Molecular Determinants of a Selective Matrix Metalloprotease-12 Inhibitor: Insights from Crystallography and Thermodynamic Studies

The molecular determinants responsible for the potency of the RXP470.1 phosphinic peptide inhibitor toward matrix metal-loprotease-12 (MMP-12) remain elusive. To address this issue, structure-activity study, X-ray crystallography, and isothermal titration calorimetry (ITC) experiments were performed. The crystal structure of MMP-12/inhibitor complex (1.15 angstrom) reveals that the inhibitor establishes multiple interactions with the MMP-12 active site, with its long P-1' side chain filling most of the S-1' deep cavity. ITC experiments indicate that the binding of this inhibitor to MMP-12 is mostly entropy driven (Delta G degrees = 13.1 kcal/mol, Delta H degrees = -2.53 kcal/mol, and -T Delta S degrees = -10.60 kcal/mol) and involves a proton uptake from the buffer. Comparing phosphinic versus hydroxamate inhibitors reveals that the chelation of the zinc ion is slightly different, leading the inhibitor backbone to adopt a position in which the hydrogen bonding with the MMP-12 active site is less favorable in phosphinic inhibitor while maintaining high affinity.