Probing proteinases: A radioactive photoaffinity probe exhibiting subnanomolar potency towards matrix metalloproteinases (MMPs) has been developed (see structure). High sensitivity in the detection of particular MMPs has been obtained; however, high variation in the cross-linking yield of MMPs with this probe may limit its ability to detect all MMP active forms in biological samples. This result suggests that a cocktail of optimized probes should be developed. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z604408_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Four phosphinic peptide libraries with compounds having the general formula p-Br-Ph-(PO2-CH2)-Xaa'-Yaa'-Zaa'-NH2 have been prepared and screened against 10 matrix metalloproteinases ( MMPs). We identified two phosphinic peptides with K-i values of 0.19 and 4.4 nM toward MMP-12 ( macrophage elastase) that are more than 2 - 3 orders of magnitude less potent toward the other MMPs tested. These highly selective MMP-12 inhibitors contain a Glu-Glu motif in their Yaa'-Zaa' positions. Incorporation of this Glu-Glu motif into the sequence of a nonspecific fluorogenic peptide cleaved by MMPs provides a highly selective substrate for MMP-12. A model of one of these inhibitors interacting with MMP-12 suggests that the selectivity observed might be due, in part, to the presence of two unique polar residues in MMP-12, Thr(239) and Lys(177). These MMP-12-selective inhibitors may have important therapeutic applications to diseases in which MMP-12 has been suggested to play a key role, such as in emphysema, atherosclerosis, and aortic abdominal aneurysm.