Interaction of papain-like cysteine proteases with dipeptide-derived nitriles

A series of 44 dipeptide nitriles with various amino acids at the P-2 position and glycine nitrile at position P-1 were prepared and evaluated as inhibitors of cysteine proteinases. With respect to the important contribution of the P-2-S-2 interaction to the formation of enzyme-inhibitor complexes, it was focused to introduce structural diversity into the P-2 side chain. Nonproteinogenic amino acids were introduced, and systematic fluorine, bromine, and phenyl scans for phenylalanine in the P-2 position were performed. Moreover, the N-terminal protection was varied. Kinetic investigations were carried out with cathepsin L, S, and K as well as papain. Changes in the backbone structure of the parent N-(tert-butoxycarbonyl)-phenylalanyl-glycinenitrile (16), such as the introduction of an R-configured amino acid or an azaamino acid into 132 as well as methylation of the P-1 nitrogen, resulted in a drastic loss of affinity. Exemplarily, the cyano group of 16 was replaced by an aldehyde or methyl ketone function. Structure-activity relationships were discussed with respect to the substrate specificity of the target enzymes.