| HIV-1 蛋白酶异位抑制剂体系的长时间分子动力学模拟 |
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| 引用本文： | 王加磊,孟现美,张庆刚,张怿慈,张少龙.HIV-1 蛋白酶异位抑制剂体系的长时间分子动力学模拟[J].山东科学,2013,26(2):1-6. |
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| 作者姓名： | 王加磊 孟现美 张庆刚 张怿慈 张少龙 |
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| 作者单位： | 山东师范大学物理与电子科学学院，山东 济南 250014 |
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| 基金项目： | 国家自然科学基金，山东省自然科学基金，高等学校博士学科点专项科研基金 |
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| 摘 要： | 采用新开发的ff12SB力场在NVIDIA CUDA GPU上对HIV-1蛋白酶的活性位抑制剂体系和异位抑制剂体系分别进行了100 ns的长时间分子动力学模拟,并用MM-PB/GBSA方法计算了活性位点抑制剂TL-3与HIV-1蛋白酶的结合自由能。异位抑制剂体系中分子片段2-甲基环己醇结合在Exo位,有利于抑制剂被束缚在活性位点附近。异位抑制剂体系中抑制剂TL-3与蛋白酶的结合自由能为-85.78 kcal/mol,活性位抑制剂体系中为-79.45 kcal/mol。这些结果有助于深入了解HIV-1 PR的动力学过程,为设计新型强效抑制剂提供了新见解。
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| 关 键 词： | HIV-I蛋白酶 异位抑制剂 MM-PB/GBSA CUDA Amber ff12SB力场 |
| 收稿时间： | 2013-01-15 |
Long-time molecular dynamics simulation of allosteric inhibitor system of HIV-1 protease |
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| WANG Jia-lei
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MENG Xian-mei
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ZHANG Qing-gang
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ZHANG Yi-ci
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ZHANG Shao-long.Long-time molecular dynamics simulation of allosteric inhibitor system of HIV-1 protease[J].Shandong Science,2013,26(2):1-6. |
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| Authors: | WANG Jia-lei MENG Xian-mei ZHANG Qing-gang ZHANG Yi-ci ZHANG Shao-long |
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| Institution: | College of Physics and Electronics, Shandong Normal University, Jinan 250014, China |
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| Abstract: | We performed 100 nanosecond molecular dynamics simulation for the allosteric inhibitor system and active site inhibitor system of HIV-1 protease on NVIDIA CUDA GPU with new developed force field ff12SB. We also calculated the bind free energy of inhibitor TL-3 and HIV-1 protease with MM-PB/GBSA. Exo site binded fragment 2-methylcyclohexanol is favorable for the binding of inhibitor near the site. The bind free energy of inhibitor TL-3 and protease is -85.78 kcal/mol in allosteric inhibitor system and -79.45 kcal/mol in active site inhibitor system. These results are benefit for the deep learning of the dynamics process of HIV-1 PR, which provides important guidelines for the design of new strong inhibitors. |
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| Keywords: | HIV-1 protease allosteric inhibitor MM-PB/GBSA CUDA Amber ff12SB force field |
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