Showing papers in "Chemical Biology & Drug Design in 2008"

The Structure of Glycosaminoglycans and their Interactions with Proteins

Abstract: Glycosaminoglycans (GAGs) are important complex carbohydrates that participate in many biological processes through the regulation of their various protein partners. Biochemical, structural biology and molecular modelling approaches have assisted in understanding the molecular basis of such interactions, creating an opportunity to capitalize on the large structural diversity of GAGs in the discovery of new drugs. The complexity of GAG–protein interactions is in part due to the conformational flexibility and underlying sulphation patterns of GAGs, the role of metal ions and the effect of pH on the affinity of binding. Current understanding of the structure of GAGs and their interactions with proteins is here reviewed: the basic structures and functions of GAGs and their proteoglycans, their clinical significance, the three-dimensional features of GAGs, their interactions with proteins and the molecular modelling of heparin binding sites and GAG–protein interactions. This review focuses on some key aspects of GAG structure–function relationships using classical examples that illustrate the specificity of GAG–protein interactions, such as growth factors, anti-thrombin, cytokines and cell adhesion molecules. New approaches to the development of GAG mimetics as possible new glycotherapeutics are also briefly covered.

Inhibition of HIV-2 Protease by HIV-1 Protease Inhibitors in Clinical Use

Abstract: Over the past 10 years, protease inhibitors have been a key component in antiretroviral therapies for HIV/AIDS. While the vast majority of HIV/AIDS cases in the world are due to HIV-1, HIV-2 infection must also be addressed. HIV-2 is endemic to Western Africa, and has also appeared in European countries such as Portugal, Spain, and Estonia. Current protease inhibitors have not been optimized for treatment of HIV-2 infection; therefore, it is important to assess the effectiveness of currently FDA-approved protease inhibitors against the HIV-2 protease, which shares only 50% sequence identity with the HIV-1 protease. Kinetic inhibition assays were performed to measure the inhibition constants (K(i)) of the HIV-1 protease inhibitors indinavir, nelfinavir, saquinavir, ritonavir, amprenavir, lopinavir, atazanavir, tipranavir, and darunavir against the HIV-2 protease. Lopinavir, saquinavir, tipranavir, and darunavir exhibit the highest potency with K(i) values of 0.7, 0.6, 0.45, and 0.17 nm, respectively. These K(i) values are 84, 2, 24, and 17 times weaker than the corresponding values against the HIV-1 protease. In general, inhibitors show K(i) ratios ranging between 2 and 80 for the HIV-2 and HIV-1 proteases. The relative drop in potency is proportional to the affinity of the inhibitor against the HIV-1 protease and is related to specific structural characteristics of the inhibitors. In particular, the potency drop is high when the maximum cap size of the inhibitors consists of very few atoms. Caps are groups located at the periphery of the molecule that are added to core structures to increase the specificity of the inhibitor to its target. The caps positioned on the HIV-1 protease inhibitors affect selectivity through interactions with distinct regions of the binding pocket. The flexibility and adaptability imparted by the higher number of rotatable bonds in large caps enables an inhibitor to accommodate changes in binding pocket geometry between HIV-1 and HIV-2 protease.

Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble.

Abstract: The influenza virus subtype H5N1 has raised concerns of a possible human pandemic threat because of its high virulence and mutation rate. Although several approved anti-influenza drugs effectively target the neuraminidase, some strains have already acquired resistance to the currently available anti-influenza drugs. In this study, we present the synergistic application of extended explicit solvent molecular dynamics (MD) and computational solvent mapping (CS-Map) to identify putative ‘hot spots’ within flexible binding regions of N1 neuraminidase. Using representative conformations of the N1 binding region extracted from a clustering analysis of four concatenated 40-ns MD simulations, CS-Map was utilized to assess the ability of small, solvent-sized molecules to bind within close proximity to the sialic acid binding region. Mapping analyses of the dominant MD conformations reveal the presence of additional hot spot regions in the 150- and 430-loop regions. Our hot spot analysis provides further support for the feasibility of developing high-affinity inhibitors capable of binding these regions, which appear to be unique to the N1 strain.

Natural Compounds: Leads or Ideas? Bioinspired Molecules for Drug Discovery

Abstract: In this article, we compare drugs of natural origin to synthetic compounds and analyze the reasons why natural compounds occupy a place of choice in the current pharmacopoeia. The observations reported here support the design of synthetic compounds inspired from plant alkaloids and their biosynthetic pathway. Our reasoning leads to very efficient syntheses of compounds which complexity matches that of indolomonoterpenic alkaloids.

