使用图形神经网络进行基于结构的QT延长风险预测:结合体内hERG试验和药监数据的综合方法
Tomoyuki Enokiya1,2, Ryosuke Kunitomo1, Takamasa Yamaguchi2
1Laboratory of Pharmacoinformatics, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka, Japan.
Clinical pharmacology and therapeutics
|February 7, 2026
概括
我们开发了一个图形神经网络 (GNN),通过整合分子结构,体外数据和安全信号来预测药物诱导的QT间隔延长风险. 这种可解释的模型增强了药物安全性评估.
科学领域:
- 药理学 药理学是指药理学的学科.
- 计算化学计算化学
- 药品安全 药品安全
背景情况:
- 药物诱导的QT间隔延长是药物开发中的一个主要安全问题,增加了Torsades de Pointes (TdP) 的风险.
- 实验室hERG抑制试验是早期查的标准,但药监数据提供了对前节律失常风险的补充见解.
- 将分子结构与多种数据源整合在一起,为预测药物心脏毒性提供了一种未被充分利用的方法.
研究的目的:
- 开发一个可解释的图形神经网络 (GNN) 框架来预测QT责任.
- 为了整合体外hERG抑制数据,FDA不良事件报告系统 (FAERS) 信号和分子结构信息.
- 通过模型解释性技术,识别有助于QT责任的结构特征.
主要方法:
- 使用 RDKit 开发了一个 GNN 框架,将 Canonical SMILES 转换为具有编码原子和键级特征的分子图形.
- 对比了四个GNN架构 (GINE,GCN,GraphSAGE,GATv2) 使用分层的五倍交叉验证对4808个具有二进制QT风险标签的小分子进行了比较.
- 利用集成梯度来解释表现最好的GATv2模型,并在独立的hERG测试数据集上验证性能.
主要成果:
- 该GATv2模型实现了0.838的交叉验证ROC-AUC,0.830的PR-AUC和0.756.756的F1得分.
- 在完整的数据集上进行重新训练,提高了ROC-AUC的0.918,PR-AUC的0.908,以及F1得分的0.847.
- 外部验证显示,ROC-AUC为0.859,灵敏度为0.80,特异性为0.82;原子度和数是关键预测因素.
结论:
- 开发的GNN框架有效地整合了结构和药理数据,以预测QT风险.
- 该模型的可解释性为药物开发提供了一个透明的,基于结构的决策支持工具.
- 这种方法与监管指南 (ICH S7B/E14) 和CIPA等加强药物安全评估的倡议保持一致.
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