki of 50 nM and a selectivity factor of 340 fold for BChE over AChE.

Development of an X-ray fluorescence holographic measurement system for protein crystals

NASA Astrophysics Data System (ADS)

Sato-Tomita, Ayana; Shibayama, Naoya; Happo, Naohisa; Kimura, Koji; Okabe, Takahiro; Matsushita, Tomohiro; Park, Sam-Yong; Sasaki, Yuji C.; Hayashi, Kouichi

2016-06-01

Experimental procedure and setup for obtaining X-ray fluorescence hologram of crystalline metalloprotein samples are described. Human hemoglobin, an α2β2 tetrameric metalloprotein containing the Fe(II) heme active-site in each chain, was chosen for this study because of its wealth of crystallographic data. A cold gas flow system was introduced to reduce X-ray radiation damage of protein crystals that are usually fragile and susceptible to damage. A χ-stage was installed to rotate the sample while avoiding intersection between the X-ray beam and the sample loop or holder, which is needed for supporting fragile protein crystals. Huge hemoglobin crystals (with a maximum size of 8 × 6 × 3 mm3) were prepared and used to keep the footprint of the incident X-ray beam smaller than the sample size during the entire course of the measurement with the incident angle of 0°-70°. Under these experimental and data acquisition conditions, we achieved the first observation of the X-ray fluorescence hologram pattern from the protein crystals with minimal radiation damage, opening up a new and potential method for investigating the stereochemistry of the metal active-sites in biomacromolecules.

Second-generation DNA-templated macrocycle libraries for the discovery of bioactive small molecules.

PubMed

Usanov, Dmitry L; Chan, Alix I; Maianti, Juan Pablo; Liu, David R

2018-07-01

DNA-encoded libraries have emerged as a widely used resource for the discovery of bioactive small molecules, and offer substantial advantages compared with conventional small-molecule libraries. Here, we have developed and streamlined multiple fundamental aspects of DNA-encoded and DNA-templated library synthesis methodology, including computational identification and experimental validation of a 20 × 20 × 20 × 80 set of orthogonal codons, chemical and computational tools for enhancing the structural diversity and drug-likeness of library members, a highly efficient polymerase-mediated template library assembly strategy, and library isolation and purification methods. We have integrated these improved methods to produce a second-generation DNA-templated library of 256,000 small-molecule macrocycles with improved drug-like physical properties. In vitro selection of this library for insulin-degrading enzyme affinity resulted in novel insulin-degrading enzyme inhibitors, including one of unusual potency and novel macrocycle stereochemistry (IC 50  = 40 nM). Collectively, these developments enable DNA-templated small-molecule libraries to serve as more powerful, accessible, streamlined and cost-effective tools for bioactive small-molecule discovery.

Cobalt-catalyzed cross-coupling reactions of alkyl halides with allylic and benzylic Grignard reagents and their application to tandem radical cyclization/cross-coupling reactions.

PubMed

Ohmiya, Hirohisa; Tsuji, Takashi; Yorimitsu, Hideki; Oshima, Koichiro

2004-11-05

Details of cobalt-catalyzed cross-coupling reactions of alkyl halides with allylic Grignard reagents are disclosed. A combination of cobalt(II) chloride and 1,2-bis(diphenylphosphino)ethane (DPPE) or 1,3-bis(diphenylphosphino)propane (DPPP) is suitable as a precatalyst and allows secondary and tertiary alkyl halides--as well as primary ones--to be employed as coupling partners for allyl Grignard reagents. The reaction offers a facile synthesis of quaternary carbon centers, which has practically never been possible with palladium, nickel, and copper catalysts. Benzyl, methallyl, and crotyl Grignard reagents can all couple with alkyl halides. The benzylation definitely requires DPPE or DPPP as a ligand. The reaction mechanism should include the generation of an alkyl radical from the parent alkyl halide. The mechanism can be interpreted in terms of a tandem radical cyclization/cross-coupling reaction. In addition, serendipitous tandem radical cyclization/cyclopropanation/carbonyl allylation of 5-alkoxy-6-halo-4-oxa-1-hexene derivatives is also described. The intermediacy of a carbon-centered radical results in the loss of the original stereochemistry of the parent alkyl halides, creating the potential for asymmetric cross-coupling of racemic alkyl halides.

An automated curation procedure for addressing chemical errors and inconsistencies in public datasets used in QSAR modelling.

PubMed

Mansouri, K; Grulke, C M; Richard, A M; Judson, R S; Williams, A J

2016-11-01

The increasing availability of large collections of chemical structures and associated experimental data provides an opportunity to build robust QSAR models for applications in different fields. One common concern is the quality of both the chemical structure information and associated experimental data. Here we describe the development of an automated KNIME workflow to curate and correct errors in the structure and identity of chemicals using the publicly available PHYSPROP physicochemical properties and environmental fate datasets. The workflow first assembles structure-identity pairs using up to four provided chemical identifiers, including chemical name, CASRNs, SMILES, and MolBlock. Problems detected included errors and mismatches in chemical structure formats, identifiers and various structure validation issues, including hypervalency and stereochemistry descriptions. Subsequently, a machine learning procedure was applied to evaluate the impact of this curation process. The performance of QSAR models built on only the highest-quality subset of the original dataset was compared with the larger curated and corrected dataset. The latter showed statistically improved predictive performance. The final workflow was used to curate the full list of PHYSPROP datasets, and is being made publicly available for further usage and integration by the scientific community.

Systematic study on the TD-DFT calculated electronic circular dichroism spectra of chiral aromatic nitro compounds: A comparison of B3LYP and CAM-B3LYP.

PubMed

Komjáti, Balázs; Urai, Ákos; Hosztafi, Sándor; Kökösi, József; Kováts, Benjámin; Nagy, József; Horváth, Péter

2016-02-15

B3LYP is one of the most widely used functional for the prediction of electronic circular dichroism spectra, however if the studied molecule contains aromatic nitro group computations may fail to produce reliable results. A test set of molecules of known stereochemistry were synthesized to study this phenomenon in detail. Spectra were computed by B3LYP and CAM-B3LYP functionals with 6-311++G(2d,2p) basis set. It was found that the range separated CAM-B3LYP gives better predictions than B3LYP for all test molecules. Fragment population analysis revealed that the nitro groups form highly localized molecule orbitals but the exact composition depends on the functional. CAM-B3LYP allows sufficient spatial overlap between the nitro group and distant parts of the molecule, which is necessary for the accurate description of excited states especially for charge transfer states. This phenomenon and the synthesized test molecules can be used to benchmark theoretical methods as well as to help the development of new functionals intended for spectroscopical studies. Copyright © 2015 Elsevier B.V. All rights reserved.