Effects of hydrophobicity on the antifungal activity of alpha-helical antimicrobial peptides.

Abstract: We utilized a series of analogs of D-V13K (a 26-residue amphipathic alpha-helical antimicrobial peptide, denoted D1) to compare and contrast the role of hydrophobicity on antifungal and antibacterial activity to the results obtained previously with Pseudomonas aeruginosa strains. Antifungal activity for zygomycota fungi decreased with increasing hydrophobicity (D-V13K/A12L/A20L/A23L, denoted D4, the most hydrophobic analog was sixfold less active than D1, the least hydrophobic analog). In contrast, antifungal activity for ascomycota fungi increased with increasing hydrophobicity (D4, the most hydrophobic analog was fivefold more active than D1). Hemolytic activity is dramatically affected by increasing hydrophobicity with peptide D4 being 286-fold more hemolytic than peptide D1. The therapeutic index for peptide D1 is 1569-fold and 62-fold better for zygomycota fungi and ascomycota fungi, respectively, compared with peptide D4. To reduce the hemolytic activity of peptide D4 and improve/maintain the antifungal activity of D4, we substituted another lysine residue in the center of the non-polar face (V16K) to generate D5 (D-V13K/V16K/A12L/A20L/A23L). This analog D5 decreased hemolytic activity by 13-fold, enhanced antifungal activity to zygomycota fungi by 16-fold and improved the therapeutic index by 201-fold compared with D4 and represents a unique approach to control specificity while maintaining high hydrophobicity in the two hydrophobic segments on the non-polar face of D5.

Reversible and competitive cinnamoyl triazole inhibitors of tissue transglutaminase.

Abstract: A series of 15 cinnamoyl triazole derivatives was prepared by Cu(I)-catalyzed azide/alkyne [3+2]-cycloaddition reactions and examined as inhibitors of guinea-pig liver transglutaminase Several compounds exhibited activity as reversible inhibitors that were competitive with acyl donor transglutaminase substrates For example, triazole 4d has a K(i) value of 174 nM and represents one of the most potent reversible transglutaminase inhibitors reported to date

Concept of Combinatorial De Novo Design of Drug‐like Molecules by Particle Swarm Optimization

Abstract: We present a fast stochastic optimization algorithm for fragment-based molecular de novo design (COLIBREE, Combinatorial Library Breeding). The search strategy is based on a discrete version of particle swarm optimization. Molecules are represented by a scaffold, which remains constant during optimization, and variable linkers and side chains. Different linkers represent virtual chemical reactions. Side-chain building blocks were obtained from pseudo-retrosynthetic dissection of large compound databases. Here, ligand-based design was performed using chemically advanced template search (CATS) topological pharmacophore similarity to reference ligands as fitness function. A weighting scheme was included for particle swarm optimization-based molecular design, which permits the use of many reference ligands and allows for positive and negative design to be performed simultaneously. In a case study, the approach was applied to the de novo design of potential peroxisome proliferator-activated receptor subtype-selective agonists. The results demonstrate the ability of the technique to cope with large combinatorial chemistry spaces and its applicability to focused library design. The technique was able to perform exploitation of a known scheme and at the same time explorative search for novel ligands within the framework of a given molecular core structure. It thereby represents a practical solution for compound screening in the early hit and lead finding phase of a drug discovery project.

PDBcal: a comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry.

Abstract: Compounds designed solely based on structure often do not result in any improvement of the binding affinity because of entropy-enthalpy compensation. Thermodynamic data along with structure provide an opportunity to gain a deeper understanding of this effect and aid in the refinement of scoring functions used in computational drug design. Here, we scoured the literature and constructed the most comprehensive hand-curated calorimetry dataset to date. It contains thermodynamic and structural data for more than 400 receptor-ligand complexes. The dataset can be accessed through a web interface at http://www.pdbcal.org. The thermodynamic data consists of free energy, enthalpy, entropy and heat capacity as measured by isothermal titration calorimetry (ITC). The dataset also contains the experimental conditions that were used to carry out the ITC experiments. The chemical structures of the ligands are also provided. Analysis of the data confirms the existence of enthalpy-entropy compensation effect for the first time using strictly ITC data.

