An enormously active and selective azapeptide inhibitor of cathepsin B

The peptidomimetic Z-Arg-Leu-Arg-Agly-Ile-Val-OMe (where Agly means alpha-aza-glycyl, -NHNHCO-) is the strongest (K(i) = 480 pM) and the most selective inhibitor of cathepsin B to date, being approximately 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 approximately cathepsin B complex suggests that, contrary to other potent inhibitors of cathepsin B, the current double Arg(1)/Arg(3) 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.