Computational Studies on the Synthesis of β-Lactams via [2+2] Thermal Cycloadditions

NASA Astrophysics Data System (ADS)

Arrieta, Ana; Lecea, Begoña; Cossío, Fernando P.

The main computational studies on the formation of β-lactams through [2+2] cycloadditions published during 1992-2008 are reported with special emphasis on the mechanistic and selectivity aspects of these reactions. Disconnection of the N1-C2 and C3-C4 bonds of the azetidin-2-one ring leads to the reaction between ketenes and imines. Computational and experimental results point to a stepwise mechanism for this reaction. The first step consists of a nucleophilic attack of the iminic nitrogen on the sp-hybridized carbon atom of the ketene. The zwitterionic intermediate thus formed yields the corresponding β-lactam by means of a four-electron conrotatoty electrocyclization. The steroecontrol and the periselectivity of the reaction support this two-step mechanism. The [2+2] cycloaddition between isocyanates and alkenes takes place via a concerted (but asynchronous) mechanism that can be interpreted in terms of a [π2s + (π2s + π2s)] interaction between both reactants. Both the regio and the stereochemistry observed are compatible with this computational model. However, the combination of solvent and substituent effects can result in a stepwise mechanism.

Coupling and Reactions of 5-Hydroxyconiferyl Alcohol in Lignin Formation

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

Elder, Thomas; Berstis, Laura; Beckham, Gregg T.

The catechol alcohols, caffeyl and 5-hydroxyconiferyl alcohol, may be incorporated into lignin either naturally or through genetic manipulation. Due to the presence of o-OH groups, these compounds form benzodioxanes, a departure from the interunit connections found in lignins derived from the cinnamyl alcohols. In nature, lignins composed of caffeyl and 5-hydroxyconiferyl alcohol are linear homopolymers and, as such, may have properties that make them amenable for use in value-added products, such as lignin-based carbon fibers. In the current work, results from density functional theory calculations for the reactions of 5-hydroxyconiferyl alcohol, taking stereochemistry into account, are reported. Dehydrogenation and quinone methide formation are found to be thermodynamically favored for 5-hydroxyconiferyl alcohol, over coniferyl alcohol. The comparative energetics of the rearomatization reactions suggest that the formation of the benzodioxane linkage is under kinetic control. Ring-opening reactions of the benzodioxane groups show that the bond dissociation enthalpy of themore » $$\\alpha$$-O cleavage reaction is lower than that of the $$\\beta$$-O reaction. In conclusion, the catechol lignins represent a novel form of the polymer that may offer new opportunities for bioproducts and genetic targets.« less

Coupling and Reactions of 5-Hydroxyconiferyl Alcohol in Lignin Formation

DOE PAGES

Elder, Thomas; Berstis, Laura; Beckham, Gregg T.; ...

2016-05-28

The catechol alcohols, caffeyl and 5-hydroxyconiferyl alcohol, may be incorporated into lignin either naturally or through genetic manipulation. Due to the presence of o-OH groups, these compounds form benzodioxanes, a departure from the interunit connections found in lignins derived from the cinnamyl alcohols. In nature, lignins composed of caffeyl and 5-hydroxyconiferyl alcohol are linear homopolymers and, as such, may have properties that make them amenable for use in value-added products, such as lignin-based carbon fibers. In the current work, results from density functional theory calculations for the reactions of 5-hydroxyconiferyl alcohol, taking stereochemistry into account, are reported. Dehydrogenation and quinone methide formation are found to be thermodynamically favored for 5-hydroxyconiferyl alcohol, over coniferyl alcohol. The comparative energetics of the rearomatization reactions suggest that the formation of the benzodioxane linkage is under kinetic control. Ring-opening reactions of the benzodioxane groups show that the bond dissociation enthalpy of themore » $$\\alpha$$-O cleavage reaction is lower than that of the $$\\beta$$-O reaction. In conclusion, the catechol lignins represent a novel form of the polymer that may offer new opportunities for bioproducts and genetic targets.« less

A New Ergosterol Analog, a New Bis-Anthraquinone and Anti-Obesity Activity of Anthraquinones from the Marine Sponge-Associated Fungus Talaromyces stipitatus KUFA 0207

PubMed Central

Noinart, Jidapa; Buttachon, Suradet; Dethoup, Tida; Gales, Luís; Pereira, José A.; Urbatzka, Ralph; Freitas, Sara; Lee, Michael; Silva, Artur M. S.; Pinto, Madalena M. M.; Vasconcelos, Vítor; Kijjoa, Anake

2017-01-01

A new ergosterol analog, talarosterone (1) and a new bis-anthraquinone derivative (3) were isolated, together with ten known compounds including palmitic acid, ergosta-4,6,8(14),22-tetraen-3-one, ergosterol-5,8-endoperoxide, cyathisterone (2), emodin (4a), questinol (4b), citreorosein (4c), fallacinol (4d), rheoemodin (4e) and secalonic acid A (5), from the ethyl acetate extract of the culture of the marine sponge-associated fungus Talaromyces stipitatus KUFA 0207. The structures of the new compounds were established based on extensive 1D and 2D spectral analysis, and in the case of talarosterone (1), the absolute configurations of its stereogenic carbons were determined by X-ray crystallographic analysis. The structure and stereochemistry of cyathisterone (2) was also confirmed by X-ray analysis. The anthraquinones 4a–e and secalonic acid A (5) were tested for their anti-obesity activity using the zebrafish Nile red assay. Only citreorosein (4c) and questinol (4b) exhibited significant anti-obesity activity, while emodin (4a) and secalonic acid A (5) caused toxicity (death) for all exposed zebrafish larvae after 24 h. PMID:28509846

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

Sato-Tomita, Ayana, E-mail: ayana.sato@jichi.ac.jp, E-mail: shibayam@jichi.ac.jp, E-mail: hayashi.koichi@nitech.ac.jp; Shibayama, Naoya, E-mail: ayana.sato@jichi.ac.jp, E-mail: shibayam@jichi.ac.jp, E-mail: hayashi.koichi@nitech.ac.jp; Okabe, Takahiro

Experimental procedure and setup for obtaining X-ray fluorescence hologram of crystalline metalloprotein samples are described. Human hemoglobin, an α{sub 2}β{sub 2} tetrameric metalloprotein containing the Fe(II) heme active-site in each chain, was chosen for this study because of its wealth of crystallographic data. A cold gas flow system was introduced to reduce X-ray radiation damage of protein crystals that are usually fragile and susceptible to damage. A χ-stage was installed to rotate the sample while avoiding intersection between the X-ray beam and the sample loop or holder, which is needed for supporting fragile protein crystals. Huge hemoglobin crystals (with amore » maximum size of 8 × 6 × 3 mm{sup 3}) were prepared and used to keep the footprint of the incident X-ray beam smaller than the sample size during the entire course of the measurement with the incident angle of 0°-70°. Under these experimental and data acquisition conditions, we achieved the first observation of the X-ray fluorescence hologram pattern from the protein crystals with minimal radiation damage, opening up a new and potential method for investigating the stereochemistry of the metal active-sites in biomacromolecules.« less

Bioactive metabolites from an endophytic Cryptosporiopsis sp. inhabiting Clidemia hirta.