Novel Molecular Targets for Antimalarial Drug Development

Abstract: Malaria with one million deaths and about 500 million new cases reported annually is a challenge to drug therapy and discovery. As current antimalarial therapeutics become increasingly ineffective because of parasitic resistance, there exists an urgent need to develop and pursue new therapeutic strategies. Antimalarial drug development can follow several strategies, ranging from minor modifications of existing agents to the design of novel agents that act against new targets. Recent advances in our knowledge of parasite biology as well as the availability of the genome sequence provide a wide range of novel targets for drug design. Several promising targets for drug intervention have been revealed in recent years. This review discusses novel molecular targets of the malaria parasite available to the drug discovery scientist.

Rhodanine derivatives as selective protease inhibitors against bacterial toxins.

Abstract: In this study, we analyzed a series of rhodanine derivatives, as potential inhibitors of bacterial toxins, namely the proteases anthrax lethal factor and the botulinum neurotoxin type A. Conducting an extensive structure-activity relationship study on rhodanine derivatives, we profiled their selectivity against the two bacterial toxins and two related human metalloproteases using in vitro assays. In addition, we examined initial in vitro ADME-Tox properties of selected compounds and their ability to protect lethal factor-induced cell death of macrophages. These data allowed the selection of one additional drug candidate for which preliminary in vivo efficacy studies against anthrax spores were conducted. Integration of these results with our structure-activity relationship studies provides a framework for the development of potential drug candidates against anthrax and botulinum.

Comparative QSAR studies of CYP1A2 inhibitor flavonoids using 2D and 3D descriptors.

Abstract: Comparative Quantitative Structure Activity Relationship (QSAR) analyses have been performed with 21 naturally occurring flavonoids for their inhibitory effects on cytochrome P450 1A2 enzyme using two-dimensional (topological, structural, and thermodynamic) and three-dimensional (spatial) descriptors. The chemometric tools used for the analyses are stepwise multiple linear regression, partial least squares, genetic function approximation, and genetic partial least squares. The data set was divided into a training set (n = 15) and test set (n = 6), based on K-means clustering technique applied on standardized two-dimensional descriptor matrix, and models were developed from the training set compounds. The best model (genetic partial least squares model using two-dimensional descriptors) was selected based on the highest external predictive R(2) (R(2)(pred)) value (0.840) and the lowest root mean square error of prediction value (0.351). The developed QSAR equations suggest the importance of the double bond present at 2 and 3 positions and requirement of absence of hydroxyl substituent or glycosidic linkage at 3 position of the 1,4-benzopyrone nucleus. Furthermore, the phenyl ring present at 2 position of the 1,4-benzopyrone ring should not be substituted with hydroxyl group. Moreover, hydroxyl groups present at 5 and 7 positions of the benzopyran nucleus should not be glycosylated for good cytochrome P450 1A2 enzyme inhibitory activity.

Pharmacophore Modelling and Virtual Screening for Identification of New Aurora‐A Kinase Inhibitors

Abstract: Aurora-A has been identified as one of the most attractive targets for cancer therapy and a considerable number of Aurora-A inhibitors have been reported recently. In order to clarify the essential structure–activity relationship for the known Aurora-A inhibitors as well as identify new lead compounds against Aurora-A, 3D pharmacophore models were developed based on the known inhibitors. The best hypothesis, Hypo1, was used to screen molecular structural databases, including Specs and China Natural Products Database for potential lead compounds. The hit compounds were subsequently subjected to filtering by Lipinski’s rules and docking study to refine the retrieved hits and as a result to reduce the rate of false positive. Finally, 39 compounds were purchased for further in vitro assay against several human tumour cell lines including A549, MCF-7, HepG2 and PC-3, in which Aurora-A is overexpressed. Two compounds show very low micromolar inhibition potency against some of these tumour cells. And they have been selected for further investigation.

Antiviral and Anticancer Optimization Studies of the DNA-binding Marine Natural Product Aaptamine

