Revisiting catalysis by chymotrypsin family serine proteases using peptidesubstrates and inhibitors with unnatural main chains

Chymotrypsin family serine proteases play essential roles in key biological and pathological processes and are frequently targets of drug discovery ef forts. This large enzyme family is also among the most advanced model syste ms for detailed studies of enzyme mechanism and structure/function relation ships. Productive interactions between these enzymes and their substrates a re widely believed to mimic the "canonical" interactions between serine pro teases and "standard" inhibitors observed in numerous protease-inhibitor co mplexes. To test this central hypothesis we have synthesized and characteri zed a series of peptide analogs, based on model substrates and inhibitors o f trypsin, that contain unnatural main chains. These results call into ques tion a long accepted theory regarding the interaction of chymotrypsin famil y serine proteases with substrates and suggest that the canonical interacti ons observed between these enzymes and standard inhibitors may represent no nproductive rather than productive, substrate-like interactions.