arXiv:2512.20958cs.LGcs.AI2025-12被引 1

用强化学习生成可合成、高亲和力的全新药物分子

ReACT-Drug: Reaction-Template Guided Reinforcement Learning for de novo Drug Design

  • 基于反应模板的强化学习,动态生成化学有效分子
  • 生成分子在亲和力和可合成性上表现优异,100%化学有效
  • 无需靶点微调,适合新药研发人员快速探索化学空间

从头药物设计是现代药物开发的关键环节,但如何在庞大的化学空间中找到可合成、高亲和力的候选分子仍具挑战。强化学习通过多目标优化和新化学空间探索,弥补了传统监督学习的不足。本文提出ReACT-Drug,一种全集成、靶点无关的分子设计框架。它利用ESM-2蛋白嵌入从PDB等知识库中识别与目标蛋白相似的蛋白质,并提取其已知配体作为片段初始搜索空间,引导智能体聚焦生物相关子结构。每个片段通过基于ChemBERTa编码的分子,由近端策略优化(PPO)代理在化学有效的反应模板动作空间中迭代演化,生成具有竞争力结合亲和力和高可合成性的全新药物候选分子。所有生成分子均满足MOSES基准的100%化学有效性和新颖性要求。该架构融合结构生物学、深度表征学习与合成规则,展现了自动化理性药物设计的巨大潜力。代码与数据集见https://github.com/YadunandanRaman/ReACT-Drug/。

原文摘要 · Abstract (English)

De novo drug design is a crucial component of modern drug development, yet navigating the vast chemical space to find synthetically accessible, high-affinity candidates remains a significant challenge. Reinforcement Learning (RL) enhances this process by enabling multi-objective optimization and exploration of novel chemical space - capabilities that traditional supervised learning methods lack. In this work, we introduce \textbf{ReACT-Drug}, a fully integrated, target-agnostic molecular design framework based on Reinforcement Learning. Unlike models requiring target-specific fine-tuning, ReACT-Drug utilizes a generalist approach by leveraging ESM-2 protein embeddings to identify similar proteins for a given target from a knowledge base such as Protein Data Base (PDB). Thereafter, the known drug ligands corresponding to such proteins are decomposed to initialize a fragment-based search space, biasing the agent towards biologically relevant subspaces. For each such fragment, the pipeline employs a Proximal Policy Optimization (PPO) agent guiding a ChemBERTa-encoded molecule through a dynamic action space of chemically valid, reaction-template-based transformations. This results in the generation of \textit{de novo} drug candidates with competitive binding affinities and high synthetic accessibility, while ensuring 100\% chemical validity and novelty as per MOSES benchmarking. This architecture highlights the potential of integrating structural biology, deep representation learning, and chemical synthesis rules to automate and accelerate rational drug design. The dataset and code are available at https://github.com/YadunandanRaman/ReACT-Drug/.

从头药物设计强化学习化学生成可合成性

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