Linker-dependent folding rationalizes PROTAC cell permeability

Proteolysis targeting chimeras (PROTACs) must be cell permeable to reach their target proteins. This is challenging as the bivalent structure of PROTACs puts them in chemical space at, or beyond, the outer limits of oral druggable space. We used NMR spectroscopy and MD simulations independently to gain insight into the origin of the differences in cell permeability displayed by three flexible cereblon PROTACs having closely related structures. Both methods revealed that the propensity of the PROTACs to adopt folded conformations with low solvent accessible 3D polar surface area in an apolar environment correlated to high cell permeability. The flexibility of the linker appeared essential for the PROTACs to populate folded conformations stabilized by intramolecular hydrogen bonds, pi-pi and van der Waals interactions. We conclude that MD simulations may be used for the prospective ranking of cell permeability in the design of cereblon PROTACs.