Abstract: Aaptamine (1; Figure 1) is commonly isolated in large yields from various species of the marine sponge genus Aaptos (Order Hadromerida: Family Suberitidae)a, along with a handful of related compounds such as isoaaptamine (2) which contain the benzonapthyridine core structure (1–7). The isolation of aaptamine from the taxonomically unrelated species Luffariella (Order Dictyoceratida: Family Thorectidae) (3), Hymeniacidon (Order Halichondrida: Family Halichondriidae) (6), and Xestospongia (7) (Order Haplosclerida: Family Petrosiidae)b, indicates the likelihood of production of aaptamine from a microbial source. In fact, several novel metabolites containing the aaptamine core have come from one particular sponge (7), underlining likely contributions of the microbial community associated with the producer of aaptamine. A number of total synthetic studies have been published along with a limited collection of semi-synthetic derivatives since its original discovery (8–16). Considering its low molecular weight, aaptamine is relatively difficult to synthesize from available starting materials. Attempts to complete the unique fused tricycle have been made through quinoline and isoquinoline precursors, the best overall yield being 13 percent over 14 steps. Although the synthetic yield is low, it is likely to be the more cost efficient choice for the production of aaptamine, unless a microbial producer is found. Figure 1 Structures of major aaptamine related marine natural products. The proposed biogenesis of aaptamine suggests a possible Pictet-Spengler type condensation commonly attributed to many other natural alkaloids (16). Likewise, three common pharmacophores can be recognized in the aaptamine scaffold: isoquinoline, the largest class of alkaloids isolated from medicinal plants; dopamine, a compound affecting the central nervous system and behavior; and finally, quinoline, known primarily for its anti-malarial properties. Aaptamine's potential for drug development is further evidenced by the actual results of a highly diverse group of molecular targets already evaluated. In addition to antiviral (5,17) and anticancer (4,6,18) activities, the aaptamines have a strong in vitro radical scavenging capacity (19) and have been shown to block α-adrenoceptor action (1) as well as inhibit α-1,3-glucanase (20) and monoamine oxidase (21). Still, compounds which are active against a variety of targets are certain to encounter problems with indiscriminant toxicities. It is important to recognize toxicity as a hurdle for the development of aaptamine as a useful drug but not let it prohibit the evaluation of its derivatives for therapeutic potential. The ‘privileged structures’ approach (22) is dependent on exploiting a scaffold's common mechanism of drug-target interaction for multiple targets. In a similar fashion, a key for the development of the aaptamine scaffold is the identification of its common mechanism of drug-target interaction. Although it is difficult to determine if broad-spectrum DNA-interaction is a compound's definitive mechanism of cytotoxicity, it is clear that DNA interaction has a measurable influence on the mechanism. Small molecules that bind to DNA do not necessarily interact in the same way, in fact, there are several modes by which a ligand can bind and affect the structure and function of this substrate (23). Of these modes, intercalation is most prevalent with planar polycyclic aromatic systems like the aaptamines which insert between adjacent base-pairs of intact DNA, depending primarily on p-bond interactions and sometimes stacking several molecules together in the same area between base pairs. The quinoline portion found in aaptamine's tri-cyclic core has already been the focus of SAR studies with derivatives of acridine (24), a structure that resembles aaptamine and is a well studied anti-cancer pharmacophore that intercalates DNA. The observed DNA binding activity of aaptamine may serve to explain some aspects of the compound's mechanism of activity against whole cell and viral pathogens. Considering the high availability of the natural material and the remarkably broad activity displayed, this heterocyclic small molecule has excellent potential as a scaffold from which numerous derivatives can be made in an attempt to improve selectivity and pharmacokinetics. Based on the synthetic work already published by Shen et al. (18), Hibino et al. (12), Pettit et al. (25,26) and Gul et al. (27) a preliminary SAR has been developed for the aaptamine scaffold in regard to cytotoxicity, antiviral and antimicrobial activity. Table 1 summarizes what has been learned of this relationship from the synthetic and natural derivatives of aaptamine. Table 1 Summary of reported relative structure activity relationships for aaptamine based on general improvements of either potency or selectivity Utilizing the information from this SAR, a semi-synthetic series of N-alkyl aaptamine derivatives was produced to complement previously published N-alkylation efforts that improved activity, and to investigate the effects of increasing the lipophilic character of the pharmacophore. In addition, it was proposed that selective demethylation of the C-9 hydroxyl would significantly increase the potency of the first generation N-alkyl derivatives. Our speculation was based on the evidence wherein 2 consistently demonstrated higher potency than 1 in a variety of biological assays; likewise the selective demethylation of the aaptamine derivatives would produce isoaaptamine analogs with higher potency. Two smaller groups of analogs were specifically produced to investigate the effect of dimerization on biological activity and the pro-drug behavior of sulfonyl esters relative to those previously studied.

A molecular basis for agonist and antagonist actions at GABA(C) receptors.

