药物设计的结构动力学关系由一个PLS模型揭示,该模型具有基于逆合成的预训练分子表示和分子动力学模拟
Feng Zhou1, Shiqiu Yin1, Yi Xiao1
1Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China.
本研究引入了一种机器学习方法,使用基于回复合成的分子表示来准确预测药物解离速率常数 (koff). 这种方法通过结合机器学习,分子动力学和相互作用指纹来提高运动药物设计,以提高选择性.
科学领域:
- 计算化学计算化学
- 药物设计 药物设计
- 机器学习 机器学习
背景情况:
- 运动性质在药物设计中越来越重要.
- 预测药物解离速率常数 (koff) 对于优化药物疗效和选择性至关重要.
- 现有的分子表示可能无法完全捕捉准确的动力预测所需的复杂性.
研究的目的:
- 开发和验证一种机器学习 (ML) 模型,用于预测药物抑制剂的解离率常数 (koff).
- 评估基于回复合成的新型预训练分子表示 (RPM) 与其他方法的性能.
- 将ML与分子动力学 (MD) 模拟和相互作用指纹 (IFP) 结合起来,以了解运动性质和选择性.
主要方法:
- 训练了一种ML模型,使用501个抑制剂在55个蛋白质中与RPM.
- 预测的Koff值为38N-终端域的热冲击蛋白90α (N-HSP90) 抑制剂.
- 利用加速的MD计算128个N-HSP90抑制剂的相对保留时间 (RT) 和蛋白质-连接体相互作用指纹 (IFP).
- 用两种新的N-HSP90抑制剂与实验koff值验证了ML模型.
主要成果:
- 基于RPM的ML模型准确地预测了N-HSP90抑制剂的Koff值.
- RPM的性能优于其他分子表示 (GEM,MPG,RDKit描述器).
- 在模拟,预测和实验值之间观察到高相关性.
- IFP提供了关于运动性质和选择性的机制的见解.
结论:
- ML,MD模拟和IFP的结合方法有效地帮助设计具有特定动力特性和选择性的药物.
- 开发的ML模型证明了对预测其他蛋白质的koff值的可转移性.
- 这种方法显著增强了基于动力学的药物设计领域.
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