用智能体+遗传算法生成更优药物分子,提升结合力和可合成性。
ToolMol: Evolutionary Agentic Framework for Multi-objective Drug Discovery

- 构建智能体驱动的进化框架,通过工具调用精准修改分子结构。
- 在三个靶点上结合力提升超10%,结合自由能预测得分领先35%以上。
- 适合药物研发人员,尤其关注高效生成高质量候选分子的研究者。
大语言模型(LLM)为小分子药物发现带来了新机遇,但现有方法常产生无效或低质量的配体,受限于分子字符串的语法缺陷。本文提出 $ exttt{ToolMol}$,一种用于从头药物设计的进化智能体框架。该框架将多目标遗传算法与智能体式 LLM 操作器结合,迭代优化配体种群。我们构建了基于 RDKit 的完整工具箱,使智能体操作器能一致地执行精确的分子修饰。$ exttt{ToolMol}$ 在多目标性质优化任务中达到当前最佳性能,在三个蛋白靶点上发现的类药物分子结合亲和力比现有方法高出超过10%。其生成的分子在金标准绝对结合自由能评分上也超越现有方法35%以上。通过分析思维链推理轨迹,我们发现工具调用使模型更忠实执行预设修改,高效利用了 LLM 中蕴含的强化学先验知识。
原文摘要 · Abstract (English)
Advances in large language models (LLMs) have recently opened new and promising avenues for small-molecule drug discovery. Yet existing LLM-based approaches for molecular generation often suffer from high rates of invalid and low-quality ligand candidates, a result of the syntactic limitations of current models with regard to molecular strings. In this paper, we introduce $\texttt{ToolMol}$, an evolutionary agentic framework for de novo drug design. $\texttt{ToolMol}$ combines a multi-objective genetic algorithm with an agentic LLM operator that iteratively updates the ligand population. We build a comprehensive toolbox of RDKit-backed functions that allows our agentic operator to consisently make precise ligand modifications. $\texttt{ToolMol}$ achieves state-of-the-art performance on multi-objective property optimization tasks, discovering drug-like and synthesizable ligands that have $>10\%$ stronger predicted binding affinity compared to existing methods, evaluated on three protein targets. $\texttt{ToolMol}$ ligands additionally achieve state-of-the-art results in gold-standard Absolute Binding Free Energy scores, gaining over existing methods by over $35\%$. By studying chain-of-thought reasoning traces, we observe that tool-calling enables the model to more faithfully execute its planned modifications, efficiently exploiting the strong chemical prior knowledge in LLMs.
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