Abstract: We modelled the N-terminal ligand-binding domain of the q1 GABAC receptor based on the Lymnaea stagnalis acetylcholine-binding protein (L-AChBP) crystal structure using comparative modelling and validated using flexible docking guided by known mutagenesis studies. A range of known q1 GABAC receptor ligands comprising seven full agonists, 10 partial agonists, 43 antagonists and 12 inactive molecules were used to evaluate and validate the models. Of the 50 models identified, six models that allowed flexible ligand docking in accordance with the experimental data were selected and used to study detailed receptor-ligand interactions. The most refined model to accommodate all known active ligands featured a cavity comprising of a volume of 488 A˚ 3 . A detailed analysis of the interaction between the q1 GABAC receptor model and the docked ligands revealed possible H-bonds and cation-p interactions between the different ligands and binding site residues. Based on quantum mechanical/molecular mechanical (QM ⁄MM) calculations, the model showed distinctive conformations of loop C that provided a molecular basis for agonist and antagonist actions. Agonists elicit loop C closure, while a more open loop C was observed upon antagonist binding. The model differentiates the role for key residues known to be involved in either binding and/or gating.

Development of Broad-Spectrum Halomethyl Ketone Inhibitors Against Coronavirus Main Protease 3CLpro

Abstract: Coronaviruses comprise a large group of RNA viruses with diverse host specificity. The emergence of highly pathogenic strains like the SARS coronavirus (SARS-CoV), and the discovery of two new coronaviruses, NL-63 and HKU1, corroborates the high rate of mutation and recombination that have enabled them to cross species barriers and infect novel hosts. For that reason, the development of broad-spectrum antivirals that are effective against several members of this family is highly desirable. This goal can be accomplished by designing inhibitors against a target, such as the main protease 3CLpro (Mpro), which is highly conserved among all coronaviruses. Here 3CLpro derived from the SARS-CoV was used as the primary target to identify a new class of inhibitors containing a halomethyl ketone warhead. The compounds are highly potent against SARS 3CLpro with Ki's as low as 300 nm. The crystal structure of the complex of one of the compounds with 3CLpro indicates that this inhibitor forms a thioether linkage between the halomethyl carbon of the warhead and the catalytic Cys 145. Furthermore, Structure Activity Relationship (SAR) studies of these compounds have led to the identification of a pharmacophore that accurately defines the essential molecular features required for the high affinity.

Antibacterial Activity of Synthesized 2,4,5‐Trisubstituted Imidazole Derivatives

Abstract: Some novel chemically synthesized 2,4,5-trisubstituted imidazoles from aryl aldehydes and 1,2-diketones or alpha-hydroxyketone were screened against eight different human pathogenic bacteria and fungi. Seven compounds were found to be active against different bacteria. These compounds showed variation in activity and were found to be active against Gram-positive as well as Gram-negative bacteria. Compound 4-(4,5-diphenyl-1H-imidazol-2-yl)-phenol, 3d was the only compound which showed activity against Klebsiella pneumoniae while rest of the compounds did not show significant activity against this micro-organism. Minimum inhibitory concentrations of the compounds were in the range of 0.50 to 6.1 microg/mL and minimum bactericidal concentration ranges from 1.11 to 12.9 microg/mL. The candidature of active compounds to be an effective and novel drug was examined based on Lipinski's rule of Five which explained ClogP, LogS, H-bond acceptors, H-Bond donors and rotational bonds. Compounds 3a-d and 3f satisfies Lipinski's rule of Five and could be proposed as potent new antibacterial drugs.

Design of Potent, Non‐Toxic Antimicrobial Agents Based Upon the Naturally Occurring Frog Skin Peptides, Ascaphin‐8 and Peptide XT‐7

Abstract: The frog skin peptides, ascaphin-8 (GFKDLLKGAAKALVKTVLF.NH2) and XT-7 (GLLGPLLKIAAKVGSNLL.NH2), show broad-spectrum antimicrobial activity but their therapeutic potential is limited by toxicity against mammalian cells. Circular dichroism spectra demonstrate that the peptides adopt an amphipathic α-helical conformation in a membrane-mimetic solvent. This study has investigated the cytolytic properties of analogs containing selected amino acid substitutions that increase cationicity while maintaining amphipathicity. Substitutions at Ala10, Val14, and Leu18 in ascaphin-8 by either l-Lys or d-Lys produced peptides that retained antimicrobial activity against the bacteria Escherichia coli and Staphylococcus aureus and the opportunistic yeast pathogen, Candida albicans but showed appreciably reduced toxicities (>10-fold) against human erythrocytes, HepG2 hepatoma-derived cells, and L929 fibroblasts. The improved therapeutic index of the l-Lys18 and d-Lys18 analogs correlated with a decrease in % helicity and in effective hydrophobicity. Substitution of Gly4 by l-Lys in XT-7 produced an analog with high potency against micro-organisms (MIC ≤ 25 μm) but low cytolytic activity against erythrocytes (LD50 > 500 μm) and this increase in therapeutic index also correlated with decreased helicity and hydrophobicity. Analogs of XT-7 with increased cationicity, containing multiple substitutions by l-Lys, not only displayed increased antimicrobial potencies, particularly against Candida albicans (MIC ≤ 6 μm), but also increased hemolytic activities.

