Evaluating the relative free energy of hydration of new thrombin inhibitorcandidates using the finite difference thermodynamic integration (FDTI) method

Thrombin is a serine protease involved in blood coagulation. Since thrombin inhibitors appear to be effective in the treatment and prevention of throm botic and embolic disorders, considerable attention has been focused on the structure and interactions of the enzyme. In this work, we calculated the relative free energies of hydration of the new thrombin inhibitor candidate s, p-substituted derivatives of benzamidine, a well-known noncovalent throm bin inhibitor. We used molecular dynamics and the finite difference thermod ynamic integration (FDTI) algorithm within the Discover program of MSI. We have shown that the orthogonality problem that occurs in the calculation of intraperturbed-group contributions to the free energy is treated adequatel y by the FDTI method. We have also shown that problems of singularity and c onvergence in free energy calculations can be properly solved using this me thod. To conclude, the calculated free energies of hydration gave the follo wing order of solvation for the candidates: p-(2-oxo-1-propyl)benzamidine > p-methylbenzamidine > p-ethylbenzamidine > p-(I-propyl)benzamidine > benza midine. (C) 2001 John Wiley & Sons, Inc.