Peptidyl ammonium methyl ketones as substrate analog inhibitors of proline-specific peptidases.

Prolyl endopeptidase (PEP) and dipeptidyl peptidase IV (DP IV) are serine enzymes cleaving highly specific prolyl peptide bonds. Both enzymes were found to be inhibited by newly designed peptidyl ammonium and pyridinium methyl ketones acting as slow binding inhibitors. The most potent inhibitor of PEP is Z-Pro-Pro-CH2N+C5H5 exhibiting a Ki* value of 1.8 nM with a first-order rate constant of Kon 0.0022 s-1 for the formation of the tight enzyme-inhibitor complex. DP IV and H-Pro-Pro-CH2N+ (CH3)3 form an enzyme-inhibitor-complex with an apparent second order rate constant of 2713 M-1 s-1. In contrast to the very stable N-terminal protected Z-Pro-Pro-CH2N+ (CH3)3, the deblocked derivative decomposes rapidly in aqueous solution.