STRUCTURAL-ANALYSIS OF THROMBIN COMPLEXED WITH POTENT INHIBITORS INCORPORATING A PHENYL GROUP AS A PEPTIDE MIMETIC AND AMINOPYRIDINES AS GUANIDINE SUBSTITUTES

The structure of the noncovalent complex of human alpha-thrombin with a nonpeptide inhibitor containing a central phenyl scaffold, lfonyloxy )phenoxy]-ethyl]-N-methyl-4-aminopyridine (1), has been determined to 2.20 Angstrom resolution. In addition, the thrombin-bound structures o f two distinct amino acid-based inhibitors (3 and 4) containing differ ent aminopyridine-derived guanidine mimetics have been determined, Eac h compound occupies the same region of the active site and projects an aminopyridine, a central hydrophobic group, and an aryl group, into t he S-1, S-2, and aryl subsites on thrombin. Nonpeptide 1 forms only on e direct intermolecular hydrogen bond to the thrombin active site and forms no hydrogen bonds to ordered molecules of solvent. Close contact s are observed between main-chain carbonyl groups on thrombin and the edges of the central phenyl and aminopyridine rings and the sulfonyl g roup of 1 such that atoms carrying opposite partial charges are juxtap osed. Aminopyridine groups in 3 and 4 also form close contacts with th e edges of carbonyl groups on thrombin and are flexibly accommodated i n the S-1 subsite. Superposition of the bound conformations of 1 and D -Phe-Pro-amidobutylguanidine (2) revealed that the central phenyl scaf fold of 1 substitutes for the peptide main chain of 2.