摘要
利用分子对接(Molecular docking)结合分子动力学(Molecular dynamics,MD)模拟方法,建立去甲斑蝥素(Norcantharidin,NCTD)与血管内皮生长因子B(Vascular endothelial growth factor B,VEGF-B)的相互作用模型,分析二者的结合方式,结合能力,探究NCTD与VEGF-B的相互作用机制。结果表明,分子对接生成稳定的NCTD/VEGF-B复合物,NCTD与VEGF-B蛋白主链的Tyr117,Cys156,Gln46形成了氢键。经4ns的MD模拟后,NCTD/VEGF-B复合物体系达到了平衡,分析动力学轨迹并计算结合自由能证明了NCTD与VEGF-B的结合稳定合理。氢键、静电作用和疏水性为NCTD与VEGF-B稳定结合的主要贡献。本工作模建结果对开展NCTD抑制VEGF-B活性来控制肿瘤发生具有一定的理论意义。
The interaction mechanism of the binding model of norcantharidin（NCTD） with vascular endothelial growth factor B（VEGF-B） is established by molecular docking and molecular dynamics（MD） simulation method.A combination of analyzing the binding mode and energy of the complex has been used to characterize the interaction of NCTD and VEGF-B.In the docking model,hydrogen bonds were formed between the NCTD molecule and the Tyrll7,Cysl56 and Gln46 of VEGF-B protein backbone.After the 4ns MD simulation,the NCTD-VEGF-B complex system reached to the balanced state and the result was obtained that the combination between NCTD and VEGF-B is stable and reasonable according to the trajectory analysis and binding free energy calculation.The hydrogen bonds,hydrophobic forces and electrostatic interaction are main binding forces in the NCTD-VEGF-B system.This work provided certain reference for the study of using NCTD to inhibit the activity of VEGF-B so that it can controls the tumor.
出处
《计算机与应用化学》
CAS
CSCD
北大核心
2014年第12期1489-1492,共4页
Computers and Applied Chemistry
基金
国家自然科学基金资助项目(No.20877072)
浙江省科技厅资助项目(2011C12043)
作者简介
郭明，男，博士，教师.联系人：郭明，E-mail：guoming@zafu．edu．cn
