Development of Noncovalent Small-Molecule Keap1-Nrf2 Inhibitors by Fragment-Based Drug Discovery

Targeting the protein–protein interaction (PPI)
between
the transcription factor nuclear factor erythroid 2-related factor
2 (Nrf2) and its repressor, Kelch-like ECH-associated protein 1 (Keap1),
constitutes a promising strategy for treating diseases involving oxidative
stress and inflammation. Here, a fragment-based drug discovery (FBDD)
campaign resulted in novel, high-affinity (Ki = 280 nM), and cell-active noncovalent small-molecule Keap1-Nrf2
PPI inhibitors. We screened 2500 fragments using orthogonal assaysfluorescence
polarization (FP), thermal shift assay (TSA), and surface plasmon
resonance (SPR)and validated the hits by saturation transfer
difference (STD) NMR, leading to 28 high-priority hits. Thirteen co-structures
showed fragments binding mainly in the P4 and P5 subpockets of Keap1’s
Kelch domain, and three fluorenone-based fragments featuring a novel
binding mode were optimized by structure-based drug discovery. We
thereby disclose several fragment hits, including their binding modes,
and show how FBDD can be performed to find new small-molecule Keap1-Nrf2
PPI inhibitors.