Computational study of the catalytic domain of human neutrophil collagenase. Specific role of the S3 and S3' subsites in the interaction with a phosphonate inhibitor

Human neutrophil collagenase (HNC,MMP-8) is one of the target enzymes for drug treatment of pathologic extracellular matrix degradation. Peptidomimetic inhibitors bind in the S'-side of the enzyme active site occupying the S1' primary specificity pocket by their large hydrophobic side-chains. The crystal structure of the complex between the catalytic domain of MMP-8 and Pro-Leu-TrpP(OH)2 (PLTP) showed that this phosphonate inhibitor binds in the S side of the active site. This finding was unexpected since it represents the first example of accomodation of the bulky Trp indolyl chain in the S1 rather than in the S1' subsite. Dynamical and structural factors favouring this uncommon mode of binding were therefore investigated. Molecular dynamics (MD) simulations performed on the uncomplexed enzyme show that its structure in aqueous solution is only slightly different from the crystal structure found in the complex with PLTP. Essential dynamics analysis of the MD simulations, performed on PLTP alternatively interacting with the S- or S'-side of the active site, shows that the enzyme fluctuation increases in both cases. The main contribution to the overall enzyme fluctuation is given by the loop 164-173. The fluctuation of this loop is spread over more degrees of freedom when PLTP interacts with the S-side. This dynamical factor can enhance the preference of PLTP for the S subsites of MMP-8. MD simulations also show that ligation of PLTP in the S subsites is further favoured by better zinc chelation, a cation-p interaction at the S3 subsite and unstrained binding conformations. The role of the S3, S3' and S1' subsites in determining the inhibitor binding is dicussed.