graph-based deep generative model
De novo PROTAC design using graph-based deep generative models
PROteolysis TArgeting Chimeras (PROTACs) are an emerging therapeutic modality for degrading a protein of interest (POI) by marking it for degradation by the proteasome. Recent developments in artificial intelligence (AI) suggest that deep generative models can assist with the de novo design of molecules with desired properties, and their application to PROTAC design remains largely unexplored. We show that a graph-based generative model can be used to propose novel PROTAC-like structures from empty graphs. Our model can be guided towards the generation of large molecules (30–140 heavy atoms) predicted to degrade a POI through policy-gradient reinforcement learning (RL). Rewards during RL are applied using a boosted tree surrogate model that predicts a molecule's degradation potential for each POI.