Affinity and Selectivity of Matrix Metalloproteinase Inhibitors:  A Chemometrical Study from the Perspective of Ligands and Proteins

Abstract

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.

Similarity of Binding Sites of Human Matrix Metalloproteinases

“…The IC 50 values for the set of 90 arylsulfonyl-1,2,3,4-tetrahydro-isoquinoline-3-carboxylates and -hydroxamates (22,35) were measured against MMP 3 and MMP 8. The correlation between the IC 50 values for these two enzymes is characterized by R 2 ϭ 0.83.…”

“…More insight is expected from examination of structural changes induced by ligand binding and the energies of the resulting complexes. The methods using the force field interaction energies of probes in individual points of a grid positioned in the binding site have a potential to provide more general results than binding studies of concrete inhibitor structures (22), especially if the binding site is treated as flexible to account for induced fit (23). The approach was used to search for the probes that have different interaction energies in individual subsites of MMPs (23).…”

“…For this purpose, the interaction energies of probes in flexible binding site are perfectly suitable. The previously used (22,23) principal component analysis (PCA) or consensus PCA (CPCA) requires omission of the repulsive interaction energies. Because the repulsive energies are extremely important in size and shape definitions of the binding site, we compared all interaction energies of all MMP pairs directly, by linear regression analysis (LRA).…”

The soluble form of a disintegrin and metalloprotease 33 promotes angiogenesis: Implications for airway remodeling in asthma

“…As ADAM33 Pro-metalloprotease E346A was inactive, it not only controlled for any effects of the V5 and 6xHis tags that had been engineered into the protein to aid purification but also demonstrated that the angiogenic activity of ADAM33 Pro-metalloprotease was unlikely to be a result of a copurified contaminant. Because these data suggested that the enzymatic activity of ADAM33 was required for the angiogenic effect, 4 synthetic carboxylate and hydroxamate compounds that are known inhibitors of metalloproteases 25 were tested for their ability to inhibit ADAM33 Pro-metalloprotease. These were found to exhibit different potencies against ADAM33-mediated peptide cleavage activity, with (3R)-(1)-[2-(4-methoxybenzenesulfonyl)-1,2,3,4-tetrahydroisoquinoline-3-hydroxamate being the most potent (inhibitory concentration 50% [IC 50 ] of 330 nmol/L; Fig E1, D).…”

Integrated Approach Using Protein and Ligand Information to Analyze Selectivity‐ and Affinity‐Determining Features of Carbonic Anhydrase Isozymes

“…[11][12][13] The second approach derives separate models for each affinity measure [14][15][16][17] and obtains selectivity information by subsequently subtracting the respective pK i values.…”