Real-Time NanoBRET Target Engagement Reveals Permeability-Activity Relationships in BET-Targeting Degraders

Membrane permeability is critical to the function of proteolysis targeting chimeras (PROTACs), yet common methods such as the parallel artificial membrane permeability assay (PAMPA) and Caco-2 transwell assays are limited by their experimental configuration and fail to directly measure a compound's ability to access the cytosolic space of a target cell. Here, we present a method to measure the membrane permeability of unmodified PROTACs and other E3 ligase ligands directly into the cytosol of living cells. By utilizing NanoBRET live-cell target engagement in real time, we quantify permeability rates that match those from transwell systems and reveal rates that transwell setups fail to measure. Several previously undetectable BET-targeting PROTACs, with subtle structural changes, display differing permeabilities that rationalize discrepancies in live-cell degradation efficiency and cytotoxicity. Ultimately, this approach enables quantitative permeability profiling of PROTACs previously considered unmeasurable in transwell assays, providing a powerful tool to guide rational design and lead optimization.