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

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.