Crystal structure of the Stromelysin-3 (MMP-11) catalytic domain complexedwith a phosphinic inhibitor mimicking the transition-state

Stromelysin-3 (ST3) is a matrix metalloproteinase (MMP-11) whose proteolyti c activity plays an important role in tumorigenicity enhancement. In breast cancer, ST3 is a bad prognosis marker: its expression is associated with a poor clinical outcome. This enzyme therefore represents an attractive ther apeutic target. The topology of matrix metalloproteinases (MMPs) is remarkably well conserv ed, making the design of highly specific inhibitors difficult. The major di fference between MMPs lies in the S-1' subsite, a well-defined hydrophobic pocket of variable depth. The present crystal structure, the first 3D-struc ture of the ST3 catalytic domain in interaction with a phosphinic inhibitor mimicking a (D, L) peptide, clearly demonstrates that its S-1' pocket corr esponds to a tunnel running through the enzyme. This open channel is filled by the inhibitor P-1' group which adopts a constrained conformation to fit this pocket, together with two water molecules interacting with the ST3-sp ecific residue Gln215. These observations provide clues for the design of m ore specific inhibitors and show how ST3 can accommodate a phosphinic inhib itor mimicking a (D, L) peptide. The presence of a water molecule interacting with one oxygen atom of the in hibitor phosphinyl group and the proline residue of the Met-turn suggests h ow the intermediate formed during proteolysis may be stabilized. Furthermor e, the hydrogen bond distance observed between the methyl of the phosphinic group and the carbonyl group of Ala182 mimics the interaction between this carbonyl group and the amide group of the cleaved peptidic bond. Our cryst al structure provides a good model to study the MMPs mechanism of proteolys is. (C) 2001 Academic Press.