PubMed

Zilla, Mahesh K; Qadri, Masroor; Pathania, Anup S; Strobel, Gary A; Nalli, Yedukondalu; Kumar, Sunil; Guru, Santosh K; Bhushan, Shashi; Singh, Sanjay K; Vishwakarma, Ram A; Riyaz-Ul-Hassan, Syed; Ali, Asif

2013-11-01

An endophytic Cryptosporiopsis sp. was isolated from Clidemia hirta and analyzed for its secondary metabolites that lead to the isolation of three bioactive molecules. The compounds were purified from the culture broth of the fungus and their structures were determined by spectroscopic methods as (R)-5-hydroxy-2-methylchroman-4-one (1), 1-(2,6-dihydroxyphenyl)pentan-1-one (2) and (Z)-1-(2-(2-butyryl-3-hydroxyphenoxy)-6-hydroxyphenyl)-3-hydroxybut-2-en-1-one (3). Compound 1 exhibited significant cytotoxic activity against the human leukemia cell line, HL-60 with an IC50 of 4 μg/ml. This compound induced G2 arrest of the HL-60 cell cycle significantly. In addition, out of these compounds, 2 and 3 were active against several bacterial pathogens. Compound 2 was active against Bacillus cereus, Escherichia coli and Staphylococcus aureus with IC50 values varying from 18 to 30 μg/ml, and compound 3 displayed activity against Pseudomonas fluorescens with an IC50 value of 6 μg/ml. Compounds 2 and 3 are novel whereas compound 1 was reported earlier but the stereochemistry of its C-2 methyl is established for the first time. Copyright © 2013 Elsevier Ltd. All rights reserved.

Synthesis and Utilization of Trialkylammonium-Substituted Cyclodextrins as Water-Soluble Chiral NMR Solvating Agents for Anionic Compounds.

PubMed

Dowey, Alison E; Puentes, Cira Mollings; Carey-Hatch, Mira; Sandridge, Keyana L; Krishna, Nikhil B; Wenzel, Thomas J

2016-04-01

Cationic trialkylammonium-substituted α-, β-, and γ-cyclodextrins containing trimethyl-, triethyl-, and tri-n-propylammonium substituent groups were synthesized and analyzed for utility as water-soluble chiral nuclear magnetic resonance (NMR) solvating agents. Racemic and enantiomerically pure (3-chloro-2-hydroxypropyl)trimethyl-, triethyl-, and tri-n-propyl ammonium chloride were synthesized from the corresponding trialkyl amine hydrochloride and either racemic or enantiomerically pure epichlorohydrin. The ammonium salts were then reacted with α-, β-, and γ-cyclodextrins at basic pH to provide the corresponding randomly substituted cationic cyclodextrins. The (1) H NMR spectra of a range of anionic, aromatic compounds was recorded with the cationic cyclodextrins. Cyclodextrins with a single stereochemistry at the hydroxy group on the (2-hydroxypropyl)trialkylammonium chloride substituent were often but not always more effective than the corresponding cyclodextrin in which the C-2 position was racemic. In several cases, the larger triethyl or tri-n-propyl derivatives were more effective than the corresponding trimethyl derivative at causing enantiomeric differentiation. None of the cyclodextrin derivatives were consistently the most effective for all of the anionic compounds studied. © 2016 Wiley Periodicals, Inc.

Stereoinversion of tertiary alcohols to tertiary-alkyl isonitriles and amines.

PubMed

Pronin, Sergey V; Reiher, Christopher A; Shenvi, Ryan A

2013-09-12

The SN2 reaction (bimolecular nucleophilic substitution) is a well-known chemical transformation that can be used to join two smaller molecules together into a larger molecule or to exchange one functional group for another. The SN2 reaction proceeds in a very predictable manner: substitution occurs with inversion of stereochemistry, resulting from the 'backside attack' of the electrophilic carbon by the nucleophile. A significant limitation of the SN2 reaction is its intolerance for tertiary carbon atoms: whereas primary and secondary alcohols are viable precursor substrates, tertiary alcohols and their derivatives usually either fail to react or produce stereochemical mixtures of products. Here we report the stereochemical inversion of chiral tertiary alcohols with a nitrogenous nucleophile facilitated by a Lewis-acid-catalysed solvolysis. The method is chemoselective against secondary and primary alcohols, thereby complementing the selectivity of the SN2 reaction. Furthermore, this method for carbon-nitrogen bond formation mimics a putative biosynthetic step in the synthesis of marine terpenoids and enables their preparation from the corresponding terrestrial terpenes. We expect that the general attributes of the methodology will allow chiral tertiary alcohols to be considered viable substrates for stereoinversion reactions.

Computation of deuterium isotope perturbation of 13C NMR chemical shifts of alkanes: a local mode zero-point level approach.

PubMed

Yang, Kin S; Hudson, Bruce

2010-11-25

Replacement of H by D perturbs the (13)C NMR chemical shifts of an alkane molecule. This effect is largest for the carbon to which the D is attached, diminishing rapidly with intervening bonds. The effect is sensitive to stereochemistry and is large enough to be measured reliably. A simple model based on the ground (zero point) vibrational level and treating only the C-H(D) degrees of freedom (local mode approach) is presented. The change in CH bond length with H/D substitution as well as the reduction in the range of the zero-point level probability distribution for the stretch and both bend degrees of freedom are computed. The (13)C NMR chemical shifts are computed with variation in these three degrees of freedom, and the results are averaged with respect to the H and D distribution functions. The resulting differences in the zero-point averaged chemical shifts are compared with experimental values of the H/D shifts for a series of cycloalkanes, norbornane, adamantane, and protoadamantane. Agreement is generally very good. The remaining differences are discussed. The proton spectrum of cyclohexane- is revisited and updated with improved agreement with experiment.

