Characterization of activity landscapes using 2D and 3D similarity methods: consensus activity cliffs.

Activity landscape characterization has been demonstrated to be a valuable tool in lead optimization, virtual screening, and computational modeling of active compounds. In this work, we present a general protocol to explore systematically the activity landscape of a lead series using 11 2D and 3D structural representations. As a test case we employed a set of 48 bicyclic guanidines (BCGs) with kappa-opioid receptor binding affinity, identified in our group.

Synthesis, in vitro and computational studies of protein tyrosine phosphatase 1B inhibition of a small library of 2-arylsulfonylaminobenzothiazoles with antihyperglycemic activity.

The 2-arylsulfonylaminobenzothiazole derivatives 1-27 were prepared using a one step reaction. The in vitro inhibitory activity of the compounds against protein tyrosine phosphatase 1B (PTP-1B) was evaluated. Compounds 4 and 16 are rapid reversible (mixed-type) inhibitors of PTP-1B with IC(50) values in the low micromolar range.

Molecular modeling and molecular dynamics studies of hydralazine with human DNA methyltransferase 1.

DNA methyltransferases (DNMTs) are a family of enzymes that methylate DNA at the C5 position of cytosine residues, and their inhibition is a promising strategy for the treatment of various developmental and proliferative diseases, particularly cancers. In the present study, a binding model for hydralazine, with a validated homology model of human DNMT, was developed by the use of automated molecular docking and molecular dynamics simulations. The docking protocol was validated by predicting the binding mode of 2'-deoxycytidine, 5-azacytidine, and 5-aza-2'-deoxycytidine.

Chemoinformatic analysis of combinatorial libraries, drugs, natural products, and molecular libraries small molecule repository.

A multiple criteria approach is presented, that is used to perform a comparative analysis of four recently developed combinatorial libraries to drugs, Molecular Libraries Small Molecule Repository (MLSMR) and natural products. The compound databases were assessed in terms of physicochemical properties, scaffolds, and fingerprints. The approach enables the analysis of property space coverage, degree of overlap between collections, scaffold and structural diversity, and overall structural novelty.

The prince and the pauper. A tale of anticancer targeted agents.

Cancer rates are set to increase at an alarming rate, from 10 million new cases globally in 2000 to 15 million in 2020. Regarding the pharmacological treatment of cancer, we currently are in the interphase of two treatment eras. The so-called pregenomic therapy which names the traditional cancer drugs, mainly cytotoxic drug types, and post-genomic era-type drugs referring to rationally-based designed.

Conformation-opioid activity relationships of bicyclic guanidines from 3D similarity analysis.

Conformation of bicyclic guanidines with kappa-opioid receptor activity derived in our laboratory from a positional scanning synthetic combinatorial library is presented in this work. We propose a common bioactive conformation and putative pharmacophoric features by means of 3D similarity methods. Our 'Y' shape molecular binding model explains structure-activity relationships and suggests that the guanidine functionality and a 4-methoxybenzyl group may be involved in key interactions with the receptor.

A similarity-based data-fusion approach to the visual characterization and comparison of compound databases.

A low-dimensional method, based on the use of multiple fusion-based similarity measures, is described for graphically depicting and characterizing relationships among molecules in compound databases. The measures are used to construct multi-fusion similarity maps that characterize the relationship of a set of 'test' molecules to a set of 'reference' molecules. The reference set is very general and can be made of molecules from, for example, the set of test molecules itself (the self-referencing case), from a small library or large compound collection, or from actives in a given assay or group of assays.

Large compound databases for structure-activity relationships studies in drug discovery.

Large libraries of chemical compounds reflect the exponentially growing data-enrichment in drug discovery that trends towards fully automated informatics solutions to study structure - activity relationships by screening docked ligand candidates to biological target structures. We review otherwise disseminated user descriptions of mainly public databases with free access and also our integrated data mining tool GPDBnet for phyto-pharmacology.

Single nucleotide polymorphisms in the promoter region of the E-cadherin gene in gastric cancer: case-control study in a young Mexican population.

Background: Gastric cancer has a tendency to present at early age in the Mexican population, and it is frequently associated with a family history. A polymorphism at position -160 at the CDH1 promoter region has been reported to lead to transcriptional downregulation of the gene in vitro, with possible increase in the risk of gastric cancer. We evaluated the role of the -160A allele in the risk of gastric cancer in a young Mexican population.

Molecular modeling of some 1H-benzimidazole derivatives with biological activity against Entamoeba histolytica: a comparative molecular field analysis study.

Comparative molecular field analysis (CoMFA) was performed on a set of 1H-benzimidazole derivatives. Molecular modeling and 3D-QSAR were employed to determine the tautomeric form that would probably fit a target receptor in Entamoeba histolytica. CoMFA results suggest that the antiamoebic activity is favored with steric bulk at position 5 of the benzimidazole ring and low electron density on the group at position 2.

Hierarchical strategy for identifying active chemotype classes in compound databases.

A general methodology is presented for analyzing patterns of activity in compound databases, which is based on the use of structural chemotypes and provides a focused, hierarchical classification of active compounds. Each node in the hierarchical tree corresponds to a specific chemotype and is labeled by a unique code or identifier. All chemotypes at a given level of the hierarchy define equivalence classes, and those of higher structural resolution have a strict parent-child (i.

Quantitative structure-activity relationship analysis of pyridinone HIV-1 reverse transcriptase inhibitors using the k nearest neighbor method and QSAR-based database mining.

We have developed quantitative structure-activity relationship (QSAR) models for 44 non-nucleoside HIV-1 reverse transcriptase inhibitors (NNRTIs) of the pyridinone derivative type. The k nearest neighbor (kNN) variable selection approach was used. This method utilizes multiple descriptors such as molecular connectivity indices, which are derived from two-dimensional molecular topology.

Molecular docking of the highly hypolipidemic agent alpha-asarone with the catalytic portion of HMG-CoA reductase.

Docking experiments using a number of published crystal structures of HMG-CoA reductase with the potent hypocholesterolemic agent alpha-asarone are described. The results indicate that alpha-asarone binds in the enzyme's active site. The methoxy groups play a key role in the binding and probably also in its biological activity, as shown by extensive SAR studies reported for analogues of alpha-asarone.

Docking-based CoMFA and CoMSIA studies of non-nucleoside reverse transcriptase inhibitors of the pyridinone derivative type.

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on a set of pyridinone derivatives. A molecular alignment obtained by docking of compounds into the non-nucleoside reverse transcriptase inhibitor binding site of HIV-1 was used. Good correlations between the calculated binding free energies and experimental inhibitory activities suggest that the binding conformations of these inhibitors are reasonable.

Flexible docking of pyridinone derivatives into the non-nucleoside inhibitor binding site of HIV-1 reverse transcriptase.

Potent non-nucleoside reverse transcriptase inhibitors (NNRTIs) of the pyridinone derivative type were docked into nine NNRTIs binding pockets of HIV-1 reverse transcriptase (RT) structures. The docking results indicate that pyridinone analogues adopt a butterfly conformation and share the same binding mode as the crystal inhibitors in the pocket geometries of nevirapine, 1051U91, 9-Cl-TIBO, Cl-alpha-APA, efavirenz, UC-781, and S-1153. The results are in agreement with the data concerning mutational and structure-activity relationships available for pyridinone analogues and aid in the understanding, at the molecular level, of the biological response of published hybrid pyridinone molecules.