Structure-Guided Conformational Restriction Leading to High-Affinity, Selective, and Cell-Active Tetrahydroisoquinoline-Based Noncovalent Keap1-Nrf2 Inhibitors

J Med Chem. 2024 Nov 14;67(21):18828-18864. doi: 10.1021/acs.jmedchem.4c01221. Epub 2024 Oct 17.

Abstract

Inhibition of the protein-protein interaction between Kelch-like ECH-associated protein 1 (Keap1) and nuclear factor erythroid 2-related factor 2 (Nrf2) has been recognized as an attractive approach for treating oxidative stress-related diseases. Here, we present a new series of noncovalent Keap1-Nrf2 inhibitors developed by a conformational restriction strategy of our fluorenone-based compounds previously identified by fragment-based drug discovery. The design was guided by X-ray cocrystal structures, and the subsequent optimization process aimed at improving affinity, cellular activity, and metabolic stability. From the noncyclic compound 7 (Ki = 2.9 μM), a new series of tetrahydroisoquinoline-based Keap1 inhibitors with up to 223-fold improvement in binding affinity (57, Ki = 13 nM), better metabolic stability, and enhanced cellular activity was obtained. In addition, the compounds showed selectivity for the Keap1 Kelch domain across a panel of 15 homologous proteins. We thereby demonstrate the utility of cyclic rigidification in the design of potent and more drug-like Keap1-Nrf2 inhibitors.

MeSH terms

  • Animals
  • Crystallography, X-Ray
  • Drug Design
  • Humans
  • Kelch-Like ECH-Associated Protein 1* / antagonists & inhibitors
  • Kelch-Like ECH-Associated Protein 1* / metabolism
  • Models, Molecular
  • Molecular Conformation
  • NF-E2-Related Factor 2* / antagonists & inhibitors
  • NF-E2-Related Factor 2* / metabolism
  • Protein Binding
  • Structure-Activity Relationship
  • Tetrahydroisoquinolines* / chemistry
  • Tetrahydroisoquinolines* / pharmacology

Substances

  • Kelch-Like ECH-Associated Protein 1
  • NF-E2-Related Factor 2
  • KEAP1 protein, human
  • Tetrahydroisoquinolines
  • NFE2L2 protein, human