Bioactivity-Guided Isolation of Potential Antidiabetic and Antihyperlipidemic Compounds from Trigonella stellata.

PubMed

Shams Eldin, Safa M; Radwan, Mohamed M; Wanas, Amira S; Habib, Abdel-Azim M; Kassem, Fahima F; Hammoda, Hala M; Khan, Shabana I; Klein, Michael L; Elokely, Khaled M; ElSohly, Mahmoud A

2018-05-25

The in vitro antidiabetic and antihyperlipidemic activities of an alcoholic extract of Trigonella stellata were evaluated in terms of the activation of PPAR α and PPAR γ in human hepatoma (HepG2) cells. The extract was investigated phytochemically, aiming at the isolation of the most active compounds to be used as a platform for drug discovery. Three new isoflavans, (3 S,4 R)-4,2',4'-trihydroxy)-7-methoxyisoflavan (1), (3 R,4 S)-4,2',4'-trihydroxy-7-methoxy-4'- O-β-d-glucopyranosylisoflavan (2), and (2 S,3 R,4 R)-4,2',4'-trihydroxy-2,7-dimethoxyisoflavan (3), were isolated and characterized along with the five known compounds p-hydroxybenzoic acid (4), 7,4'-dihydroxyflavone (5), dihydromelilotoside (6), quercetin-3,7- O-α-l-dirhamnoside (7), and soyasaponin I (8). The structures of 1-3 were elucidated using various spectroscopic techniques including HRESIMS and 1D and 2D NMR. The absolute stereochemistry of the new isoflavans (1-3) was determined using both experimental and calculated electronic circular dichroism as well as DP4 calculations. The isolated compounds were tested for their PPAR α and PPAR γ activation effects in HepG2 cells.

Resolving Structural Isomers of Monosaccharide Methyl Glycosides Using Drift Tube and Traveling Wave Ion Mobility Mass Spectrometry

PubMed Central

Li, Hongli; Giles, Kevin; Bendiak, Brad; Kaplan, Kimberly; Siems, William F.; Hill, Herbert H.

2013-01-01

Monosaccharide structural isomers including sixteen methyl-D-glycopyranosides and four methyl-N-acetylhexosamines were subjected to ion mobility measurements by electrospray ion mobility mass spectrometry. Two ion mobility-MS systems were employed: atmospheric pressure drift tube ion mobility time-of-flight mass spectrometry and a Synapt G2 HDMS system which incorporates a low pressure traveling wave ion mobility separator. All the compounds were investigated as [M+Na]+ ions in the positive mode. A majority of the monosaccharide structural isomers exhibited different mobility drift times in either system, depending on differences in their anomeric and stereochemical configurations. In general, drift time patterns (relative drift times of isomers) matched between the two instruments. Higher resolving power was observed using the atmospheric pressure drift tube. Collision cross section values of monosaccharide structural isomers were directly calculated from the atmospheric pressure ion mobility experiments and a collision cross section calibration curve was made for the traveling wave ion mobility instrument. Overall, it was demonstrated that ion mobility-mass spectrometry using either drift tube or traveling wave ion mobility is a valuable technique for resolving subtle variations in stereochemistry among the sodium adducts of monosaccharide methyl glycosides. PMID:22339760

A prebiotic template-directed peptide synthesis based on amyloids.

PubMed

Rout, Saroj K; Friedmann, Michael P; Riek, Roland; Greenwald, Jason

2018-01-16

The prebiotic replication of information-coding molecules is a central problem concerning life's origins. Here, we report that amyloids composed of short peptides can direct the sequence-selective, regioselective and stereoselective condensation of amino acids. The addition of activated DL-arginine and DL-phenylalanine to the peptide RFRFR-NH 2 in the presence of the complementary template peptide Ac-FEFEFEFE-NH 2 yields the isotactic product FRFRFRFR-NH 2 , 1 of 64 possible triple addition products, under conditions in which the absence of template yields only single and double additions of mixed stereochemistry. The templating mechanism appears to be general in that a different amyloid formed by (Orn)V(Orn)V(Orn)V(Orn)V-NH 2 and Ac-VDVDVDVDV-NH 2 is regioselective and stereoselective for N-terminal, L-amino-acid addition while the ornithine-valine peptide alone yields predominantly sidechain condensation products with little stereoselectivity. Furthermore, the templating reaction is stable over a wide range of pH (5.6-8.6), salt concentration (0-4 M NaCl), and temperature (25-90 °C), making the amyloid an attractive model for a prebiotic peptide replicating system.

Antifreeze glycopeptide diastereomers.

PubMed

Nagel, Lilly; Budke, Carsten; Dreyer, Axel; Koop, Thomas; Sewald, Norbert

2012-01-01

Antifreeze glycopeptides (AFGPs) are a special class of biological antifreeze agents, which possess the property to inhibit ice growth in the body fluids of arctic and antarctic fish and, thus, enable life under these harsh conditions. AFGPs are composed of 4-55 tripeptide units -Ala-Ala-Thr- glycosylated at the threonine side chains. Despite the structural homology among all the fish species, divergence regarding the composition of the amino acids occurs in peptides from natural sources. Although AFGPs were discovered in the early 1960s, the adsorption mechanism of these macromolecules to the surface of the ice crystals has not yet been fully elucidated. Two AFGP diastereomers containing different amino acid configurations were synthesized to study the influence of amino acid stereochemistry on conformation and antifreeze activity. For this purpose, peptides containing monosaccharide-substituted allo-L- and D-threonine building blocks were assembled by solid-phase peptide synthesis (SPPS). The retro-inverso AFGP analogue contained all amino acids in D-configuration, while the allo-L-diastereomer was composed of L-amino acids, like native AFGPs, with replacement of L-threonine by its allo-L-diastereomer. Both glycopeptides were analyzed regarding their conformational properties, by circular dichroism (CD), and their ability to inhibit ice recrystallization in microphysical experiments.

