用深度学习精准预测GPCR配体,加速新药发现
GPCR-Filter: a deep learning framework for efficient and precise GPCR modulator discovery
- 结合蛋白质语言模型与图神经网络,融合受体与配体信息
- 在超9万对实验数据上训练,对未见受体/配体泛化能力强
- 成功发现5-HT1A受体微摩尔级激动剂,化学结构新颖
G蛋白偶联受体(GPCRs)调控多种生理过程,是现代药物研发的核心靶点。然而,其激活常由复杂的变构效应引发,而非直接结合亲和力,传统筛选方法耗时、昂贵且难以捕捉动态特性。本文提出GPCR-Filter,一个专为GPCR调节剂发现设计的深度学习框架。构建了超过9万对经实验验证的GPCR-配体数据集,作为训练与评估基础。该框架融合ESM-3蛋白语言模型生成高保真受体序列表征,结合图神经网络编码配体结构,并通过注意力机制融合,学习受体-配体功能关系。在多个评估场景中,其性能持续优于现有化合物-蛋白相互作用模型,并展现出对未见受体与配体的强大泛化能力。尤其成功识别出具有不同化学骨架的5-HT₁ₐ受体微摩尔级激动剂。结果表明,GPCR-Filter是一种可扩展、高效的计算方法,推动复杂信号系统的AI辅助药物研发。
原文摘要 · Abstract (English)
G protein-coupled receptors (GPCRs) govern diverse physiological processes and are central to modern pharmacology. Yet discovering GPCR modulators remains challenging because receptor activation often arises from complex allosteric effects rather than direct binding affinity, and conventional assays are slow, costly, and not optimized for capturing these dynamics. Here we present GPCR-Filter, a deep learning framework specifically developed for GPCR modulator discovery. We assembled a high-quality dataset of over 90,000 experimentally validated GPCR-ligand pairs, providing a robust foundation for training and evaluation. GPCR-Filter integrates the ESM-3 protein language model for high-fidelity GPCR sequence representations with graph neural networks that encode ligand structures, coupled through an attention-based fusion mechanism that learns receptor-ligand functional relationships. Across multiple evaluation settings, GPCR-Filter consistently outperforms state-of-the-art compound-protein interaction models and exhibits strong generalization to unseen receptors and ligands. Notably, the model successfully identified micromolar-level agonists of the 5-HT\textsubscript{1A} receptor with distinct chemical frameworks. These results establish GPCR-Filter as a scalable and effective computational approach for GPCR modulator discovery, advancing AI-assisted drug development for complex signaling systems.
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