Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts:   Target Concepts:
Query: EC:3.4.24.17 (MMP-3)
 3,419 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A novel strategy to understand affinity and selectivity for enzyme inhibitors using information from ligands and target protein 3D structures is described. It was applied to 2-arylsulfonyl-1,2,3, 4-tetrahydro-isoquinoline-3-carboxylates and -hydroxamates as inhibitors of the matrix metalloproteinases MMP-3 (stromelysin-1) and MMP-8 (human neutrophil collagenase). As the first step, consistent and predictive 3D-QSAR models were derived using CoMFA, CoMSIA, and GRID/Golpe approaches, leading to the identification of binding regions where steric, electronic, or hydrophobic effects are important for affinity. These models were validated using multiple analyses using two or five randomly chosen cross-validation groups and randomizations of biological activities. Second, 3D-QSAR models were derived based on the affinity ratio IC(50)(MMP-8)/IC(50)(MMP-3), allowing the identification of key ligand determinants for selectivity toward one of both enzymes. In addition to this ligands' view, the third step encompasses a chemometrical approach based on principal component analysis (PCA) of multivariate GRID descriptors to uncover the major differences between both protein binding sites with respect to their GRID probe interaction pattern. The resulting information, based on the accurate knowledge of the target protein 3D structures, led to a consistent picture in good agreement with experimentally observed differences in selectivity toward MMP-8 or MMP-3. The interpretation of all three classes of statistical models leads to detailed SAR information for MMP inhibitors, which is in agreement with available data for binding site topologies, ligand affinities, and selectivities. Thus the combined chemical analyses provide guidelines and accurate activity predictions for designing novel, selective MMP inhibitors.
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PMID:Affinity and selectivity of matrix metalloproteinase inhibitors: a chemometrical study from the perspective of ligands and proteins. 1057 15

A theoretical study was performed on the structure of both the native and inhibited metalloproteinase Ht-d (E.C. 3.4.24.42) solved at 2.0 A resolution. The energy maps calculated by program GRID clearly showed the extended binding site of Ht-d and allowed localization and characterization of the pockets S1-S3 and S1'-S3'. The GRID energy contour maps point out the particular shape of the S1' pocket in agreement with experimental density maps and inhibited Ht-d structures. Based on the high degree of sequence homology of the Ht-d active site to that of mammalian metalloproteinases, the characterization of active site pockets was extended to neutrophil collagenase, fibroblast collagenase, stromelysin 1 and 2. Thirty residues of the Ht-d propeptide were modeled and optimized with reference to the Ht-d structure, giving insight to the mechanism of natural inhibition in metalloproteinase proenzymes. Kinetic measurements of Ht-d inhibition by a series of synthetic peptides show, in agreement with our Ht-d propeptide model, the crucial role of cysteine and adjacent residues in the specificity of Ht-d propeptide. This study suggests the structural link between Ht-d and mammalian metalloproteinases, contributing to the understanding of the mechanism of natural and synthetic inhibitor binding to metalloproteinases. Therefore, Ht-d is a good model system for the design of novel inhibitors against these enzymes with enhanced potency and specificity.
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PMID:Structure-based analysis of inhibitor binding to Ht-d. 1529 48