11分钟的无偏向分子动力学 药物解锁 揭示过渡状态 稳定相互作用
1Michigan State University , East Lansing, Michigan 48823, United States.
Journal of the American Chemical Society
|January 6, 2018
概括
本研究使用WExplore算法在药理上相关的时间尺度上进行了第一个完整的药物解锁模拟. 这些发现揭示了多种解绑途径,并提供了通过动力学优化药物有效性的见解.
科学领域:
- 计算化学和分子动力学
- 药理学和药物发现
背景情况:
- 对药物的特异性和疗效至关重要.
- 与热力学计算相比,模拟药物解锁在计算上具有挑战性.
- 可溶性环氧化酶 (sEH) 是优化疗效的临床相关酶标.
研究的目的:
- 在没有偏差力的情况下,在药物相关的时间尺度上进行第一个药物解结的完整模拟.
- 研究抑制剂TPPU从可溶性环氧化酶 (sEH) 的解结过程.
- 开发和应用构造空间网络来分析解绑路径和罕见事件.
主要方法:
- 使用基于权重组合的算法WExplore进行无偏的模拟.
- 在药理上相关的时间尺度上模拟了TPPU与sEH的解结.
- 采用形态空间网络来分析结,溶解和不平衡的自由能量.
主要成果:
- 使用形态空间网络观察到多个解结路径和罕见事件,包括连接物方向逆转.
- 预测了过渡状态组合,并确定了稳定其关键的蛋白质 - 连接体相互作用.
- 从模拟中计算出42秒的停留时间 (具有广泛的误差范围),接近实验中的11分钟.
结论:
- 构造空间网络为可视化和分析复杂的分子过程提供了强大的工具.
- 这项研究证明了模拟复杂分子过程的可行性,用于更广泛的时间尺度.
- 这些发现为SEH抑制剂的动力学优化提供了洞察力,并为药物修改策略提出了新的假设.
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