Conformational Dynamics in the Cell Membrane Interactions of Bispecific Targeted Degrader Therapeutics

Proteolysis targeting chimeras (PROTACs) offer vast new therapeutic opportunities, but their physicochemical properties are difficult to combine with optimal cell permeability and exposure at the target sites. We have systematically analyzed a data set of more than 3500 PROTACs to investigate how the choice of ubiquitin E3 ligands, linker design, and global molecular properties can be optimized to achieve the desired cell membrane interactions and ultimately membrane permeability and intracellular exposure. We find that conformational flexibility leads to environment-dependent shielding of polar functions and improved interactions with cell membranes but that at the same time, extended, linear conformations within the membrane are beneficial. Linker composition was a major factor in determining the folding propensity. Collectively, our results suggest that strategies to rationally design linkers and to shield polarity selectively within the protein-of-interest (POI) ligand and/or E3 ligand domains rather than more extensive folding may be beneficial in the design of permeable and effective PROTACs.