自由能量扰动模拟与复制交换分子动力学相结合,可以研究具有分布式结合位点的联体吗?
Christopher Lockhart1, Xingyu Luo1, Audrey Olson1
1School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States.
Journal of chemical information and modeling
|August 2, 2023
概括
复制交换的自由能量扰动 (FEP/REST) 准确地估计了连接体结合的自由能量变化,即使对于具有多种姿势的分子. 这种方法对于分析约束能量和构造组合非常有价值.
科学领域:
- 计算化学是一种计算化学.
- 分子动力学模拟的模拟.
- 生物物理学的生物物理.
背景情况:
- 准确计算连接体结合的自由能量对于药物发现至关重要.
- 自由能量扰动与复制品交换 (FEP/REST) 是计算相对自由能量变化的严格方法.
- 评估FEP/REST适用于具有不同结合姿势的配体的适用性是必不可少的.
研究的目的:
- 为了验证FEP/REST的技术性能和对分布式结合态的配体的融合.
- 估计进口α抑制剂的结合自由能量 (ΔΔG) 的变化.
- 确定FEP/REST模拟对于构造结合分析的有用性.
主要方法:
- 使用FEP/REST模拟,对三种与importin-α结合的抑制剂 (I0,I1,I2) 的两种化学转化进行了模拟.
- 专注于改变连接体极性 (I0 → I1 和 I0 → I2) 的转换.
- 采用多个独立的轨迹,而不是扩展的单个轨迹,以获得更好的FEP/REST战略.
主要成果:
- FEP/REST的实施表现出了适当的形式主义,并产生了趋同的 ΔΔG 估计.
- 转换导致了轻微的结合自由能量变化,I1显示了略微增加的亲和力,I2则减少了亲和力.
- 静电相互作用占主导地位,驱动体变化,而体变化则控制了结合亲和力.
- 根据之前的直接结合模拟,验证了FEP/REST估计值.
结论:
- 从技术上讲,FEP/REST是合理的,并提供结合的有约束力的自由能源估计.
- 该方法适用于研究连接体结合的能量,即使没有定义的姿势,以及微小的亲和力差异 (红色ΔΔG红色0.5 kcal/mol).
- 在FEP/REST模拟中,可以有效地取样连接体结合的形状组合,从而有助于结合分析.
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