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

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

  • J Med Chem. 2021 Dec 23;64(24):18082-18101. doi: 10.1021/acs.jmedchem.1c01496.
Victoria G Klein 1 Adam G Bond 2 Conner Craigon 2 R Scott Lokey 1 Alessio Ciulli 2
Affiliations

Affiliations

  • 1 Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States.
  • 2 Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K.
Abstract

Criteria for predicting the druglike properties of "beyond Rule of 5" Proteolysis Targeting Chimeras (PROTAC) degraders are underdeveloped. PROTAC components are often combined via amide couplings due to their reliability. Amides, however, can give rise to poor absorption, distribution, metabolism, and excretion (ADME) properties. We hypothesized that a bioisosteric amide-to-ester substitution could lead to improvements in both physicochemical properties and bioactivity. Using model compounds, bearing either amides or esters, we identify parameters for optimal lipophilicity and permeability. We applied these learnings to design a set of novel amide-to-ester-substituted, VHL-based BET degraders with the goal to increase permeability. Our ester PROTACs retained intracellular stability, were overall more potent degraders than their amide counterparts, and showed an earlier onset of the hook effect. These enhancements were driven by greater cell permeability rather than improvements in ternary complex formation. This largely unexplored amide-to-ester substitution provides a simple strategy to enhance PROTAC permeability and bioactivity and may prove beneficial to other beyond Ro5 molecules.

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