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arXiv · 2412.09661

Language model driven: a PROTAC generation pipeline with dual constraints of structure and property

Jinsong Shao·Qineng Gong·Zeyu Yin·Yu Chen·Yajie Hao·Lei Zhang·Linlin Jiang·Min Yao·Jinlong Li·Fubo Wang·Li Wang
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Abstract

The imperfect modeling of ternary complexes has limited the application of computer-aided drug discovery tools in PROTAC research and development. In this study, an AI-assisted approach for PROTAC molecule design pipeline named LM-PROTAC was developed, which stands for language model driven Proteolysis Targeting Chimera, by embedding a transformer-based generative model with dual constraints on structure and properties, referred to as the DCT. This study utilized the fragmentation representation of molecules and developed a language model driven pipeline. Firstly, a language model driven affinity model for protein compounds to screen molecular fragments with high affinity for the target protein. Secondly, structural and physicochemical properties of these fragments were constrained during the generation process to meet specific scenario requirements. Finally, a two-round screening of the preliminary generated molecules using a multidimensional property prediction model to generate a batch of PROTAC molecules capable of degrading disease-relevant target proteins for validation in vitro experiments, thus achieving a complete solution for AI-assisted PROTAC drug generation. Taking the tumor key target Wnt3a as an example, the LM-PROTAC pipeline successfully generated PROTAC molecules capable of inhibiting Wnt3a. The results show that DCT can efficiently generate PROTAC that targets and hydrolyses Wnt3a.

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Jinsong Shao, Qineng Gong, Zeyu Yin, Yu Chen, Yajie Hao, Lei Zhang, Linlin Jiang, Min Yao, Jinlong Li, Fubo Wang, Li Wang. 2024-12-12. Language model driven: a PROTAC generation pipeline with dual constraints of structure and property. https://arxiv.org/abs/2412.09661

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