The Challenges of PROTAC Permeability Prediction

Abstract: Cell permeability is a key bottleneck for PROTAC development, and public data available to model it is scarce and inconsistent. We adapt an expert-in-the-loop LLM extraction workflow to mine PAMPA measurements from the primary literature, recovering image-only structures by optical chemical structure recognition and hand-verifying every record, expanding the public record from 31 PROTACs to 87. Ridge models trained on PROTAC-DB 3.0 reach $R² = 0.67$ within that resource but collapse on the newly extracted chemistry ($ρ= 0.12$), while models trained on the new compounds transfer back successfully ($ρ= 0.80$). We conclude that the current composition of the published records, and not dataset size, is limiting the construction of more generalizable models, and we outline what would need to change in reporting practices for better data-driven permeability models.