Di- and triorganotin(IV) esters of 3,4-methylenedioxyphenylpropenoic acid: synthesis, spectroscopic characterization and biological screening for antimicrobial, cytotoxic and antitumor activities.

Abstract: Nine biologically significant organotin(IV) esters of 3,4-Methylenedioxyphenylpropenoic acid (L) were synthesized with the general formulae [R2SnL2], where R includes Me(1), Et(3), But(4), Oct(5), Ph(8), and [R3SnL], in which R is Me(2), Cy(6), Ph(7), and But(9). The acid and its compounds were characterized by basic analytical techniques comprising elemental analysis, FTIR and mass spectrometry in solid state and by Multinuclear (1H, 13C and 119Sn) NMR in solution form, which provides some important information about the different coordination behaviors of metal in both solid and solution. Methylenedioxy moiety in these compounds enhances the biological activity of these compounds. These compounds were screened for a range of biological activities. Antibacterial activities were determined against six pathogenic bacterial strains, three gram-positive and three gram-negative, the activities were measured in terms of inhibition zones (mm). Results demonstrate that diorganotin derivatives are more active than triorganotin derivatives and ligand acid. Antifungal activity was determined against six pathogenic fungal strains, cytotoxicity by the brine shrimp lethality assay, and antitumor activity by crown gall tumor inhibition (potato disc) assay. Results for antifungal activity, cytotoxicity, and antitumor activity of these compounds demonstrate that triorganotin derivatives are more active than diorganotin derivatives and ligand. Finally, the results were compared with similar reports in the literature.

Chiral N‐Phosphonyl Imine Chemistry: Asymmetric Aza‐Henry Reaction

Abstract: A series of chiral N-phosphonyl imines have been synthesized and utilized successfully in asymmetric aza-Henry reaction. The chiral auxiliary was optimized for this reaction by varying different R groups on the nitrogen atoms. The reaction is convenient to perform to give excellent yields and good diastereoselectivities. The absolute stereochemistry was unambiguously determined by converting a resulting vicinal nitroamine into its N-Boc derivative which serves as a known compound.

Mapping Ligand–receptor Interfaces: Approaching the Resolution Limit of Benzophenone‐based Photoaffinity Scanning

Abstract: Photoaffinity crosslinking has yielded important insights in the study of G protein-coupled receptors and the mode of ligand binding. The most widely used photolabile moiety is p-benzoylphenylalanine largely because of its reportedly high site specificity, reduced reactivity to water and light, photokinetics, and ease of incorporation into peptide ligands during synthesis. However, in the course of our studies directed at characterizing the binding of parathyroid hormone to its cognate G protein-coupled receptor, we find that inherent properties of p-benzoylphenylalanine, such as its size and conformational flexibility, limit the resulting resolution of the ligand–receptor structure. Here, we examine and define these limits.

Methods for computer-aided chemical biology. Part 3: analysis of structure-selectivity relationships through single- or dual-step selectivity searching and Bayesian classification.

Abstract: The identification of small molecules that are selective for individual targets within target families is an important task in chemical biology. We aim at the development of computational approaches for the study of structure-selectivity relationships and prediction of target-selective ligands. In previous studies, we have introduced the concept of selectivity searching. Here we study compound selectivity on the basis of 18 selectivity sets that are designed to contain target-selective molecules and compounds that are comparably active against related targets. These sets consist of a total of 432 compounds and focus on eight targets belonging to four target families. This compound source has enabled us to evaluate different computational approaches to search for target-selective compounds in large databases. These investigations have revealed a preferred search strategy to enrich database selection sets with target-selective compounds. The selectivity sets reported here are made publicly available to support the development of other computational tools for applications in chemical biology and medicinal chemistry.

CXCR4, inhibitors and mechanisms of action.

Abstract: In this review, the author discusses recent advances in anti-HIV inhibitors, targeting CXCR4, including natural and modified chemokines, peptides and organic compounds, their mechanisms of action, and the molecular process of virus invasion of immune cells. Peptides with strong anti-HIV activity exhibit several common features, such as electrostatic charges, cyclization, beta-turns and dimerization induced by a sulphide bond. Organic compounds, such as cyclams, display a unique metal-mediated mechanism in the binding process to its target CXCR4. Understanding of their mechanisms of action may be useful for the design of more effective drugs. Consecutive interactions of viral glycoprotein gp120 with CD4 and the co-receptor, CXCR4 or another co-receptor CCR5 on the cell surface leads to virus invasion into host cells. The molecular details of the binding between HIV glycoproteins and the co-receptors also provide a basis for anti-HIV therapy.

