Abstract
Thrombin is a serine protease responsible for blood coagulation. Since thrombin inhibitors appear to be effective in the treatment and prevention of thrombotic and embolic disorders, considerable attention has been focused on the structure and interactions of this enzyme. In this work, to evaluate the relative free energies of hydration and binding to thrombin for some benzamidine derivatives, we used the finite difference thermodynamic integration (FDTI) algorithm within the Discover program of MSI. By this method, two possible orders of hydration for the candidates were obtained: p-amidinophenylpyruvate > p-(2-oxo-1-propyl)benzamidine > p-methylbenzamidine > p-ethylbenzamidine > p-(1-propyl)benzamidine > benzamidine and p-amidinophenylpyruvate > p-(2-oxo-1-propyl)benzamidine > p-methylbenzamidine > p-ethylbenzamidine > benzamidine > p-(1-propyl)benzamidine. We also obtained the following order for thrombin binding: p-(2-oxo-1-propyl)benzamidine > p-ethylbenzamidine > p-(1-propyl)benzamidine > p-methylbenzamidine > benzamidine > p-amidinophenylpyruvate.
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