Peptide2Mol: A Diffusion Model for Generating Small Molecules as Peptide Mimics for Targeted Protein Binding

• URL: http://arxiv.org/abs/2511.04984v1
• Date: Fri, 07 Nov 2025 05:02:51 GMT
• Title: Peptide2Mol: A Diffusion Model for Generating Small Molecules as Peptide Mimics for Targeted Protein Binding
• Authors: Xinheng He, Yijia Zhang, Haowei Lin, Xingang Peng, Xiangzhe Kong, Mingyu Li, Jianzhu Ma,
• Abstract summary: We present an E(3)-equivariant graph neural network diffusion model that generates small molecules by referencing both the original peptide binders and their surrounding protein pocket environments.<n>The model achieves state-of-the-art performance in non-autoregressive generative tasks and produces molecules with similarity to the original peptide binder.
• Score: 30.495863416651414
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Structure-based drug design has seen significant advancements with the integration of artificial intelligence (AI), particularly in the generation of hit and lead compounds. However, most AI-driven approaches neglect the importance of endogenous protein interactions with peptides, which may result in suboptimal molecule designs. In this work, we present Peptide2Mol, an E(3)-equivariant graph neural network diffusion model that generates small molecules by referencing both the original peptide binders and their surrounding protein pocket environments. Trained on large datasets and leveraging sophisticated modeling techniques, Peptide2Mol not only achieves state-of-the-art performance in non-autoregressive generative tasks, but also produces molecules with similarity to the original peptide binder. Additionally, the model allows for molecule optimization and peptidomimetic design through a partial diffusion process. Our results highlight Peptide2Mol as an effective deep generative model for generating and optimizing bioactive small molecules from protein binding pockets.

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