Comparison of the Anti-inflammatory Activities of Imidazole Antimycotics in Relation to Molecular Structure

Abstract: The objective of this study was to compare the anti-inflammatory potencies of the imidazole antimycotics, fluconazole, itraconazole, ketoconazole and voriconazole (0.5 and 5 microM) in relation to their molecular structures. Anti-inflammatory activity was determined according to the magnitude of inhibition of production of leukotriene B4 and influx of Ca2+ following activation of the cells with the chemo-attractant platelet-activating factor (200 nM), using enzyme-linked immunosorbent assay and spectrofluorometric procedures, respectively. Treatment of platelet-activating factor-activated neutrophils with the imidazole antimycotics resulted in inhibition of production of leukotriene B4 and attenuation of Ca2+ influx, the order of potency being itraconazole > ketoconazole > fluconazole = voriconazole. These observations demonstrate the requirement for both the diazole/triazole moiety (all four agents), and the substituted phenylpiperazinyl ether side chain (itraconazole and ketoconazole only) for maximal anti-inflammatory activity of this class of pharmacological agents.

Experimental and QSAR of acetophenones as antibacterial agents.

Abstract: Antibacterial activity of 20 acetophenone derivatives was evaluated against two Gram-positive and three Gram-negative organisms, namely, Bacillus subtilis NCIM 2718, Staphylococcus aureus NCIM5021, Salmonella typhi NCIM2501, Enterobacter aerogenes NCIM5139, and Proteus vulgaris NCIM2813 by two-fold dilution method. The most active amongst this group of compounds were 4-methyl, 2-hydroxy, 3-bromo, 4-ethoxy, 3-nitro and 4-nitro acetophenones. Quantitative structure-activity relationships were developed by dividing the data into training and validation sets, the former was used to develop and the latter was used to test the models. Spatial, electronic and topological descriptors were predominantly found to influence the activity. The statistical measures such as r( 2) (0.76-0.91), cross-validated r( 2) (0.56-0.85), F-ratio and predicted residual sum of square values were found to be in the acceptable range. The developed models were able to predict the activity of the validation data set within the 99% confidence limit (except for two data points). 4-Nitroacetophenone was found to be the most slimicidal in nature. Bacterial Adhesion to Hydrocarbons (BATH) assay indicated that Staphylococcus aureus NCIM5021 had the most hydrophobic cell surface of these five organisms. Cell surface hydrophobicity of organisms also had an impact on the antibacterial activity of the acetophenones.

Reversible Binding of Antidiabetic Drugs, Repaglinide and Gliclazide, with Human Serum Albumin

Abstract: Mechanism of interaction of antidiabetic drugs, repaglinide and gliclazide, to human serum albumin has been studied using fluorescence spectroscopic technique. Repaglinide had much higher affinity for human serum albumin when compared with gliclazide. The order of association constants was 10(5) for both the drugs. The size, hydrophobicity and flexibility of the drug molecules play a major role in explaining the binding behaviour of these drugs. Hydrophobic interactions are predominantly involved in the binding. However, drugs do not share common sites with 1-anilinonaphthalene-8-sulphonate on the human serum albumin molecule. Both tyrosine and tryptophan residues participate in the interaction. Repaglinide and gliclazide are bound to site II on the human serum albumin molecule, and the aromatic ring of 411Tyr appears to be involved in binding within site II. Although they do not bind at site I, their binding at site II may cause conformational changes thereby affecting the binding of other ligands to site I. Site-specificity can be useful in predicting the competitive displacement of these drugs by other co-administered drugs, resulting in fluctuations of the blood glucose levels in diabetic patients. Stern-Volmer analysis of quenching data indicated that the tryptophan residues are not fully accessible to the drugs and predominantly dynamic quenching mechanism is involved in the binding.

Chiral N-Phosphonyl Imine Chemistry: Asymmetric Additions of Ester Enolates for the Synthesis of β-Amino Acids

Abstract: Chiral phosphonyl imines attached by 1-naphthyl protection group were found to react with lithium ester enolates smoothly and give chiral beta-amino esters in good yields (70-88%) and up to excellent diastereoselectivity (>99:1 dr). Triisopropoxytitanium (IV) chloride was found to enhance diastereoseletivity when used as the Lewis acid promoter. The chiral auxiliary can be readily removed by treating with HBr to give free amino esters. The absolute structure has been unambiguously determined by converting one of the products into an authentic sample. This reaction provides an easy access to beta-amino acid derivatives.

