Design and structure-activity relationship of thrombin inhibitors with an azaphenylalanine scaffold: Potency and selectivity enhancements via P2 optimization

Theoretical and structural studies followed by the directed synthesis and i n vitro biological tests lead us to novel noncovalent thrombin pseudopeptid e inhibitors. We have incorporated an azapeptide scaffold into the central part of the classical tripeptide D-Phe-Pro-Arg inhibitor structure thus eli minating one stereogenic center from the molecule. A series of compounds ha s been designed to optimize the occupancy of tile S2 pocket of thrombin. in creased hydrophobicity at P2 provides an enhanced fit into this active site S2 pocket. In the present paper, we also report oil the structure of these inhibitors in solution and conformational analysis of inhibitors in the ac tive site in order to asses the consequences of tile replacement of the cen tral alpha -CH by a nitrogen functionality. In vitro biological testing of the designed inhibitors shows that elimination of R, S stereoisomerism and restriction of conformational freedom influences the binding of inhibitors in a favorable fashion. (C) 2001 Elsevier Science Ltd. All rights reserved.