Antifreeze glycopeptide diastereomers

PubMed Central

Nagel, Lilly; Budke, Carsten; Dreyer, Axel; Koop, Thomas

2012-01-01

Summary Antifreeze glycopeptides (AFGPs) are a special class of biological antifreeze agents, which possess the property to inhibit ice growth in the body fluids of arctic and antarctic fish and, thus, enable life under these harsh conditions. AFGPs are composed of 4–55 tripeptide units -Ala-Ala-Thr- glycosylated at the threonine side chains. Despite the structural homology among all the fish species, divergence regarding the composition of the amino acids occurs in peptides from natural sources. Although AFGPs were discovered in the early 1960s, the adsorption mechanism of these macromolecules to the surface of the ice crystals has not yet been fully elucidated. Two AFGP diastereomers containing different amino acid configurations were synthesized to study the influence of amino acid stereochemistry on conformation and antifreeze activity. For this purpose, peptides containing monosaccharide-substituted allo-L- and D-threonine building blocks were assembled by solid-phase peptide synthesis (SPPS). The retro-inverso AFGP analogue contained all amino acids in D-configuration, while the allo-L-diastereomer was composed of L-amino acids, like native AFGPs, with replacement of L-threonine by its allo-L-diastereomer. Both glycopeptides were analyzed regarding their conformational properties, by circular dichroism (CD), and their ability to inhibit ice recrystallization in microphysical experiments. PMID:23209499

Muramyl peptides in mammalian tissues and their effects at the cellular level.

PubMed

Karnovsky, M L

1986-10-01

Muramyl peptides (MPs), presumably breakdown products of bacterial cell walls, have been found in the brain, liver, and kidney of the rat. They exert multiple physiological effects on higher animals as immunoadjuvants, activators of macrophages, pyrogens, antitumor agents, inducers of contractility of smooth muscle, and promoters of slow-wave sleep, as well as nonspecific protectors of animals against infection. Structure-function relationships of these substances have been extensively studied, especially with respect to somnogenicity. In the role an intact muramyl ring is required, and the 1,6-anhydro form is active. The presence of free carboxyls or amides on the glutamyl and diaminopimelyl entities have important effects. The stereochemistry is crucial: the alanine adjacent to the N-acetylmuramyl entity must be L, and the glutamate must be D. Studies were carried out with murine macrophages to establish mechanisms of action of these glycopeptides. There are two populations of binding sites for MPs on those cells. When compounds of different structure are compared, binding ability correlates with pyrogenic and somnogenic activity. Serotonin competes with these agents for binding sites. Binding of that substance induces at least one macrophage response characteristic of the binding of MP.

Protein Loop Structure Prediction Using Conformational Space Annealing.

PubMed

Heo, Seungryong; Lee, Juyong; Joo, Keehyoung; Shin, Hang-Cheol; Lee, Jooyoung

2017-05-22

We have developed a protein loop structure prediction method by combining a new energy function, which we call E PLM (energy for protein loop modeling), with the conformational space annealing (CSA) global optimization algorithm. The energy function includes stereochemistry, dynamic fragment assembly, distance-scaled finite ideal gas reference (DFIRE), and generalized orientation- and distance-dependent terms. For the conformational search of loop structures, we used the CSA algorithm, which has been quite successful in dealing with various hard global optimization problems. We assessed the performance of E PLM with two widely used loop-decoy sets, Jacobson and RAPPER, and compared the results against the DFIRE potential. The accuracy of model selection from a pool of loop decoys as well as de novo loop modeling starting from randomly generated structures was examined separately. For the selection of a nativelike structure from a decoy set, E PLM was more accurate than DFIRE in the case of the Jacobson set and had similar accuracy in the case of the RAPPER set. In terms of sampling more nativelike loop structures, E PLM outperformed E DFIRE for both decoy sets. This new approach equipped with E PLM and CSA can serve as the state-of-the-art de novo loop modeling method.

A site-saturated mutagenesis study of pentaerythritol tetranitrate reductase reveals that residues 181 and 184 influence ligand binding, stereochemistry and reactivity.

PubMed

Toogood, Helen S; Fryszkowska, Anna; Hulley, Martyn; Sakuma, Michiyo; Mansell, David; Stephens, Gill M; Gardiner, John M; Scrutton, Nigel S

2011-03-21

We have conducted a site-specific saturation mutagenesis study of H181 and H184 of flavoprotein pentaerythritol tetranitrate reductase (PETN reductase) to probe the role of these residues in substrate binding and catalysis with a variety of α,β-unsaturated alkenes. Single mutations at these residues were sufficient to dramatically increase the enantiopurity of products formed by reduction of 2-phenyl-1-nitropropene. In addition, many mutants exhibited a switch in reactivity to predominantly catalyse nitro reduction, as opposed to CC reduction. These mutants showed an enhancement in a minor side reaction and formed 2-phenylpropanal oxime from 2-phenyl-1-nitropropene. The multiple binding conformations of hydroxy substituted nitro-olefins in PETN reductase were examined by using both structural and catalytic techniques. These compounds were found to bind in both active and inhibitory complexes; this highlights the plasticity of the active site and the ability of the H181/H184 couple to coordinate with multiple functional groups. These properties demonstrate the potential to use PETN reductase as a scaffold in the development of industrially useful biocatalysts. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal structure of bis-[tetra-kis-(tetra-hydro-furan-κO)lithium] bis[μ-2,2',2''-methanetriyltris(4,6-di-tert-butylphenolato)-κ4O,O':O',O'']-dimagnesiate.

PubMed

Zhou, Hongyan; Wang, Lei

2017-07-01

The title ion-association metal complex, [Li(C 4 H 8 O) 4 ] 2 [Mg 2 (C 43 H 61 O 3 ) 2 ], has been synthesized from the tridentate phenolic ligand tris-(3,5-di- tert -butyl-2-hy-droxy-phen-yl)methane in tetra-hydro-furan (THF). The aryl-oxo magnesiate complex anion is binuclear with each Mg 2 O 4 complex unit inversion-related and bridged through the two tridentate chelating phenolate O-donors of the ligand. The complex centres have a distorted tetra-hedral stereochemistry [Mg-O range 1.8796 (17)-2.0005 (16) Å] and an Mg⋯Mg separation of 2.9430 (14) Å]. The LiO 4 coodination sphere of the cation comprises four THF O-donor atoms and has a slightly distorted tetra-hedral conformation [Li-O range 1.899 (5)- 1.953 (5) Å]. In the crystal, a number of stabilizing intra-anion C-H⋯O hydrogen-bonding inter-actions are present but no inter-species associations are found.

Optimizing separations in online comprehensive two‐dimensional liquid chromatography

PubMed Central

Gargano, Andrea F.G.; Schoenmakers, Peter J.

