用AI生成更有效、更可合成的药物分子,提升成功率。
Toward Closed-loop Molecular Discovery via Language Model, Property Alignment and Strategic Search
- 结合语言模型与搜索策略,智能组装分子片段。
- 生成分子在亲和力、成药性上分别提升7.85%、11.10%。
- 适合需要高效设计新药分子的研究者使用。
药物发现过程耗时且成本高昂,传统高通量筛选和基于对接的虚拟筛选面临成功率低和扩展性差的问题。近年来,自回归、扩散和流模型等生成方法突破了枚举式筛选的限制,实现了从头药物分子设计。然而这些模型普遍存在泛化能力不足、可解释性差,且过度关注结合亲和力而忽视关键药代动力学性质的问题,限制了其实际应用。本文提出Trio框架,整合基于片段的分子语言建模、强化学习与蒙特卡洛树搜索,实现高效且可解释的闭环靶向分子设计。通过三大组件,Trio支持上下文感知的片段组装,确保理化性质与合成可行性,并平衡新化学类型探索与结合口袋内潜力中间体的利用。实验表明,Trio能稳定生成化学有效且药理性能优越的配体,相比先进方法在结合亲和力(+7.85%)、类药性(+11.10%)和合成可及性(+12.05%)上均有显著提升,同时分子多样性扩大四倍以上。Trio融合泛化性、合理性与可解释性,建立新的闭环生成范式,为下一代AI驱动药物发现提供变革性基础。
原文摘要 · Abstract (English)
Drug discovery is a time-consuming and expensive process, with traditional high-throughput and docking-based virtual screening hampered by low success rates and limited scalability. Recent advances in generative modelling, including autoregressive, diffusion, and flow-based approaches, have enabled de novo ligand design beyond the limits of enumerative screening. Yet these models often suffer from inadequate generalization, limited interpretability, and an overemphasis on binding affinity at the expense of key pharmacological properties, thereby restricting their translational utility. Here we present Trio, a molecular generation framework integrating fragment-based molecular language modeling, reinforcement learning, and Monte Carlo tree search, for effective and interpretable closed-loop targeted molecular design. Through the three key components, Trio enables context-aware fragment assembly, enforces physicochemical and synthetic feasibility, and guides a balanced search between the exploration of novel chemotypes and the exploitation of promising intermediates within protein binding pockets. Experimental results show that Trio reliably achieves chemically valid and pharmacologically enhanced ligands, outperforming state-of-the-art approaches with improved binding affinity (+7.85%), drug-likeness (+11.10%) and synthetic accessibility (+12.05%), while expanding molecular diversity more than fourfold. By combining generalization, plausibility, and interpretability, Trio establishes a closed-loop generative paradigm that redefines how chemical space can be navigated, offering a transformative foundation for the next era of AI-driven drug discovery.
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