Macrocyclic Inhibitors of Penicillopepsin. 2. X-ray Crystallographic Analyses of Penicillopepsin Complexed with a P3−P1 Macrocyclic Peptidyl Inhibitor and with Its Two Acyclic Analogues

Macrocyclic inhibitor 1 {methyl [cyclo-7[(2R)-((N-valyl) amino)-2-(hydroxyl-(1S)-1-methyoxycarbonyl-2-phenylethoxy)phosphinyloxyethyl]-1-naphthaleneacetamide] sodium salt} was designed according to the conformation of the acyclic analogue Iva-l-Val-l-Val-l-LeuP-(O)Phe-OMe [LeuP = the phosphinic acid and analogue of l-leucine; (O)Phe = l-3-phenyllactic acid; OMe = methyl ester] (4) bound to penicillopepsin, by linking the P1 and P3 side chains of the penicillopepsin inhibitor. This compound and its two acyclic derivatives, {methyl (2S)-[1-(((N-Formyl)-l-valyl)amino-2-(2-naphthyl)ethyl)hydroxyphosphinyloxy]-3-phenylpropanoate, sodium salt} (2) and {methyl (2S)-[1-(((N-(1-naphthaleneacetyl))-l-valyl)aminomethyl)hydroxyphosphinyloxy]-3-phenylpropanoate, sodium salt} (3), have been synthesized and evaluated as inhibitors of penicillopepsin. Their binding affinity to the enzyme was found to be inversely related to the predicted degree of conformational flexibility across the series: 3 (Ki = 110 μM), 2 (Ki = 7....