动态优化肽序列,自动找可改位点并提升多目标性能
PepEVOLVE: Position-Aware Dynamic Peptide Optimization via Group-Relative Advantage
- 通过动态掩码和上下文无关的路由机制,自动发现可优化位点
- 在真实药物靶点测试中平均得分0.8,最优达0.95,优于基线模型
- 适合未知最佳修饰位置的肽类药物设计,提升研发效率
大环肽是一类兼具生物制剂高亲和力与小分子易开发性的新兴药物形式,但其庞大的组合空间及多目标优化需求使先导化合物优化过程缓慢且困难。以往生成方法如PepINVENT需化学家预先指定可变位点,而这些信息往往难以事先确定,且依赖静态预训练和固定优化算法,限制了模型泛化能力。我们提出PepEVOLVE,一种位置感知的动态框架,可同时学习何处修改以及如何动态优化肽序列以实现多目标改进。该方法(i)通过动态掩码和CHUCKLES扰动增强预训练,提升泛化性;(ii)采用无上下文的多臂老虎机路由策略,识别高收益残基;(iii)结合新颖的进化优化算法与组相对优势机制,稳定强化学习更新。在体外评估中,路由策略能可靠聚焦于影响肽性质的化学有意义位点。在治疗性靶点Rev-结合大环肽基准测试中,PepEVOLVE平均得分达0.8(对比PepINVENT的0.6),最优候选者得分为0.95(对比0.87),且在满足结构约束下优化渗透性和脂溶性时收敛步数更少。整体上,PepEVOLVE为未知最优编辑位点的肽类先导优化提供了可复现、高效的实际路径,显著提升多目标设计质量。
原文摘要 · Abstract (English)
Macrocyclic peptides are an emerging modality that combines biologics-like affinity with small-molecule-like developability, but their vast combinatorial space and multi-parameter objectives make lead optimization slow and challenging. Prior generative approaches such as PepINVENT require chemists to pre-specify mutable positions for optimization, choices that are not always known a priori, and rely on static pretraining and optimization algorithms that limit the model's ability to generalize and effectively optimize peptide sequences. We introduce PepEVOLVE, a position-aware, dynamic framework that learns both where to edit and how to dynamically optimize peptides for multi-objective improvement. PepEVOLVE (i) augments pretraining with dynamic masking and CHUCKLES shifting to improve generalization, (ii) uses a context-free multi-armed bandit router that discovers high-reward residues, and (iii) couples a novel evolving optimization algorithm with group-relative advantage to stabilize reinforcement updates. During in silico evaluations, the router policy reliably learns and concentrates probability on chemically meaningful sites that influence the peptide's properties. On a therapeutically motivated Rev-binding macrocycle benchmark, PepEVOLVE outperformed PepINVENT by reaching higher mean scores (approximately 0.8 vs. 0.6), achieving best candidates with a score of 0.95 (vs. 0.87), and converging in fewer steps under the task of optimizing permeability and lipophilicity with structural constraints. Overall, PepEVOLVE offers a practical, reproducible path to peptide lead optimization when optimal edit sites are unknown, enabling more efficient exploration and improving design quality across multiple objectives.
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