QUANTUM CALCULATION OF PROTEIN SOLVATION AND PROTEIN-LIGAND BINDING FREE ENERGY FOR HIV-1 PROTEASE/WATER COMPLEX

被引：22

作者：

Tong, Yan ^{[3
]}

Mei, Ye ^{[1
]}

Zhang, John Z. H. ^{[2
]}

Duan, Li L. ^{[4
]}

Zhang, Qing-Gang ^{[4
]}

机构：

[1] E China Normal Univ, State Key Lab Precis Spect, Dept Phys, Shanghai 200062, Peoples R China

[2] New York Univ, Dept Chem, New York, NY 10003 USA

[3] Nanjing Univ, Inst Theoret & Computat Chem, Key Lab Mesoscop Chem, Sch Chem & Chem Engn,Minist Educ, Nanjing 210093, Peoples R China

[4] Shandong Normal Univ, Coll Phys & Elect, Jinan 250014, Peoples R China

来源：

JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY | 2009年 / 8卷 / 06期

基金：

中国国家自然科学基金;

关键词：

HIV-1; protease; quantum mechanics (QM); MFCC; CPCM; free energy; MOLECULAR-ORBITAL METHOD; AB-INITIO COMPUTATION; IMPLICIT SOLVENT; POTENT INHIBITOR; HYDROGEN-BOND; FORCE-FIELD; MM-PBSA; DYNAMICS; MECHANICS; RNA;

D O I：

10.1142/S0219633609005313

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

HIV-1 protease (PR) is a primary target for anti-HIV therapeutics. A well conserved water molecule, denoted as W301, is found in almost all the crystallographic structures of PR/inhibitor complexes and it plays an important role in PR/inhibitor binding. As the PR/inhibitor interaction depends on the ionization state of the cleavage site which contains an aspartyl dyad (Asp25/Asp25'), the determination of the protonation states of aspartyl dyad in PR may be essential for drug design. In this study, a linear scaling quantum mechanical method, molecular fragmentation with conjugate caps (MFCC), is used for interaction study of PR/ABT-538 and W301 at four different monoprotonation states of the Asp25/Asp25'. Combined method of MFCC and conductor-like polarizable continuum model (CPCM) is applied in binding affinity calculation for four minimum energy structures which are extracted from four different molecular dynamics trajectories corresponding to four different monoprotonation states of Asp25/Asp25'. Our result is

引用

页码：1265 / 1279

页数：15

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