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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。
Molecular docking and molecular dynamics (MD) simulation were used to establish the interaction between Norcantharidin (NCTD) and vascular endothelial growth factor B (VEGF-B) Model, the combination of the two methods, combined with the ability to explore the interaction between NCTD and VEGF-B mechanism. The results showed that NCTD and NCTD formed hydrogen bonds with Tyr117, Cys156 and Gln46 in the backbone of VEGF-B protein. After 4 ns MD simulation, the equilibrium of NCTD / VEGF-B complex system was reached. The kinetic trajectory and the calculated free energy of binding demonstrated that the binding of NCTD and VEGF-B was stable and reasonable. Hydrogen bonding, electrostatic interaction and hydrophobicity are the main contributions of stable binding of NCTD to VEGF-B. The modeling results of this work to carry out NCTD inhibit VEGF-B activity to control tumor has a certain theoretical significance.