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学科主题: 计算机化学与化学信息学
题名: Interpretation of the Binding Affinities of PTP1B Inhibitors with the MM-GB/SA Method and the X-Score Scoring Function
其他题名: Interpretation of the Binding Affinities of PTP1B Inhibitors with the MM-GB/SA Method and the X-Score Scoring Function
作者: Zhang XL(张兴龙) ; Li X(李勋) ; Wang RX(王任小)
通讯作者: 王任小
刊名: J. Chem Inf. Model.
发表日期: 2009
卷: 49, 期:4, 页:1033-1048
收录类别: SCI
部门归属: 上海有机所
英文摘要: We have studied the binding affinities of a set of 45 small-molecule inhibitors to protein tyrosine phosphatase 1B (PTP1B) through computational approaches. All of these compounds share a common oxalylamino benzoic acid (OBA) moiety. The complex structure of each compound was modeled by using the GOLD program plus the ASP scoring function. Each complex structure was then subjected to a molecular dynamics (MID) simulation of 2 ns long by using the AMBER program. Based on the configurational ensembles retrieved from MD trajectories, both MM-GB/SA and MM-PB/SA were employed to compute the binding free energies of all 45 PTP1B inhibitors. The correlation coefficient between the MM-GB/SA results and experimental binding data was 0.87 and the standard deviation was 0.60 kcal/mol. The performance of MM-PB/SA was slightly inferior to that of MM-GB/SA. Several aspects of the MM-GB(PB)/SA method were explored in our study to obtain optimized results. The X-Score scoring function was found to produce equally good results as MM-GB/SA on both the complex structures prepared by molecular docking and the configurational ensembles obtained through lengthy MD simulations. The structure-activity relationship of this set of compounds is also discussed based on the computed results. The computational approaches validated in cur study are hopefully applicable to the study of other classes of PTP1B inhibitors.
语种: 英语
相关网址: 查看原文
WOS记录号: WOS:000265528400027
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内容类型: 期刊论文
URI标识: http://ir.sioc.ac.cn/handle/331003/28707
Appears in Collections:计算机化学与化学信息学研究室_期刊论文

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Recommended Citation:
Zhang XL,Li X,Wang RX. Interpretation of the Binding Affinities of PTP1B Inhibitors with the MM-GB/SA Method and the X-Score Scoring Function[J]. J. Chem Inf. Model.,2009,49(4):1033-1048.
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