An enormously active and selective azapeptide inhibitor of cathepsin B

The peptidomimetic Z‐Arg‐Leu‐Arg‐Agly‐Ile‐Val‐OMe (where Agly means α‐aza‐glycyl, ‐NHNHCO‐) is the strongest (Ki = 480 pM) and the most selective inhibitor of cathepsin B to date, being ∼2310 times as active to cathepsin B as to cathepsin K. In this paper we introduce the peptide and seek to rationalize its structure‐activity relationships using molecular dynamics (MD) and NMR. It is shown that the ‐Agly‐moiety restrains the peptide backbone to a bent shape, contrary to its parent peptide (with Gly in position 4), having its backbone extended and flexible. This fold is maintained in the plug covalently bound to the cathepsin B Cys29, in compliance with similar bends already observed in two other azapeptides attached to the active sites of cathepsin B. The MD simulation of the Z‐Arg‐Leu‐Arg‐Agly ∼ cathepsin B complex suggests that, contrary to other potent inhibitors of cathepsin B, the current double Arg1/Arg3 inhibitor, while maintaining the fold is able to form a unique ion cluster involving both Arg residues on the inhibitor part and two acidic Glu171 and Glu245 on the cathepsin B part, thus enhancing the affinity and subsequently the inhibiting power and selectivity of Z‐Arg‐Leu‐Arg‐Agly‐Ile‐Val‐OMe to the observed extreme extent. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.