Coupling protein engineering with probe design to inhibit and image matrix metallo proteases with controlled specificity

Matrix metalloproteinases (MMPs) are zinc-endopeptidases that play roles in numerous pathophysiological processes and therefore are promising drug targets. However, the large size of this family and a lack of highly selective compounds that can be used for imaging or inhibition of specific MMPs members has limited efforts to better define their biological function. Here we describe a protein engineering strategy coupled with small molecule probe design to selectively target individual members of the MMP family. Specifically, we introduce a cysteine residue near the active site of a selected protease that does not alter its overall activity or function but allows direct covalent modifi-cation by a small molecule probe containing a reactive electrophile. This specific engineered interaction between the probe and the target protease provides a means to both image and inhibit the modified protease with absolute specificity. Here we demonstrate the feasibility of the approach for two distinct MMP proteases, MMP-12 and MT1-MMP (MMP-14).