Much of the PROTAC target-engagement spread is exposure, not E3 recognition
- Twenty PROTACs with varied E3 ligands, linkers and target binders were profiled in intracellular NanoBRET competition assays against cereblon and VHL tracers.
- Apparent potency spread widely when referenced to applied concentration, and passive Caco-2 permeability explained little of it.
- Correcting for measured intracellular unbound exposure shrank the spread dramatically, matching values from permeabilized cells.
💡 Points
Before I read a PROTAC SAR table as E3 affinity, I'd now ask what the cell actually saw. If most of the shift is unbound exposure, linker tweaks that look like potency gains may just be permeability gains, and measuring exposure early keeps us from chasing the wrong variable.