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Molecular docking and molecular dynamics simulation studies of GPR40 receptor-agonist interactions

文献类型：期刊论文

作者Lu, Shao-Yong2; Jiang, Yong-Jun3; Lv, Jing2; Wu, Tian-Xing2; Yu, Qing-Sen2; Zhu, Wei-Liang1
刊名JOURNAL OF MOLECULAR GRAPHICS & MODELLING
出版日期2010-06
卷号28期号:8页码:766-774
关键词GPR40 Molecular docking Molecular dynamics simulation AutoDock GROMACS
ISSN号1093-3263
DOI10.1016/j.jmgm.2010.02.001
文献子类Article
英文摘要In order to explore the agonistic activity of small-molecule agonists to GPR40, AutoDock and GROMACS software were used for docking and molecular dynamics studies. A molecular docking of eight structurally diverse agonists (six carboxylic acids (CAs) agonist, and two non-carboxylic acids (non-CAs) agonist) was performed and the differences in their binding modes were investigated. Moreover, a good linear relationship based on the predicted binding affinities (pK(i)) determined by using AutoDock and experimental activity values (pEC50) was obtained. Then, the 10 ns molecular dynamics (MD) simulations of three obtained ligand-receptor complexes embedded into the phospholipid bilayer were carried out. The position fluctuations of the ligands located inside the transmembrane domain were explored, and the stable binding modes of the three studied agonists were determined. Furthermore, the residue-based decomposition of interaction energies in three systems identified several critical residues for ligand binding. (C) 2010 Elsevier Inc. All rights reserved.
WOS关键词FATTY-ACID RECEPTOR ; INSULIN-SECRETION ; ADRENERGIC-RECEPTOR ; LIPID-BILAYER ; PROTEIN ; DISCOVERY ; ANTAGONISTS ; BINDING ; SPECTROSCOPY ; RECOGNITION
资助项目National High Technology Research and Development Program of China[2007AA02Z301] ; National High Technology Research and Development Program of China[2006AA02Z336] ; Natural Science Foundation of China[20803063]
WOS研究方向Biochemistry & Molecular Biology ; Computer Science ; Crystallography ; Mathematical & Computational Biology
语种英语
WOS记录号WOS:000278414800007
出版者ELSEVIER SCIENCE INC
源URL[http://119.78.100.183/handle/2S10ELR8/278888]  
专题药物发现与设计中心
通讯作者Jiang, Yong-Jun
作者单位1.Chinese Acad Sci, Drug Discovery & Design Ctr, Shanghai Inst Mat Med, Shanghai 201203, Peoples R China
2.Zhejiang Univ, Dept Chem, Hangzhou 310027, Peoples R China;
3.Zhejiang Univ, Key Lab Mol Design & Nutr Engn, Ningbo Inst Technol, Ningbo 315104, Peoples R China;
推荐引用方式
GB/T 7714		 Lu, Shao-Yong,Jiang, Yong-Jun,Lv, Jing,et al. Molecular docking and molecular dynamics simulation studies of GPR40 receptor-agonist interactions[J]. JOURNAL OF MOLECULAR GRAPHICS & MODELLING,2010,28(8):766-774.
APA Lu, Shao-Yong,Jiang, Yong-Jun,Lv, Jing,Wu, Tian-Xing,Yu, Qing-Sen,&Zhu, Wei-Liang.(2010).Molecular docking and molecular dynamics simulation studies of GPR40 receptor-agonist interactions.JOURNAL OF MOLECULAR GRAPHICS & MODELLING,28(8),766-774.
MLA Lu, Shao-Yong,et al."Molecular docking and molecular dynamics simulation studies of GPR40 receptor-agonist interactions".JOURNAL OF MOLECULAR GRAPHICS & MODELLING 28.8(2010):766-774.

入库方式： OAI收割

来源：上海药物研究所

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