Advancing PROTAC Discovery Through Artificial Intelligence: Opportunities, Challenges, and Future Directions

Proteolysis Targeting Chimeras (PROTACs) represent a transformative modality in drug discovery, enabling the selective degradation of disease-relevant proteins through the ubiquitin proteasome system. Despite their therapeutic promise, the rational design of PROTACs remains a complex and resource-intensive process, involving multiple parameters such as target and ligase compatibility, ternary complex formation, linker optimization, and degradation efficiency. Recent advances in artificial intelligence (AI) have provided new strategies to address these obstacles, ranging from structure-based modeling of ternary complexes to degradability prediction, generative linker design, and pharmacokinetic property estimation. This review aims to explore how AI can be leveraged directly or indirectly in the PROTAC development pipeline. First, we analyze existing applications of AI, such as ternary complex structure prediction, degradability prediction, linker design, and ADME prediction. We further discuss how other approaches from the related fields may be adapted to address the challenges of PROTAC discovery. Lastly, we discuss challenges that current AI models face, such as limited data, poor interpretability, and low generalizability. Taken together, overcoming these barriers will enable AI-driven strategies to accelerate PROTAC discovery and provide a more rational framework for targeted protein degrader development.