Design and synthesis of thrombin substrates with modified kinetic parameters

For the continuous registration of thrombin formation in plasma (1), selective thrombin substrates are required, that show moderate binding affinities (high Km) and low turnover numbers (low kcat). Previously we have used SQ68 (CH3O-CO-CH2-CO-Aib-Arg-pNA) for this purpose. In order to find more substrates suitable for this application, we synthesized a series of 25 peptide p-nitroanilides. As lead structures SQ68 and S2238 (H-D-Phe-Pip-Arg-pNA) were used. By introduction of specific structure modifications we tried to alter the kinetic data in the required direction. The modifications were designed on basis of existing knowledge on the structure of the thrombin active-site and its surroundings. We indeed obtained a number of substrates with the kinetic constants in the desired range.