Journal
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY
Volume 7, Issue 4, Pages 485-503Publisher
WORLD SCIENTIFIC PUBL CO PTE LTD
DOI: 10.1142/S0219633608003915
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A series of HIV-1 protease (PR) inhibitors are designed to increase the binding affinity with PR subsites based on the quantum analysis of the contributions of molecular fragments in six FDA-approved PR drugs to the total binding interaction. The binding free energies were estimated by modified linear interaction energy approach [Zoete H, Michielin O, Karplus M, J Comput Aided Mol Des 17: 861, 2003], in which the binding free energy is written as a linear combination of the electrostatic interaction energy between PR and the ligand, E-elec, the van der Waals interaction energy between PR and the ligand, E-vdW, and the difference of the solvation free energies of the complex, the receptor and the isolated ligand, Delta G(solv). The parameters of these energy terms were fitted for a training set of 14 HIV-1 protease-inhibitor complexes of known 3D structure with a correlation coefficient of 0.91 and an unsigned mean error of 0.83 kcal/mol.
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