机器学习揭示了SARS-CoV-2 Mpro 抑制剂的结合性亲和和药物相似性之间的对抗性趋势
Anacleto Silva de Souza1, Vitor Martins de Freitas Amorim1, Eduardo Pereira Soares1
1Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo 05508-000, Brazil.
设计SARS-CoV-2 Mpro抑制剂需要平衡目标亲和力和类似药物的特性. 机器学习和模拟显示,优化结合可能会对药理动力学产生负面影响,突出显示需要一种平衡的计算方法.
科学领域:
- 计算化学是一种计算化学.
- 药物发现 药物发现
- 在药理学中的机器学习.
背景情况:
- SARS-CoV-2 主蛋白酶 (Mpro) 是抗病毒疗法的关键标,但由于需要优化标亲和力和药物样性质,开发有效的抑制剂具有挑战性.
- 很少有Mpro抑制剂在临床上取得进展,这表明了解如何在药物设计过程中平衡药理动力学 (PD) 和药理动力学 (PK) 特性存在差距.
研究的目的:
- 整合机器学习 (ML),分子对接和分子动力学 (MD) 模拟,以调查Mpro抑制剂设计中的PD和PK特性之间的相互作用.
- 根据实验数据和结构见解,开发预测ML模型来对Mpro抑制剂进行分类.
- 确定影响结合亲和和药物相似性的关键分子特征和相互作用.
主要方法:
- 开发了ML模型,包括支持矢量机 (SVM) 和后勤回归,以使用分子描述符和MD模拟数据对Mpro抑制剂进行分类.
- 利用分子对接和MD模拟来分析Mpro子站点 (S2,S3/S4) 内的结构见解和相互作用.
- 使用训练和测试准确度以及接收器操作特征 (ROC) 曲线下的区域 (AUC) 评估了ML模型的性能.
主要成果:
- 通过ML模型实现了强大的性能:SVM (训练精度0.84,ROC AUC 0.91;测试精度0.79,ROC AUC 0.86) 和后勤回归 (训练精度0.78,ROC AUC 0.85;测试精度0.76,ROC AUC 0.83).
- 观察到PD和PK特性之间的对抗性趋势:水友特征改善了结合亲和力,但恶化了PK,而S2和S3/S4亚位点的相互作用对结合至关重要.
- 使用集成的ML/MD方法首次证明了PK和PD特征之间的对抗关系.
结论:
- 均衡的方法对于Mpro抑制剂设计至关重要,战略地准S2和S3/S4等子站点,以优化结合亲和力和药物相似性.
- 集成的ML/MD计算框架为设计下一代具有临床前和临床潜力的SARS-CoV-2 Mpro抑制剂提供了合理的方法.
- 这项研究为击中到的优化提供了宝贵的见解,指导了新型抗病毒化合物的开发.
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