Linker-Determined Folding and Hydrophobic Interactions Explain a Major Difference in PROTAC Cell Permeability

Area of Science:

• Biochemistry
• Chemical Biology
• Drug Discovery

Background:

• PROTACs (proteolysis-targeting chimeras) require low polar surface area for efficient passive cell permeability.
• Linker design is critical for PROTAC conformational flexibility and cell penetration.

Purpose of the Study:

• To investigate how linker modifications in VHL PROTACs affect their conformational behavior and cell permeability.
• To elucidate the relationship between PROTAC conformation, solvent accessibility, and passive cell permeability.

Main Methods:

• Molecular dynamics (MD) simulations to analyze PROTAC conformational dynamics.
• NMR spectroscopy to determine PROTAC structures in different environments.
• Comparison of two VHL PROTACs with differing linker chemistries (alkyl vs. PEG).

Main Results:

• The alkyl-linker PROTAC exhibited environment-dependent conformations, adopting extended, polar forms in nonpolar media (low permeability) and folded, less polar forms in water.
• The PEG-linker PROTAC maintained similar conformations and polarities across polar and nonpolar environments, correlating with high permeability.
• Hydrophobic interactions significantly influenced the conformational behavior of the alkyl-linker PROTAC.

Conclusions:

• PROTAC linker chemistry profoundly impacts conformational adaptability and, consequently, cell permeability.
• Environment-dependent conformational changes in PROTACs can be a major determinant of their passive cell permeability.
• Rational design of PROTAC linkers, considering environmental conformational effects, is crucial for optimizing cell permeability in drug discovery.