3D‐Quantitative Structure–Activity Relationship Studies on Benzothiadiazepine Hydroxamates as Inhibitors of Tumor Necrosis Factor‐α Converting Enzyme

Abstract: A set of 29 benzothiadiazepine hydroxamates having selective tumor necrosis factor-alpha converting enzyme inhibitory activity were used to compare the quality and predictive power of 3D-quantitative structure-activity relationship, comparative molecular field analysis, and comparative molecular similarity indices models for the atom-based, centroid/atom-based, data-based, and docked conformer-based alignment. Removal of two outliers from the initial training set of molecules improved the predictivity of models. Among the 3D-quantitative structure-activity relationship models developed using the above four alignments, the database alignment provided the optimal predictive comparative molecular field analysis model for the training set with cross-validated r(2) (q(2)) = 0.510, non-cross-validated r(2) = 0.972, standard error of estimates (s) = 0.098, and F = 215.44 and the optimal comparative molecular similarity indices model with cross-validated r(2) (q(2)) = 0.556, non-cross-validated r(2) = 0.946, standard error of estimates (s) = 0.163, and F = 99.785. These models also showed the best test set prediction for six compounds with predictive r(2) values of 0.460 and 0.535, respectively. The contour maps obtained from 3D-quantitative structure-activity relationship studies were appraised for activity trends for the molecules analyzed. The comparative molecular similarity indices models exhibited good external predictivity as compared with that of comparative molecular field analysis models. The data generated from the present study helped us to further design and report some novel and potent tumor necrosis factor-alpha converting enzyme inhibitors.

Docking and quantitative structure-activity relationship studies for the bisphenylbenzimidazole family of non-nucleoside inhibitors of HIV-1 reverse transcriptase.

Abstract: Molecular docking studies on a set of bisphenylbenzimidazole derivatives were conducted to identify the compounds binding orientations within the HIV-1 reverse transcriptase non-nucleoside binding pocket. A good correlation between the calculated binding free energies and the experimental inhibitory activities suggests that the identified binding conformations of these inhibitors are reliable. Based on obtained bisphenylbenzimidazoles binding conformations, a predictive quantitative structure-activity relationship model based on radial distribution function descriptors was developed. The obtained quantitative structure-activity relationship model was predictive according to internal and external validation experiments and might provide guidelines for the design of novel non-nucleoside HIV-1 reverse transcriptase inhibitors based on the 1-benzyl-2-arylbenzimidazole scaffold.

A novel macrocyclic polyamine cationic lipid containing an imidazolium salt group: synthesis, characterization and its transfection activity as a gene delivery vector.

Abstract: The synthesis and characterization of a novel macrocyclic polyamine cationic lipid containing an imidazolium salt group is reported. Its interaction with plasmid DNA was studied by gel electrophoresis and fluorescence quenching experiments. The transfection activity of target compound as a gene delivery vector was also investigated. The results showed that the synthesized macrocyclic polyamine cationic lipid has high binding and condensation ability of DNA under physiological conditions probably because of the cooperation effect of macrocyclic polyamine (Cyclen) and an imidazolium salt group. This novel lipid could transfer plasmid DNA into cell in in vitro experiment without the use of any extraneous agent.

Novel method for probing the specificity binding profile of ligands: applications to HIV protease.

Abstract: A detailed understanding of factors influencing the binding specificity of a ligand to a set of desirable targets and undesirable decoys is a key step in the design of potent and selective therapeutics. We have developed a general method for optimizing binding specificity in ligand–receptor complexes based on the theory of electrostatic charge optimization. This methodology can be used to tune the binding of a ligand to a panel of potential targets and decoys, along the continuum from narrow binding to only one partner to broad binding to the entire panel. Using HIV-1 protease as a model system, we probe specificity in three distinct ways. First, we probe interactions that could make the promiscuous protease inhibitor pepstatin more selective toward HIV-1 protease. Next, we study clinically approved HIV-1 protease inhibitors and probe ways to broaden the binding profiles toward both wild-type HIV-1 protease and drug-resistant mutants. Finally, we study a conformational ensemble of wild-type HIV-1 protease to “design in” broad specificity to known drugs before resistance mutations arise. The results from this conformational ensemble were similar to those from the drug-resistant ensemble, suggesting the use of a conformational wild-type ensemble as a tool to develop escape-mutant resistant inhibitors.