Diastereomeric Branched-Ester dBET1 Analogs Exhibit Conformation-Dependent Differences in Passive Membrane Permeability

Proteolysis-targeting
chimeras (PROTACs) represent a promising
therapeutic modality, but their clinical translation is often hindered
by poor pharmacokinetic properties associated with their location
in the “beyond Rule of 5” chemical space. Using the
BRD4 degrader dBET1 as a model, this study explored a dual approach
to improve the cellular permeability of PROTACs by combining amide-to-ester
substitution with the strategic linker methylation to induce stereochemistry-driven
conformational modulation. Substitution with ester enhanced both permeability
and degradation potency, while methylation afforded two diastereomers
with different permeability profiles. Steered molecular dynamics and
enhanced conformational sampling in polar and nonpolar environments
revealed distinct chameleonic behaviors, with the more permeable diastereomer 2b adopting folded conformations with a lower solvent-accessible
3D polar surface area in the nonpolar environment. These findings
were supported by 2D NMR and hydrogen-bond acidity analyses (ANMR). Notably, low-energy “congruent
conformation” accessible in both environments was identified
for 2b. This work establishes a viable strategy for the
design of membrane-permeable PROTACs.