Dynamics of stromelysin/inhibitor interactions studied by N-15 NMR relaxation measurements: Comparison of ligand binding to the S-1-S-3 and S-1 '-S-3' subsites

This report describes the backbone amide dynamics of the uniformly N-15 lab eled catalytic domain of human stromelysin complexed to PNU-99533, a hydrox amate-containing ligand that binds to the S-1'-S-3' region (right side) of the stromelysin active site, and to PNU-107859 and PNU-142372, both thiadia zole-containing ligands that bind to the S-1-S-3 region (left side) of the stromelysin active site. N-15 R-1, R-2 and NOE NMR relaxation measurements were recorded and analyzed for each complex. Different dynamic behaviors we re observed for stromelysin complexed to the two classes of ligands, indica ting that it may be possible to use protein dynamics to distinguish between different binding orientations. In the absence of bound ligand at the S-1- S-3 subsites, the S-1-S-3 residues were found to be relatively rigid. In co ntrast, the S-1'-S-3' subsites were found to be flexible in the absence of interactions with ligand. The relative rigidness of the S-1-S-3 subsites ma y be responsible for MMP binding specificity by discriminating between liga nds of different shapes. By contrast, the inherent flexibility of the S-1'- S-3' subsites allows structural rearrangement to accommodate a broad range of incoming substrates or inhibitors. Similarities and differences in dynam ics observed for each complex provide insights into the interactions respon sible for protein-ligand recognition. The relevance of protein dynamics to structure-based drug design is discussed.