利用强化学习和基于结构的药物设计鉴定纳摩尔级别的腺苷 A 受体配体。

Identification of nanomolar adenosine A receptor ligands using reinforcement learning and structure-based drug design.

作者信息

Thomas Morgan, Matricon Pierre G, Gillespie Robert J, Napiórkowska Maja, Neale Hannah, Mason Jonathan S, Brown Jason, Harwood Kaan, Fieldhouse Charlotte, Swain Nigel A, Geng Tian, O'Boyle Noel M, Deflorian Francesca, Bender Andreas, de Graaf Chris

机构信息

Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK.

Nxera Pharma, Steinmetz Building, Granta Park, Great Abington, Cambridge, UK.

出版信息

Nat Commun. 2025 Jul 1;16(1):5485. doi: 10.1038/s41467-025-60629-0.

Abstract

Generative chemical language models (CLMs) have demonstrated success in learning language-based molecular representations for de novo drug design. Here, we integrate structure-based drug design (SBDD) principles with CLMs to go from protein structure to novel small-molecule ligands, without a priori knowledge of ligand chemistry. Using Augmented Hill-Climb, we successfully optimise multiple objectives within a practical timeframe, including protein-ligand complementarity. Resulting de novo molecules contain known or promising adenosine A receptor ligand chemistry that is not available in commercial vendor libraries, accessing commercially novel areas of chemical space. Experimental validation demonstrates a binding hit rate of 88%, with 50% having confirmed functional activity, including three nanomolar ligands and two novel chemotypes. The two strongest binders are co-crystallised with the A receptor, revealing their binding mechanisms that can be used to inform future iterations of structure-based de novo design, closing the AI SBDD loop.

摘要

生成式化学语言模型(CLMs)已在从头药物设计中学习基于语言的分子表示方面取得成功。在这里,我们将基于结构的药物设计(SBDD)原则与CLMs相结合,从蛋白质结构出发设计新型小分子配体,而无需预先了解配体化学。通过增强爬山法,我们在实际时间范围内成功优化了多个目标,包括蛋白质-配体互补性。所得的从头设计分子包含商业供应商库中没有的已知或有前景的腺苷A受体配体化学结构,进入了化学空间中的商业新领域。实验验证表明结合命中率为88%,其中50%具有已确认的功能活性,包括三种纳摩尔级配体和两种新型化学类型。两种最强的结合剂与A受体共结晶,揭示了它们的结合机制,可用于为基于结构的从头设计的未来迭代提供信息,从而闭合人工智能SBDD循环。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6d3e/12216625/68b33ec6f339/41467_2025_60629_Fig1_HTML.jpg

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