2017-01-01

Abstract Online comprehensive two‐dimensional liquid chromatography has become an attractive option for the analysis of complex nonvolatile samples found in various fields (e.g. environmental studies, food, life, and polymer sciences). Two‐dimensional liquid chromatography complements the highly popular hyphenated systems that combine liquid chromatography with mass spectrometry. Two‐dimensional liquid chromatography is also applied to the analysis of samples that are not compatible with mass spectrometry (e.g. high‐molecular‐weight polymers), providing important information on the distribution of the sample components along chemical dimensions (molecular weight, charge, lipophilicity, stereochemistry, etc.). Also, in comparison with conventional one‐dimensional liquid chromatography, two‐dimensional liquid chromatography provides a greater separation power (peak capacity). Because of the additional selectivity and higher peak capacity, the combination of two‐dimensional liquid chromatography with mass spectrometry allows for simpler mixtures of compounds to be introduced in the ion source at any given time, improving quantitative analysis by reducing matrix effects. In this review, we summarize the rationale and principles of two‐dimensional liquid chromatography experiments, describe advantages and disadvantages of combining different selectivities and discuss strategies to improve the quality of two‐dimensional liquid chromatography separations. PMID:29027363

Molecular structure of dextran sulphate sodium in aqueous environment

NASA Astrophysics Data System (ADS)

Yu, Miao; Every, Hayley A.; Jiskoot, Wim; Witkamp, Geert-Jan; Buijs, Wim

2018-03-01

Here we propose a 3D-molecular structural model for dextran sulphate sodium (DSS) in a neutral aqueous environment based on the results of a molecular modelling study. The DSS structure is dominated by the stereochemistry of the 1,6-linked α-glucose units and the presence of two sulphate groups on each α-glucose unit. The structure of DSS can be best described as a helix with various patterns of di-sulphate substitution on the glucose rings. The presence of a side chain does not alter the 3D-structure of the linear main chain much, but affects the overall spatial dimension of the polymer. The simulated polymers have a diameter similar to or in some cases even larger than model α-hemolysin nano-pores for macromolecule transport in many biological processes, indicating a size-limited translocation through such pores. All results of the molecular modelling study are in line with previously reported experimental data. This study establishes the three-dimensional structure of DSS and summarizes the spatial dimension of the polymer, serving as the basis for a better understanding on the molecular level of DSS-involved electrostatic interaction processes with biological components like proteins and cell pores.

Stereochemical diversity in lignan biosynthesis of Arctium lappa L.

PubMed

Suzuki, Shiro; Umezawa, Toshiaki; Shimada, Mikio

2002-06-01

The stereochemistry of lignan biosynthesis in Arctium lappa L. is regulated organ-specifically. (+)-Secoisolariciresinol [81% enantiomeric excess (e.e.)] was isolated from A. lappa petioles. In sharp contrast, lignans whose predominant enantiomers have the opposite absolute configuration to that of (+)-secoisolariciresinol [i.e., (-)-matairesinol (>99% e.e.), (-)-arctigenin (>99% e.e.), and (-)-secoisolariciresinol (65% e.e.)] were isolated from seeds of the species. The stereochemical diversity of secoisolariciresinol was demonstrated with enzyme preparations from A. lappa petioles and seeds. Thus, a petiole enzyme preparation catalyzed the formation of (+)-pinoresinol (33% e.e.), (+)-lariciresinol (30% e.e.), and (+)-secoisolariciresinol (20% e.e.) from achiral coniferyl alcohol in the presence of NADPH and H202, whereas that from ripening seeds catalyzed the formation of (-)-pinoresinol (22% e.e.), (-)-lariciresinol (>99% e.e.), and (-)-secoisolariciresinol (38% e.e.) under the same conditions. In addition, the ripening seed enzyme preparation mediated the selective formation of the optically pure (>99% e.e.) (-)-enantiomer of matairesinol from racemic (+/-)-secoisolariciresinols in the presence of NADP. These results indicate that the stereochemical mechanism for lignan biosynthesis in A. lappa varies with organs, suggesting that multiple lignan-synthesizing isozymes are involved in the stereochemical control of lignan formation in A. lappa.

Coarse graining of atactic polystyrene and its derivatives

NASA Astrophysics Data System (ADS)

Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

2014-03-01

Capturing large length scales in polymers and soft matter while retaining atomistic properties is imperative to computational studies of dynamic systems. Here we present a new methodology developing coarse-grain model based on atomistic simulation of atactic polystyrene (PS). Similar to previous work by Fritz et al., each monomer is described by two coarse grained beads. In contrast to this earlier work where intramolecular potentials were based on Monte Carlo simulation of both isotactic and syndiotactic single PS molecule to capture stereochemistry, we obtained intramolecular interactions from a single molecular dynamics simulation of an all-atom atactic PS melts. The non-bonded interactions are obtained using the iterative Boltzmann inversion (IBI) scheme. This methodology has been extended to coarse graining of poly-(t-butyl-styrene) (PtBS). An additional coarse-grained bead is used to describe the t-butyl group. Similar to the process for PS, the intramolecular interactions are obtained from a single all atom atactic melt simulation. Starting from the non-bonded interactions for PS, we show that the IBI method for the non-bonded interactions of PtBS converges relatively fast. A generalized scheme for substituted PS is currently in development. We would like to acknowledge Prof. Kurt Kremer for helpful discussions during this work.

Alkaloid venom weaponry of three Megalomyrmex thief ants and the behavioral response of Cyphomyrmex costatus host ants.

PubMed

Adams, Rachelle M M; Jones, Tappey H; Longino, John T; Weatherford, Robert G; Mueller, Ulrich G

2015-04-01

Social parasites exploit other societies by invading and stealing resources. Some enter protected nests using offensive chemical weaponry made from alkaloid-based venom. We characterized the venoms of three Megalomyrmex thief ant species (M. mondabora, M. mondaboroides, and M. silvestrii) that parasitize the fungus-growing ants, and developed an ethogram to describe host ant reactions to raiding M. mondaboroides and M. silvestrii parasites. We compared piperidine, pyrrolidine, and pyrolizidine venom alkaloid structures with synthetic samples from previous studies, and describe the novel stereochemistry of trans 2-hexyl-5-[8-oxononyl]-pyrrolidine (3) from M. mondabora. We showed that workers of Cyphomyrmex costatus, the host of M. mondaboroides and M. silvestrii, react to a sting by Megalomyrmex parasites mainly with submissive behavior, playing dead or retreating. Host submission also followed brief antennal contact. The behavior of C. costatus ants observed in this study was similar to that of Cyphomyrmex cornutus, host of M. mondabora, suggesting that the alkaloidal venoms with pyrrolidines from M. mondabora, piperidines from M. mondaboroides, and pyrolizidines from M. silvestrii may function similarly as appeasement and repellent allomones against host ants, despite their different chemical structure. With the use of these chemical weapons, the Megalomyrmex thief ants are met with little host resistance and easily exploit host colony resources.

