Wu XiaoYun, Wan ShanHe, Wang GuangFa, Jin Hong, Li ZhongHuang, Tian YuanXin, Zhu ZhengGuang, Zhang JiaJie
School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
J Mol Graph Model. 2015 Mar;56:103-12. doi: 10.1016/j.jmgm.2014.12.006. Epub 2014 Dec 24.
Vascular endothelial growth factors receptor-2 (VEGFR-2) inhibitors have been proved as very effective anticancer agents. Structurally similar ligands 1 and 2 show almost the same inhibitory activities against VEGFR-2, but they bind to the enzyme in distinct binding mode. Ligand 1 targets DFG-in active conformation of VEGFR-2, known as Type I inhibitor. On the other hand, ligand 2 targets DFG-out inactive conformation of VEGFR-2, known as Type II inhibitor or allosteric kinase inhibitor. Ligand 2 shows high inhibitory activity, while the compound 3, a close analog of 2 with the cyclopropylamide replaced by tert-butylamide, exhibits drastically diminished potency. In this work, molecular dynamics simulations and free energy calculations were performed on inhibitors 1-3 binding to active and inactive conformation of VEGFR-2. Molecular dynamics simulations find that the active conformation binding to Type I inhibitor 1 appears more flexible when compared to the unbound form. In contrast, binding of Type II inhibitor 2 to the inactive conformation helps to stabilize the inactive conformation of the protein. Binding free energy calculations verify that inhibitors 1 and 2 have almost the same activities against VEGFR-2, and that ligand 1 binds to and stabilizes the DFG-in conformation of VEGFR-2, which is in agree with the experimental observation. Molecular dynamics simulations and binding free energy calculations of 3 binding to VEGFR-2 can give a good explanation of the drastically diminished potency. Free energy analysis revealed that van der Waals interactions provided the substantial driving force for the binding process. The important hydrophobic property of the terminal 4-Cl phenyl was required to be Type II inhibitors. Furthermore, per-residue free energy decomposition analysis revealed that the most favorable contribution came from Leu840, Val848, Ala866, Lys868, Leu889, Val899, Thr916, Phe918, Cys919, Leu1035, Cys1045, Asp1046, and Phe1047. These results are expected to be useful for future rational design of novel potent VEGFR-2 inhibitors.
血管内皮生长因子受体-2（VEGFR-2）抑制剂已被证明是非常有效的抗癌药物。结构相似的配体1和2对VEGFR-2显示出几乎相同的抑制活性，但它们以不同的结合模式与该酶结合。配体1靶向VEGFR-2的DFG-in活性构象，被称为I型抑制剂。另一方面，配体2靶向VEGFR-2的DFG-out非活性构象，被称为II型抑制剂或变构激酶抑制剂。配体2显示出高抑制活性，而化合物3是2的紧密类似物，其中环丙基酰胺被叔丁基酰胺取代，其效力急剧下降。在这项工作中，对抑制剂1-3与VEGFR-2的活性和非活性构象的结合进行了分子动力学模拟和自由能计算。分子动力学模拟发现，与未结合形式相比，与I型抑制剂1结合的活性构象显得更灵活。相反，II型抑制剂2与非活性构象的结合有助于稳定蛋白质的非活性构象。结合自由能计算证实，抑制剂1和2对VEGFR-2具有几乎相同的活性，并且配体1与VEGFR-2的DFG-in构象结合并使其稳定，这与实验观察结果一致。对3与VEGFR-2结合的分子动力学模拟和结合自由能计算可以很好地解释其效力的急剧下降。自由能分析表明，范德华相互作用为结合过程提供了主要驱动力。末端4-氯苯基的重要疏水性质是成为II型抑制剂所必需的。此外，每个残基的自由能分解分析表明，最有利的贡献来自Leu840、Val848、Ala866、Lys868、Leu889、Val899、Thr916、Phe918、Cys919、Leu1035、Cys1045、Asp1046和Phe1047。这些结果有望对未来新型高效VEGFR-2抑制剂的合理设计有用。
