arXiv:2604.23307cs.LGcs.AI2026-04ICML被引 4

用组合搜索生成能同时作用两个靶点的药物分子,兼顾活性与可合成性。

CombiMOTS: Combinatorial Multi-Objective Tree Search for Dual-Target Molecule Generation

论文配图:CombiMOTS: Combinatorial Multi-Objective Tree Search for Dual-Target Molecule Generation
图 1 · 摘自论文原文
  • 基于向量优化的蒙特卡洛树搜索,同时优化结合能力和分子性质。
  • 在真实数据库上生成的分子兼具高对接得分、多样性和平衡药理特性。
  • 适合需要多靶点药物设计的研究者,尤其关注合成可行性与疗效平衡。

双靶点分子生成旨在发现可同时作用于两个靶蛋白的化合物,具有提升治疗效率、安全性及抗耐药性的潜力。现有方法存在两大挑战:一是将复杂的双目标优化问题简化为单目标组合,难以捕捉靶点结合与分子性质间的权衡;二是通常未将合成规划融入生成过程。为此,本文提出CombiMOTS,一种基于帕累托蒙特卡洛树搜索(PMCTS)的框架,可在可合成片段空间中探索,并通过向量化优化约束同时建模靶点亲和力与理化性质。在真实世界数据库上的大量实验表明,CombiMOTS生成的新型双靶点分子具有高对接分数、增强的多样性以及均衡的药理特征,展现出作为双靶点药物发现强大工具的潜力。代码与数据已公开于 https://github.com/Tibogoss/CombiMOTS。

原文摘要 · Abstract (English)

Dual-target molecule generation, which focuses on discovering compounds capable of interacting with two target proteins, has garnered significant attention due to its potential for improving therapeutic efficiency, safety and resistance mitigation. Existing approaches face two critical challenges. First, by simplifying the complex dual-target optimization problem to scalarized combinations of individual objectives, they fail to capture important trade-offs between target engagement and molecular properties. Second, they typically do not integrate synthetic planning into the generative process. This highlights a need for more appropriate objective function design and synthesis-aware methodologies tailored to the dual-target molecule generation task. In this work, we propose CombiMOTS, a Pareto Monte Carlo Tree Search (PMCTS) framework that generates dual-target molecules. CombiMOTS is designed to explore a synthesizable fragment space while employing vectorized optimization constraints to encapsulate target affinity and physicochemical properties. Extensive experiments on real-world databases demonstrate that CombiMOTS produces novel dual-target molecules with high docking scores, enhanced diversity, and balanced pharmacological characteristics, showcasing its potential as a powerful tool for dual-target drug discovery. The code and data is accessible through https://github.com/Tibogoss/CombiMOTS.

分子生成双靶点蒙特卡洛药物设计

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