Chemical Physics Program, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA.
J Phys Chem B. 2010 Apr 22;114(15):5144-53. doi: 10.1021/jp911085d.
Survivin is an anticancer drug target due to its overexpression in tumor cells in a homodimer form. Abbott Laboratories has identified a small molecule binding site near the dimerization interface in a high-throughput-screening (HTS)-NMR experiment. A benchmarking of the binding mode of the compound Abbott8 aided in the search for the ligand-induced-fit receptor structure by exploring the conformational space of the survivin dimer. We performed ensemble dockings with Abbott8 against a large set of conformations sampled via replica exchange molecular dynamics (REMD). This enhanced sampling allowed the reproduction of the holo-NMR experimental binding mode. Surprisingly, the major structural change in the best-REMD snapshot corresponding to the small molecule induced-fit happens in the so-called "survivin mitosis/apoptosis switch loop", consistent with the X-ray crystal structure of survivin-monomer/borealin/INCENP chromosomal passenger complex (CPC), as the distance between Phe93 and Phe101 increased. To verify this hypothetical pathway for the induced-fit conformational change, we utilized morphed intermediate structures that combined the X-ray data and the best-REMD snapshot, and the potential of mean force (PMF) of the survivin dimer was constructed with umbrella sampling (US) followed by a multiple Bennett acceptance ratio estimator (MBAR). It revealed a 3-4 kcal/mol free energy barrier along the reaction coordinate, and the complex is stabilized by the gain of the binding energies of Abbott8. This free energy barrier might prohibit the reproduction of the experimental binding mode from the regular NTP-MD ensemble docking that we had tried. The combination of REMD generalized ensemble sampling with ensemble docking and free energy pathway analysis may provide a novel research protocol for the simulation of protein-ligand induced-fit recognition.
生存素是一种抗癌药物靶点，因为它以同源二聚体的形式在肿瘤细胞中过度表达。雅培实验室在高通量筛选（HTS）-NMR 实验中鉴定了一个靠近二聚化界面的小分子结合位点。通过探索生存素二聚体的构象空间，对化合物 Abbott8 的结合模式进行基准测试，有助于搜索配体诱导的受体结构。我们使用 Abbott8 对通过 replica exchange 分子动力学（REMD）采样的大量构象进行了整体对接。这种增强的采样允许复制全构象-NMR 实验的结合模式。令人惊讶的是，与小分子诱导适应相关的最佳 REMD 快照中的主要结构变化发生在所谓的“生存素有丝分裂/凋亡开关环”中，这与生存素单体/ borealin/INCENP 染色体乘客复合物（CPC）的 X 射线晶体结构一致，因为 Phe93 和 Phe101 之间的距离增加了。为了验证这种诱导适应构象变化的假设途径，我们利用了组合了 X 射线数据和最佳 REMD 快照的变形中间结构，并用伞状采样（US）构建了生存素二聚体的平均力势能（PMF），然后使用多个 Bennett 接受率估计器（MBAR）。它揭示了沿着反应坐标的 3-4 kcal/mol 自由能障碍，并且该复合物通过 Abbott8 的结合能的增加而稳定。该自由能障碍可能会阻止我们尝试的常规 NTP-MD 整体对接从实验结合模式中重现。REMD 广义集合采样与集合对接和自由能途径分析的结合可能为模拟蛋白质-配体诱导适应识别提供新的研究方案。
