Superimposing the 27 crystal protein/inhibitor complexes of β-secretase to calculate the binding affinities by the linear interaction energy method

被引：7

作者：

Liu, Shu ^{[1
]}

Zhou, Li-Hua ^{[1
]}

Wang, Hua-Qiao ^{[1
]}

Yao, Zhi-Bin ^{[1
]}

机构：

[1] Sun Yat Sen Univ, Zhong Shan Sch Med, Dept Anat, Guangzhou 510080, Guangdong, Peoples R China

来源：

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS | 2010年 / 20卷 / 22期

基金：

美国国家科学基金会;

关键词：

BACE-1; LIE; Superimposing; Free binding energy; POTENT BACE-1 INHIBITORS; CENTRAL CORE; DISCOVERY; DOCKING; DESIGN;

D O I：

10.1016/j.bmcl.2010.09.050

中图分类号：

R914 [药物化学];

学科分类号：

100701 ;

摘要：

BACE-1 is an important target for designing therapeutic agents for the treatment of Alzheimer's disease. An improved linear interaction energy (LIE) model has been developed to calculate the binding free energies of beta-secretase (BACE-1) by superimposing the 27 crystal BACE-1/inhibitor complexes to put a diverse set of 27 co-crystallized ligands into the binding pocket. These co-crystallized conformations of ligands were set as the initial binding conformations for LIE simulation. The effects of two protein conformations (i.e., 1W51 and 1FKN), two sampling methods (i.e., energy minimization and hybrid Monte Carlo [HMC]), and energy terms were studied. Using 1W51 crystal structure and HMC sampling technique, the best binding affinity model for the full set of ligands was found to have a root-mean-square error of 0.996 kcal/mol. (C) 2010 Elsevier Ltd. All rights reserved.

引用

页码：6533 / 6537

页数：5

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