SynPROTAC: synthesizable PROTACs design through synthesis constrained generative model and reinforcement learning

Xu, M.; Deng, Q.; Zhang, H.; Qiao, A.; Wang, Z.; Hsieh, C.-Y.; Chen, H.; lei, j.

doi:10.64898/2025.12.10.693572

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bioRxiv · 10.64898/2025.12.10.693572

SynPROTAC: synthesizable PROTACs design through synthesis constrained generative model and reinforcement learning

Xu, M.·Deng, Q.·Zhang, H.·Qiao, A.·Wang, Z.·Hsieh, C.-Y.·Chen, H.·lei, j.

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Abstract

Protein hydrolysis targeting chimeric (PROTAC) has emerged as a promising technology in degrading disease-related proteins for drug design. Recent deep generative models can accelerate PROTAC design, but the generated molecules are often difficult to synthesize. Here we develop SynPROTAC model, which employs Graphormer encoded warhead or E3 ligand as input, and autoregressively samples reaction templates and building blocks through transformer based decoder for PROTAC construction. The model is also fine-tuned via reinforcement learning for generating PROTACs with favorable binding properties. The comprehensive evaluations indicated that SynPROTAC is capable of generating novel PROTACs with feasible synthetic routes, reasonable physico-chemical and binding related properties.

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Xu, M., Deng, Q., Zhang, H., Qiao, A., Wang, Z., Hsieh, C.-Y., Chen, H., lei, j.. 2025-12-12. SynPROTAC: synthesizable PROTACs design through synthesis constrained generative model and reinforcement learning. https://doi.org/10.64898/2025.12.10.693572

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