arXiv:2505.02887q-bio.BMcs.AI2025-05被引 3

用深度学习设计高亲和力靶向肽,突破自然变体有限的瓶颈。

CreoPep: A Universal Deep Learning Framework for Target-Specific Peptide Design and Optimization

  • 结合掩码语言建模与渐进式掩码,生成多样肽突变体。
  • 对α7烟碱受体抑制剂实现亚微摩尔级活性,验证效果显著。
  • 可发现新型结构基序,适合药物研发人员快速筛选新肽药。

靶向肽(如Conotoxins)对离子通道和受体具有极高的结合亲和力与选择性,但其治疗潜力受限于天然变体多样性不足及传统优化策略耗时费力。本文提出CreoPep,一种基于深度学习的条件生成框架,融合掩码语言建模与渐进式掩码策略,设计高亲和力肽突变体并揭示新型结构基序。该方法采用整合增强流程,结合FoldX能量筛选与温度控制的多项式采样,生成在结构和功能上均具多样性的肽,同时保持关键药理性质。通过设计针对α7烟碱乙酰胆碱受体的Conotoxin抑制剂,在电生理实验中达到亚微摩尔级效力。结构分析显示,CreoPep生成的变异体既保留保守结合模式,也出现新型结合方式,包括无二硫键形式,突破传统设计范式。整体而言,CreoPep提供了一个稳健且通用的平台,连接计算设计与实验验证,加速下一代肽类药物的发现。

原文摘要 · Abstract (English)

Target-specific peptides, such as conotoxins, exhibit exceptional binding affinity and selectivity toward ion channels and receptors. However, their therapeutic potential remains underutilized due to the limited diversity of natural variants and the labor-intensive nature of traditional optimization strategies. Here, we present CreoPep, a deep learning-based conditional generative framework that integrates masked language modeling with a progressive masking scheme to design high-affinity peptide mutants while uncovering novel structural motifs. CreoPep employs an integrative augmentation pipeline, combining FoldX-based energy screening with temperature-controlled multinomial sampling, to generate structurally and functionally diverse peptides that retain key pharmacological properties. We validate this approach by designing conotoxin inhibitors targeting the $α$7 nicotinic acetylcholine receptor, achieving submicromolar potency in electrophysiological assays. Structural analysis reveals that CreoPep-generated variants engage in both conserved and novel binding modes, including disulfide-deficient forms, thus expanding beyond conventional design paradigms. Overall, CreoPep offers a robust and generalizable platform that bridges computational peptide design with experimental validation, accelerating the discovery of next-generation peptide therapeutics.

肽设计深度学习药物发现生成模型

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