Extended Data Fig. 9: NRF2 peptide- and ligand-binding sites, rationale for binder versus displacer.

Here we show the docking pose of one of the hit compounds (iKeap9, green ball-and-stick representation) bound to KEAP1, together with the NRF2 peptide (PDB ID: 4IFL; peptide in violet). iKeap9 is a tight binder (180 nM by steady-state SPR) but cannot displace NRF2. Left, the top view. Right, the side view of the cross-section of KEAP1 along the central plane. The violet box indicates the docking region (where the ligands were allowed to bind), which was used in the virtual screening. The site of interest includes a part of the deep pocket/tunnel of the β-barrel-shaped KEAP1, as it enables ligands to bind more tightly by insertion into the channel than on a shallow surface. However, the deep tunnel is largely non-overlapping with the peptide-binding site (which binds to the entrance site of the tunnel). Thus, binding molecules might only partially interfere with peptide binding, which could reduce or eliminate the ability of small-molecule binders to displace the peptide. The ability of a small molecule to displace the peptide is difficult to predict, and was not attempted in this study. In some cases, small molecules can also act as molecular glues and strengthen the interaction between NRF2 and KEAP1.