ClusterCAD: a computational platform for type I modular polyketide synthase design

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

Eng, Clara H.; Backman, Tyler W H; Bailey, Constance B.

Here, we present ClusterCAD, a web-based toolkit designed to leverage the collinear structure and deterministic logic of type I modular polyketide synthases (PKSs) for synthetic biology applications. The unique organization of these megasynthases, combined with the diversity of their catalytic domain building blocks, has fueled an interest in harnessing the biosynthetic potential of PKSs for the microbial production of both novel natural product analogs and industrially relevant small molecules. However, a limited theoretical understanding of the determinants of PKS fold and function poses a substantial barrier to the design of active variants, and identifying strategies to reliably construct functional PKSmore » chimeras remains an active area of research. In this work, we formalize a paradigm for the design of PKS chimeras and introduce ClusterCAD as a computational platform to streamline and simplify the process of designing experiments to test strategies for engineering PKS variants. ClusterCAD provides chemical structures with stereochemistry for the intermediates generated by each PKS module, as well as sequence- and structure-based search tools that allow users to identify modules based either on amino acid sequence or on the chemical structure of the cognate polyketide intermediate. ClusterCAD can be accessed at https://clustercad.jbei.org and at http://clustercad.igb.uci.edu.« less

Kinetics and stereochemistry of hydrolysis of an N-(phenylacetyl)-α-hydroxyglycine ester catalyzed by serine β-lactamases and DD-peptidases.

PubMed

Pelto, Ryan B; Pratt, R F

2012-09-28

The α-hydroxydepsipeptide 3-carboxyphenyl N-(phenylacetyl)-α-hydroxyglycinate (5) is a quite effective substrate of serine β-lactamases and low molecular mass DD-peptidases. The class C P99 and ampC β-lactamases catalyze the hydrolysis of both enantiomers of 5, although they show a strong preference for one of them. The class A TEM-2 and class D OXA-1 β-lactamases and the Streptomyces R61 and Actinomadura R39 DD-peptidases catalyze hydrolysis of only one enantiomer of at any significant rate. Experiments show that all of the above enzymes strongly prefer the same enantiomer, a surprising result since β-lactamases usually prefer L(S) enantiomers and DD-peptidases D(R). Product analysis, employing peptidylglycine α-amidating lyase, showed that the preferred enantiomer is D(R). Thus, it is the β-lactamases that have switched preference rather than the DD-peptidases. Molecular modeling of the P99 β-lactamase active site suggests that the α-hydroxyl 5 of may interact with conserved Asn and Lys residues. Both α-hydroxy and α-amido substituents on a glycine ester substrate can therefore enhance its productive interaction with the β-lactamase active site, although their effects are not additive; this may also be true for inhibitors.

Fluorinated End-Groups in Electrolytes Induce Ordered Electrolyte/Anode Interface Even at Open-Circuit Potential as Revealed by Sum Frequency Generation Vibrational Spectroscopy

DOE PAGES

Horowitz, Yonatan; Han, Hui-Ling; Ralston, Walter T.; ...

2017-05-12

Fluorine-based additives have a tremendously beneficial effect on the performance of lithium-ion batteries, yet the origin of this phenomenon is unclear. This study shows that the formation of a solid-electrolyte interphase (SEI) on the anode surface in the first five charge/discharge cycles is affected by the stereochemistry of the electrolyte molecules on the anode surface starting at open-circuit potential (OCP). This study shows an anode-specific model system, the reduction of 1,2-diethoxy ethane with lithium bis(trifluoromethane)sulfonimide, as a salt on an amorphous silicon anode, and compares the electrochemical response and SEI formation to its fluorinated version, bis(2,2,2-trifluoroethoxy) ethane (BTFEOE), by summore » frequency generation (SFG) vibrational spectroscopy under reaction conditions. The SFG results suggest that the —CF 3 end-groups of the linear ether BTFEOE change their adsorption orientation on the a-Si surface at OCP, leading to a better protective layer. Finally, supporting evidence from ex situ scanning electron microscopy and X-ray photoelectron spectroscopy depth profiling measurements shows that the fluorinated ether, BTFEOE, yields a smooth SEI on the a-Si surface and enables lithium ions to intercalate deeper into the a-Si bulk.« less

Fluorinated End-Groups in Electrolytes Induce Ordered Electrolyte/Anode Interface Even at Open-Circuit Potential as Revealed by Sum Frequency Generation Vibrational Spectroscopy

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

Horowitz, Yonatan; Han, Hui-Ling; Ralston, Walter T.

Fluorine-based additives have a tremendously beneficial effect on the performance of lithium-ion batteries, yet the origin of this phenomenon is unclear. This study shows that the formation of a solid-electrolyte interphase (SEI) on the anode surface in the first five charge/discharge cycles is affected by the stereochemistry of the electrolyte molecules on the anode surface starting at open-circuit potential (OCP). This study shows an anode-specific model system, the reduction of 1,2-diethoxy ethane with lithium bis(trifluoromethane)sulfonimide, as a salt on an amorphous silicon anode, and compares the electrochemical response and SEI formation to its fluorinated version, bis(2,2,2-trifluoroethoxy) ethane (BTFEOE), by summore » frequency generation (SFG) vibrational spectroscopy under reaction conditions. The SFG results suggest that the —CF 3 end-groups of the linear ether BTFEOE change their adsorption orientation on the a-Si surface at OCP, leading to a better protective layer. Finally, supporting evidence from ex situ scanning electron microscopy and X-ray photoelectron spectroscopy depth profiling measurements shows that the fluorinated ether, BTFEOE, yields a smooth SEI on the a-Si surface and enables lithium ions to intercalate deeper into the a-Si bulk.« less

Spin Choreography: Basic Steps in High Resolution NMR (by Ray Freeman)

NASA Astrophysics Data System (ADS)

Minch, Michael J.

1998-02-01

There are three orientations that NMR courses may take. The traditional molecular structure course focuses on the interpretation of spectra and the use of chemical shifts, coupling constants, and nuclear Overhauser effects (NOE) to sort out subtle details of structure and stereochemistry. Courses can also focus on the fundamental quantum mechanics of observable NMR parameters and processes such a spin-spin splitting and relaxation. More recently there are courses devoted to the manipulation of nuclear spins and the basic steps of one- and two-dimensional NMR experiments. Freeman's book is directed towards the latter audience. Modern NMR methods offer a myriad ways to extract information about molecular structure and motion by observing the behavior of nuclear spins under a variety of conditions. In Freeman's words: "We can lead the spins through an intricate dance, carefully programmed in advance, to enhance, simplify, correlate, decouple, edit or assign NMR spectra." This is a carefully written, well-illustrated account of how this dance is choreographed by pulse programming, double resonance, and gradient effects. Although well written, this book is not an easy read; every word counts. It is recommended for graduate courses that emphasize the fundamentals of magnetic resonance. It is not a text on interpretation of spectra.

