1. Mechanism and inhibition kinetics of peptide P13 as thrombin inhibitor
- Author
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Fangyuan Chen and Guangrong Huang
- Subjects
Peptide ,02 engineering and technology ,Biochemistry ,Antithrombins ,03 medical and health sciences ,Thrombin ,Structural Biology ,medicine ,Humans ,Molecular Biology ,Peptide sequence ,Protein secondary structure ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Anticoagulant drug ,Chemistry ,General Medicine ,021001 nanoscience & nanotechnology ,Amino acid ,Enzyme ,Docking (molecular) ,Peptides ,0210 nano-technology ,medicine.drug - Abstract
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.
- Published
- 2020