New Multiparameter Index Is a Strong Predictor of Oral Bioavailability for Heterobifunctional Degraders

Ligand-directed degraders (LDDs) are heterobifunctional molecules that degrade proteins by engaging the ubiquitin-protein-ligase (E3) system. LDDs (also known as proteolysis-targeting chimeras) consist of a target-engaging moiety, an E3 ligase-binding moiety, and a bridging linker. Due to their size and physicochemical complexity, these molecules do not adhere to well-established rules of lead optimization. Achieving oral bioavailability remains a key challenge in the optimization of LDDs as therapeutic agents. In this study, we build on the previously established Balanced Permeability Index (BPI) (a metric that integrates size, polarity, and lipophilicity) by incorporating an additional descriptor to account for molecular shape. Our new combined metric, termed Bifunctional Bioavailability Index (BBI), can differentiate oral bioavailability of LDDs in our data set more effectively than polarity, lipophilicity, or size separately. Notably, BBI is also more effective than in vitro cell permeability assays in predicting orally bioavailable LDDs. These results support the use of BBI as a computational tool for designing and optimizing bioavailable bifunctional degraders.