arXiv:2503.08160cs.LG2025-03

基于概念驱动的分子生成框架,提升靶向蛋白药物分子的可合成性与结合力。

Concept-Driven Deep Learning for Enhanced Protein-Specific Molecular Generation

  • 构建蛋白子口袋与分子臂概念神经网络,融合相互作用力与几何互补性
  • 生成骨架的扩散模型使分子可合成性提升6%,类药性提高4%
  • 通过显式交互数据增强可解释性,适合药物设计与分子工程研究

近年来,深度学习在靶向分子生成方面取得显著进展,推动了药物发现的发展。然而,现有方法存在明显局限:原子级生成常缺乏可合成性、类药性和可解释性,而片段生成方法则常忽视影响蛋白质-分子相互作用的综合因素。为此,我们提出一种针对特定蛋白的新型片段生成框架。该方法首先构建基于蛋白子口袋与分子臂概念的神经网络,系统整合相互作用力信息与几何互补性,以采样适配特定蛋白子口袋的分子臂。随后引入扩散模型生成连接这些臂的分子骨架,确保结构完整性和化学多样性。实验表明,该方法显著提升了可合成性与结合亲和力,类药性提升4%,可合成性提高6%。通过概念模型显式融入交互数据,框架增强了可解释性,为分子设计过程提供了重要洞见。

原文摘要 · Abstract (English)

In recent years, deep learning techniques have made significant strides in molecular generation for specific targets, driving advancements in drug discovery. However, existing molecular generation methods present significant limitations: those operating at the atomic level often lack synthetic feasibility, drug-likeness, and interpretability, while fragment-based approaches frequently overlook comprehensive factors that influence protein-molecule interactions. To address these challenges, we propose a novel fragment-based molecular generation framework tailored for specific proteins. Our method begins by constructing a protein subpocket and molecular arm concept-based neural network, which systematically integrates interaction force information and geometric complementarity to sample molecular arms for specific protein subpockets. Subsequently, we introduce a diffusion model to generate molecular backbones that connect these arms, ensuring structural integrity and chemical diversity. Our approach significantly improves synthetic feasibility and binding affinity, with a 4% increase in drug-likeness and a 6% improvement in synthetic feasibility. Furthermore, by integrating explicit interaction data through a concept-based model, our framework enhances interpretability, offering valuable insights into the molecular design process.

分子生成深度学习药物设计可解释性

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