Impact of Linker Composition on VHL PROTAC Cell Permeability

J Med Chem. 2025 Jan 9;68(1):638-657. doi: 10.1021/acs.jmedchem.4c02492. Epub 2024 Dec 18.

Abstract

The discovery of cell permeable and orally bioavailable von Hippel-Lindau (VHL) proteolysis targeting chimeras (PROTACs) is challenging as their structures locates them at, or beyond, the outer limits of oral druggable space. We have designed a set of nine VHL PROTACs and found that the linker had a profound impact on passive cell permeability. Determination of the solution ensembles in a nonpolar solvent revealed that high permeability was correlated to the ability of the PROTACs to adopt folded conformations that have a low solvent accessible 3D polar surface area. Our results suggest that the design of cell permeable VHL PROTACs could focus on linkers that facilitate shielding of polar surface area in the VHL ligand in a nonpolar but not in a polar environment. In addition, we found that not only intramolecular hydrogen bonds, but also NH-π and π-π interactions contribute to the stabilization of low-polarity conformations, and thereby to high cell permeability.

MeSH terms

  • Cell Membrane Permeability* / drug effects
  • Humans
  • Hydrogen Bonding
  • Ligands
  • Proteolysis* / drug effects
  • Von Hippel-Lindau Tumor Suppressor Protein* / chemistry
  • Von Hippel-Lindau Tumor Suppressor Protein* / metabolism

Substances

  • Von Hippel-Lindau Tumor Suppressor Protein
  • VHL protein, human
  • Ligands