提出CMOMO框架,实现多属性优化与药物约束的动态平衡。
Balancing property optimization and constraint satisfaction for constrained multi-property molecular optimization
- 采用动态协同优化机制处理多种约束条件。
- 在两个基准任务中超越五种先进方法,显著提升分子性能。
- 适用于真实药物靶点发现,可生成高潜力候选分子。
分子优化旨在从庞大的化学空间中发现更优分子,是化学研发的关键步骤。尽管人工智能技术在该任务中已表现出高效性,但多数方法未兼顾属性优化与约束满足,难以获得兼具理想性质和合规性的高质量分子。为此,本文提出约束型多属性分子优化框架(CMOMO),一种灵活高效的算法,可在满足多种药物类约束的同时协同优化多个分子属性。CMOMO基于动态协同优化机制,自适应处理不同场景下的约束;同时在隐式分子空间中通过分子演化过程,协作评估多个属性以引导搜索。实验表明,CMOMO在两个基准任务中优于五种主流方法,实现对多个非生物活性属性的联合优化并满足两项结构约束。此外,在两个实际任务中验证其应用价值:成功发现β2-肾上腺素受体GPCR的候选配体及糖原合成酶激酶-3β的候选抑制剂,均具备优异性质且符合药物类约束。
原文摘要 · Abstract (English)
Molecular optimization, which aims to discover improved molecules from a vast chemical search space, is a critical step in chemical development. Various artificial intelligence technologies have demonstrated high effectiveness and efficiency on molecular optimization tasks. However, few of these technologies focus on balancing property optimization with constraint satisfaction, making it difficult to obtain high-quality molecules that not only possess desirable properties but also meet various constraints. To address this issue, we propose a constrained multi-property molecular optimization framework (CMOMO), which is a flexible and efficient method to simultaneously optimize multiple molecular properties while satisfying several drug-like constraints. CMOMO improves multiple properties of molecules with constraints based on dynamic cooperative optimization, which dynamically handles the constraints across various scenarios. Besides, CMOMO evaluates multiple properties within discrete chemical spaces cooperatively with the evolution of molecules within an implicit molecular space to guide the evolutionary search. Experimental results show the superior performance of the proposed CMOMO over five state-of-the-art molecular optimization methods on two benchmark tasks of simultaneously optimizing multiple non-biological activity properties while satisfying two structural constraints. Furthermore, the practical applicability of CMOMO is verified on two practical tasks, where it identified a collection of candidate ligands of $β$2-adrenoceptor GPCR and candidate inhibitors of glycogen synthase kinase-3$β$ with high properties and under drug-like constraints.
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