Deconstructing Noncovalent Kelch-like ECH-Associated Protein 1 (Keap1) Inhibitors into Fragments to Reconstruct New Potent Compounds

J Med Chem. 2021 Apr 22;64(8):4623-4661. doi: 10.1021/acs.jmedchem.0c02094. Epub 2021 Apr 5.

Abstract

Targeting the protein-protein interaction (PPI) between nuclear factor erythroid 2-related factor 2 (Nrf2) and Kelch-like ECH-associated protein 1 (Keap1) is a potential therapeutic strategy to control diseases involving oxidative stress. Here, six classes of known small-molecule Keap1-Nrf2 PPI inhibitors were dissected into 77 fragments in a fragment-based deconstruction reconstruction (FBDR) study and tested in four orthogonal assays. This gave 17 fragment hits of which six were shown by X-ray crystallography to bind in the Keap1 Kelch binding pocket. Two hits were merged into compound 8 with a 220-380-fold stronger affinity (Ki = 16 μM) relative to the parent fragments. Systematic optimization resulted in several novel analogues with Ki values of 0.04-0.5 μM, binding modes determined by X-ray crystallography, and enhanced microsomal stability. This demonstrates how FBDR can be used to find new fragment hits, elucidate important ligand-protein interactions, and identify new potent inhibitors of the Keap1-Nrf2 PPI.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Crystallography, X-Ray
  • Drug Stability
  • Humans
  • Kelch-Like ECH-Associated Protein 1 / antagonists & inhibitors*
  • Kelch-Like ECH-Associated Protein 1 / metabolism
  • Ligands
  • Magnetic Resonance Spectroscopy
  • Microsomes / metabolism
  • Molecular Dynamics Simulation
  • NF-E2-Related Factor 2 / chemistry
  • NF-E2-Related Factor 2 / metabolism
  • Protein Binding
  • Protein Interaction Maps / drug effects
  • Small Molecule Libraries / chemistry*
  • Small Molecule Libraries / metabolism
  • Small Molecule Libraries / pharmacology
  • Structure-Activity Relationship
  • Surface Plasmon Resonance

Substances

  • KEAP1 protein, human
  • Kelch-Like ECH-Associated Protein 1
  • Ligands
  • NF-E2-Related Factor 2
  • Small Molecule Libraries