Amide-to-Ester Substitution as a Strategy for Optimizing PROTAC Permeability and Cellular Activity.

Area of Science:

• Medicinal Chemistry
• Drug Discovery
• Chemical Biology

Background:

• Predicting drug-like properties for "beyond Rule of 5" Proteolysis Targeting Chimeras (PROTACs) remains challenging.
• Amide couplings, common in PROTAC synthesis, can negatively impact absorption, distribution, metabolism, and excretion (ADME) properties.
• Developing strategies to improve PROTAC physicochemical properties is crucial for advancing their therapeutic potential.

Purpose of the Study:

• To investigate the impact of bioisosteric amide-to-ester substitution on PROTAC physicochemical properties and bioactivity.
• To design and evaluate novel ester-substituted PROTACs for enhanced cell permeability and degradation.
• To explore the potential of amide-to-ester substitution as a general strategy for improving beyond Rule of 5 molecules.

Main Methods:

• Synthesis and characterization of model compounds with amide and ester linkages.
• Identification of optimal lipophilicity and permeability parameters using model systems.
• Design and synthesis of VHL-based BET degraders with amide-to-ester substitutions.
• Assessment of intracellular stability, degradation potency, and hook effect onset in ester PROTACs.

Main Results:

• Amide-to-ester substitution improved cell permeability without compromising intracellular stability.
• Ester PROTACs demonstrated enhanced degradation potency compared to their amide counterparts.
• Earlier onset of the hook effect was observed with ester PROTACs, linked to improved permeability.
• The primary driver for enhanced potency was increased cell permeability, not ternary complex formation.

Conclusions:

• Bioisosteric amide-to-ester substitution is a viable strategy to enhance PROTAC permeability and bioactivity.
• This approach offers a simple method to overcome ADME limitations associated with amide linkages in PROTACs.
• The findings suggest potential benefits of amide-to-ester substitution for other "beyond Rule of 5" drug candidates.