STRUCTURE OF A RETRO-BINDING PEPTIDE INHIBITOR COMPLEXED WITH HUMAN ALPHA-THROMBIN

The crystallographic structure of the ternary complex between human al pha-thrombin, hirugen and the peptidyl inhibitor Phe-allo Thr-Phe-O-CH 3, which is acylated at its N terminus with 4-guanidino butanoic acid (BMS-183507), has been determined at 2.6 Angstrom resolution. The stru cture reveals a unique ''retro-binding'' mode for this tripeptide acti ve site inhibitor. The inhibitor binds with its alkyl-guanidine moiety in the primary specificity pocket and its two phenyl rings occupying the hydrophobic proximal and distal pockets of the thrombin active sit e. In this arrangement the backbone of the tripeptide forms a parallel beta-strand to the thrombin main-chain at the binding site. This is o pposite to the orientation of the natural substrate, fibrinogen, and a ll the small active site-directed thrombin inhibitors whose bound stru ctures have been previously reported. BMS-183507 is the first syntheti c inhibitor proved to bind in a retro-binding fashion to thrombin, in a fashion similar to that of the N-terminal residues of the natural in hibitor hirudin. Furthermore, this new potent thrombin inhibitor (K-i = 17.2 nM) is selective for thrombin over other serine proteases teste d and may be a template to be considered in designing hirudin-based th rombin inhibitors with interactions at the specificity pocket.