分子动力学研究2-乙酸苯并噻吩在HIV-1蛋白酶与抑制剂结合中的作用
收稿日期: 2013-03-25
网络出版日期: 2013-05-24
基金资助
项目受山东省自然科学基金(No. ZR2011HM048)和国家自然科学基金(No. 11274206)资助.
Molecular Dynamics Study on Function of 2-ylacetic acid-Benzothiophene in Binding of HIV-1 Protease and Inhibitor
Received date: 2013-03-25
Online published: 2013-05-24
Supported by
Project supported by the Natural Science Foundation of Shandong Province (No. ZR2011HM048) and the National Natural Science Foundation of China (No. 11274206).
为了研究别构小分子2-乙酸苯并噻吩(2FX)在HIV-1蛋白酶与抑制剂结合中的作用, 利用分子动力学方法分别对未结合和结合2FX的HIV-1蛋白酶抑制剂体系进行了100 ns的模拟, 模拟计算中对每种体系均采用两种新的分子力场ff99SBildn和ff12SB. 研究了2FX对体系构象的影响和两体系在不同力场下的动力学行为, 分析了两体系的均方根偏差和残基的B因子, 比较了计算结构和晶体结构, 最后采用MM-PB/GBSA两种方法计算了两体系的结合自由能. 研究表明, 两种力场计算的结果虽有差异, 但都说明2FX的结合导致蛋白酶构象的变化, 使得体系更加稳定, 尤其是flap的柔性减弱, 使得蛋白酶和抑制剂的结合更牢固; 另外, 还发现ff12SB力场动力学过程更稳定. 研究结果有助于为设计新的别构抑制剂提供理论依据.
关键词： HIV-I蛋白酶; 抑制剂; 分子动力学模拟; MM-PB/GBSA方法; 别构抑制剂
孟现美 , 王加磊 , 张少龙 , 张庆刚 . 分子动力学研究2-乙酸苯并噻吩在HIV-1蛋白酶与抑制剂结合中的作用[J]. 化学学报, 2013 , 71(08) : 1167 -1174 . DOI: 10.6023/A13030327
In order to study the role of allosteric fragment 2-ylacetic acid-benzothiophene (2FX) in the binding of HIV-1 protease (PR) and inhibitor, the molecular dynamics simulations of 100 nanoseconds have been successfully performed on two systems of HIV-1 protease and inhibitor, respectively, one of which 2FX is attached to and another is not. Both types of new force fields, ff99SBildn and ff12SB, and GPU parallel computing technology have been used for each of the two systems in the simulations. By investigating the influence of 2FX on the protease, it is found that the binding of 2FX induces a conformational change of the protease. The dynamics behaviors of the two systems under the two force fields are compared with the VMD visualization software and it is found that, to a certain extent, there exist differences between those from the different forces. The root-mean-square deviations (RMSD), the B-factors of the two systems, and structure superposition between the calculated and X-ray crystal structures, which display that the system with 2FX has a more stable dynamics process and the vibration extent of the residues decreases, indicate that the 2FX bound in the protease can stabilize the system. The binding free energies have been calculated using the two force fields and using two methods, MM-PB/GBSA, respectively. The resulting free energy values, ff99SBildn: -70.52 and -68.42 kcal/mol (PB), -86.72 and -89.40 kcal/mol (GB); ff12SB: -75.40 and -77.68 kcal/mol (PB), -87.01 and -93.75 kcal/mol (GB), 2FX-system being generally of greater magnitudes, also suggest the allosteric fragment stabilizes the binding of inhibitor and PR. The present results, despite the discrepancies between those from the two different force fields, demonstrate that the allosteric fragment 2FX unambiguously gives rise to subtle changes of structure of the PR and make the inhibitor and PR combine more firmly. In particular, it is clear that the fragment acts to weaken the flexibility of the flap, strengthening the combination of the inhibitor and PR. In addition, it is also found that, with ff12SB force field, the dynamics processes are more stable, the calculated binding free energies are more favorable, and the results are better consistent with the experiments than with ff99SBildn. It is expected that this work could be helpful to design new allosteric inhibitors in the future.
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