Novel syn intramolecular pathway in base-catalyzed 1,2-elimination reactions of beta-acetoxy esters.

PubMed

Mohrig, Jerry R; Carlson, Hans K; Coughlin, Jane M; Hofmeister, Gretchen E; McMartin, Lea A; Rowley, Elizabeth G; Trimmer, Elizabeth E; Wild, Andrew J; Schultz, Steve C

2007-02-02

As part of a comprehensive investigation of electronic effects on the stereochemistry of base-catalyzed 1,2-elimination reactions, we observed a new syn intramolecular pathway in the elimination of acetic acid from beta-acetoxy esters and thioesters. 1H and 2H NMR investigation of reactions using stereospecifically labeled tert-butyl (2R*,3R*)-3-acetoxy-2,3-2H2-butanoate (1) and its (2R*,3S*) diastereomer (2) shows that 23 +/- 2% syn elimination occurs. The elimination reactions were catalyzed with KOH or (CH3)4NOH in ethanol/water under rigorously non-ion-pairing conditions. By contrast, the more sterically hindered beta-trimethylacetoxy ester produces only 6 +/- 1% syn elimination. These data strongly support an intramolecular (Ei) syn path for elimination of acetic acid, most likely through the oxyanion produced by nucleophilic attack at the carbonyl carbon of the beta-acetoxy group. The analogous thioesters, S-tert-butyl (2R*,3R*)-3-acetoxy-2,3-2H2-butanethioate (3) and its (2R*,3S*) diastereomer (4), showed 18 +/- 2% syn elimination, whereas the beta-trimethylacetoxy substrate gave 5 +/- 1% syn elimination. The more acidic thioester substrates do not produce an increased amount of syn stereoselectivity even though their elimination reactions are at the E1cb interface.

Mycobacterium tuberculosis hemoglobin N displays a protein tunnel suited for O2 diffusion to the heme

PubMed Central

Milani, Mario; Pesce, Alessandra; Ouellet, Yannick; Ascenzi, Paolo; Guertin, Michel; Bolognesi, Martino

2001-01-01

Macrophage-generated oxygen- and nitrogen-reactive species control the development of Mycobacterium tuberculosis infection in the host. Mycobacterium tuberculosis ‘truncated hemoglobin’ N (trHbN) has been related to nitric oxide (NO) detoxification, in response to macrophage nitrosative stress, during the bacterium latent infection stage. The three-dimensional structure of oxygenated trHbN, solved at 1.9 Å resolution, displays the two-over-two α-helical sandwich fold recently characterized in two homologous truncated hemoglobins, featuring an extra N-terminal α-helix and homodimeric assembly. In the absence of a polar distal E7 residue, the O2 heme ligand is stabilized by two hydrogen bonds to TyrB10(33). Strikingly, ligand diffusion to the heme in trHbN may occur via an apolar tunnel/cavity system extending for ∼28 Å through the protein matrix, connecting the heme distal cavity to two distinct protein surface sites. This unique structural feature appears to be conserved in several homologous truncated hemoglobins. It is proposed that in trHbN, heme Fe/O2 stereochemistry and the protein matrix tunnel may promote O2/NO chemistry in vivo, as a M.tuberculosis defense mechanism against macrophage nitrosative stress. PMID:11483493

Rotational Spectrum and Carbon Atom Structure of Dihydroartemisinic Acid

NASA Astrophysics Data System (ADS)

Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

2016-06-01

Dihydroartemisinic acid (DHAA, C15H24O2, five chiral centers) is a precursor in proposed low-cost synthetic routes to the antimalarial drug artemisinin. In one reaction process being considered in pharmaceutical production, DHAA is formed from an enantiopure sample of artemisinic acid through hydrogenation of the alkene. This reaction needs to properly set the stereochemistry of the asymmetric carbon for the synthesis to produce artemisinin. A recrystallization process can purify the diastereomer mixture of the hydrogenation reaction if the unwanted epimer is produced in less than 10% abundance. There is a need in the process analytical chemistry to rapidly (less than 1 min) measure the diastereomer excess and current solutions, such a HPLC, lack the needed measurement speed. The rotational spectrum of DHAA has been measured at 300:1 signal-to-noise ratio in a chirped-pulsed Fourier transform microwave spectrometer operating from 2-8 GHz using simple heating of the compound. The 13C isotope analysis provides a carbon atom structure that confirms the diastereomer. This structure is in excellent agreement with quantum chemistry calculations at the B2PLYPD3/ 6-311++G** level of theory. The DHAA spectrum is expected to be fully resolved from the unwanted diastereomer raising the potential for fast diastereomer excess measurement by rotational spectroscopy in the pharmaceutical production process.

Synthesis and biological evaluation of enantiomerically pure cyclopropyl analogues of combretastatin A4.

PubMed

Ty, Nancy; Pontikis, Renée; Chabot, Guy G; Devillers, Emmanuelle; Quentin, Lionel; Bourg, Stéphane; Florent, Jean-Claude

2013-03-01

To evaluate the influence of stereochemistry on biological activities of cis-cyclopropyl combretastatin A4 (CA4) analogues, we have prepared several cyclopropyl compounds in their pure enantiomeric forms. The key reactions in our synthesis are the cyclopropanation of a (Z)-alkenylboron compound bearing a chiral auxiliary, and the cross-coupling of both enantiomeric cyclopropyl trifluoroborate salts with aryl and olefinic halides. Three pairs of cis-cyclopropyl CA4 analogues were evaluated for their potential antivascular activities. The diarylcyclopropyl compounds with SR-configuration (-)-1b, (-)-2b and the cyclopropylvinyl enantiomer (+)-3a with RR-configuration were the most potent tubulin polymerization inhibitors. A correlation was noted between anti-tubulin activity and rounding up activity of endothelial cells. The cytotoxic activity on B16 melanoma cells was in the submicromolar range for most compounds, but unlike the anti-tubulin activity, there was no difference in cytotoxic activity between racemic and enantiomerically pure forms for the three series of compounds. Molecular docking studies within the colchicine binding site of tubulin were in good agreement with the tubulin polymerization inhibitory data and confirmed the importance of the configuration of the synthesized cis-cyclopropyl CA4 analogues for potential antivascular activities. Copyright © 2013. Published by Elsevier Ltd.