arXiv:2505.08774q-bio.BMcs.LG2025-05被引 5

提出可精细控制合成难易度的分子生成框架,兼顾高效设计与实际可合成性。

Generative Molecular Design with Steerable and Granular Synthesizability Control

  • 通过可调节的合成约束实现多目标分子生成
  • 在1420亿分子库中仅用8GB显卡生成32万分子并发现有效候选
  • 适合药物研发中需精准控制反应路径的场景

设计兼具优异性质和高可合成性的分子是药物发现的核心挑战。现有方法虽能生成分子并预测合成路线,但对合成难易度的灵活控制仍不足,且难以应对超大规模化学空间(如百亿级)的虚拟筛选。本文提出一种统一框架,结合合成约束分子设计与超大规模虚拟筛选,实现可调节、细粒度的合成可行性控制。生成分子满足多参数优化目标,其合成路线可包含或排除特定反应、使用特定原料、最小化步骤数。在针对BRD4的内部实验中,设计出依赖特定反应与原料的分子,成功合成了六种化合物,并发现了两种微摩尔级结合物。进一步验证表明,该框架可高效导航超大可定制化学空间:在Chemspace Freedom 4.0(1420亿分子)中,单张消费级显卡(8GB显存)生成约32万分子(占0.00023%),并在60个合成候选中识别出一个微摩尔级Wee1抑制剂。该统一框架实现了新颖可合成分子生成与目录就绪候选检索,为缓解合成瓶颈提供灵活解决方案。

原文摘要 · Abstract (English)

Designing molecules that are both property-optimal and readily synthesizable is a central challenge in drug discovery. Existing works that do consider synthesizability can jointly output predicted synthesis routes for generated molecules. However, there has been minimal attention in addressing the ease of synthesis and with flexibility to incorporate desired reaction constraints. On the other hand, virtual screening searches for commercially available compounds, but imposes challenges when scaling to ultra-large (billion-size and beyond) chemical spaces. Here, we propose a generative design framework that unifies synthesis-constrained molecular design and ultra-large-scale virtual screening through steerable and granular synthesizability control. Generated molecules satisfy arbitrary multi-parameter optimization objectives with predicted synthesis routes satisfying mix-and-match constraints: including or avoiding certain reactions, incorporating specific building blocks, and minimizing synthesis route length. In an end-to-end in-house campaign targeting BRD4, we designed molecules synthesizable with specific selected reactions and building blocks, synthesized all six selected compounds, and identified two micromolar binders. We further demonstrate that reaction control enables efficient navigation of ultra-large make-on-demand chemical spaces to identify property-optimal candidates. By applying our framework to Chemspace's Freedom 4.0 make-on-demand space (142 billion molecules), we generated ~320k molecules (0.00023% of the library) on a single consumer-grade GPU (with only 8 GB GPU memory) and identified a micromolar Wee1 binder amongst 60 synthesized candidates. The single unified framework thus enables generating novel synthesizable molecules and retrieving catalogue-ready candidates, offering a flexible solution to mitigating the synthesizability bottleneck.

分子生成合成控制药物发现超大化学空间

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