Pu Chunlan, Yan Guoyi, Shi Jianyou, Li Rui
Cancer Center , West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , 610041 Sichuan , P. R. China . Email:
Individualized Medication Key Laboratory of Sichuan Province , Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital , Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital , School of Medicine , Center for Information in Medicine , University of Electronic Science and Technology of China , Chengdu , 610072 Sichuan , P. R. China . Email:
Medchemcomm. 2017 May 22;8(7):1452-1458. doi: 10.1039/c7md00184c. eCollection 2017 Jul 1.
Over-expressed polo-like kinases 1, a key regulator of cell mitosis, is associated with carcinogenesis and poor prognosis. It is very necessary to develop a reliable computational affinity prediction protocol targeting PLK1. In this study, the performance of different docking scoring function, free energy perturbation, MM-GBSA and QM/MM-GBSA were evaluated. The ranking capability of FEP is the best with = 0.854. However, the obtained from MM-GBSA can reach 0.767, which requires only about one-eighth of the simulation time of FEP. As for the sampling method, single long molecular dynamics (SLMD) surpass the multiple short molecular dynamics (MSMD) in ranking of the 20 congeneric compounds by about 0.1 in . In addition, ligands treated by QM can significantly improve the ranking performance. As for the docking scoring functions, a force field-based scoring function is more suitable for ranking congeneric compounds.
过表达的polo样激酶1是细胞有丝分裂的关键调节因子，与肿瘤发生和不良预后相关。开发一种针对PLK1的可靠计算亲和力预测方案非常必要。在本研究中，评估了不同对接评分函数、自由能微扰、MM-GBSA和QM/MM-GBSA的性能。FEP的排名能力最佳，r = 0.854。然而，MM-GBSA得到的r可达0.767，而这只需要FEP约八分之一的模拟时间。至于采样方法，在对20种同类化合物进行排名时，单组长分子动力学（SLMD）在r方面比多组短分子动力学（MSMD）高出约0.1。此外，经量子力学（QM）处理的配体可显著提高排名性能。至于对接评分函数，基于力场的评分函数更适合对同类化合物进行排名。
