基于生成式强化学习的支架跳跃

Scaffold Hopping with Generative Reinforcement Learning.

作者信息

Rossen Luke, Sirockin Finton, Schneider Nadine, Grisoni Francesca

机构信息

Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.

Novartis Biomedical Research, Novartis Campus, 4002 Basel, Switzerland.

出版信息

J Chem Inf Model. 2025 Jul 14;65(13):6513-6525. doi: 10.1021/acs.jcim.5c00029. Epub 2025 Jun 26.

Abstract

Scaffold hopping-the design of novel scaffolds for existing lead candidates-is a multifaceted and nontrivial task, for medicinal chemists and computational approaches alike. Generative reinforcement learning can iteratively optimize desirable properties of designs, thereby offering opportunities to accelerate scaffold hopping. Current approaches confine the generation to a predefined molecular substructure (e.g., a linker or scaffold) for scaffold hopping. This confined generation may limit the exploration of the chemical space and require intricate molecule (dis)assembly rules. In this work, we aim to advance reinforcement learning for scaffold hopping, by allowing "unconstrained", full-molecule generation. This is achieved via the (einforcement Learning for nconstrained caffold opping) approach. RuSH steers the generation toward the design of full molecules having a high three-dimensional and pharmacophore similarity to a reference molecule, but low scaffold similarity. In this first study, we show the flexibility and effectiveness of RuSH in exploring analogs of known scaffold-hops and in designing scaffold-hopping candidates that match known binding mechanisms. Finally, the comparison between RuSH and two established methods highlights the benefit of its unconstrained molecule generation to systematically achieve scaffold diversity while preserving optimal three-dimensional properties.

摘要

支架跳跃——为现有先导化合物设计新型支架——对于药物化学家以及计算方法而言,都是一项多方面且复杂的任务。生成式强化学习可以迭代优化设计的理想属性,从而为加速支架跳跃提供机会。当前的方法将支架跳跃的生成限制在预定义的分子子结构(例如连接子或支架)上。这种受限的生成可能会限制化学空间的探索,并需要复杂的分子(解)组装规则。在这项工作中,我们旨在通过允许“无约束”的全分子生成来推进用于支架跳跃的强化学习。这是通过“无约束支架跳跃的强化学习”(RuSH)方法实现的。RuSH将生成导向与参考分子具有高三维及药效团相似性,但支架相似性低的全分子设计。在这项首次研究中,我们展示了RuSH在探索已知支架跳跃类似物以及设计与已知结合机制匹配的支架跳跃候选物方面的灵活性和有效性。最后,RuSH与两种既定方法的比较突出了其无约束分子生成在系统实现支架多样性同时保留最佳三维属性方面的优势。

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