Mechanism and inhibition kinetics of peptide P13 as thrombin inhibitor

• Published in: International journal of biological macromolecules 2020-05, Vol.150, p.1046-1052
• Main Authors: Chen, Fangyuan, Huang, Guangrong
• Format: Article
• Language: English
• Subjects: Antithrombins - chemical synthesis; Antithrombins - chemistry; Humans; Inhibitory mechanism; Peptides - chemical synthesis; Peptides - chemistry; Thrombin; Thrombin - antagonists & inhibitors; Thrombin - chemistry; Thrombin inhibitor
• ISSN: 0141-8130; 1879-0003
• DOI: 10.1016/j.ijbiomac.2019.10.109

Excessive coagulation can easily lead to arterial and venous thrombosis, which is the main reason for the evolution of myocardial infarction and cerebrovascular accidents. As a key coagulation factor for the coagulation pathway, thrombin has become a remarkable target for the control of thrombosis. The synthesized peptide P13 with amino acid sequence of N-RGDAGFAGDDAPR was expected to be an inhibitor with higher antithrombotic activity. The results showed that the IC50 (50% inhibition of thrombin activity) of the peptide P13 was determined by colorimetric method to be 115 µM. And enzyme kinetic experiments showed that P13 was a competitive inhibitor of thrombin with Ki = 106 µM. Fluorescence spectra and three-dimensional fluorescence showed that P13 could alter the secondary structure of thrombin and the microenvironment of certain chromogenic amino acids. P13 can spontaneously bind with thrombin exosite 1 in the form of 1:1 mainly through hydrogen bonding and van der Waals force. And the optimal docking mode of P13 and thrombin was revealed by molecular docking with “-CDOCKER_Energy” of 178.679 kcal mol−1. This study revealed P13 may become a potential anticoagulant drug widely used after further studies in preclinical and clinical trials.