Byungwoong Yoo
UNLABELLED: The Keap1-Nrf2-ARE pathway coordinates cellular antioxidant defence and is a potential target for limiting oxidative and neuroinflammatory injury. Natural products can activate Nrf2 through several mechanisms, but persistent non-covalent occupancy of the Keap1 ETGE pocket has rarely been demonstrated experimentally. We compared catalpol, geniposide, loganin, morroniside and coptisine using a uniform workflow based on docking to the human Keap1 Kelch domain, independently replicated all-atom molecular dynamics, and conformational and interaction analyses for the full panel; a quality-controlled endpoint-energy sensitivity check was restricted to the reproducibly retained catalpol and geniposide complexes. Protein compactness, correlated Cα motions, conformational probability density, ligand displacement, pocket contacts, hydrogen bonding, solvent burial and anchor-residue behaviour were assessed across replicates. Catalpol and geniposide were retained most reproducibly near the ETGE pocket, whereas loganin showed heterogeneous excursions, morroniside was not reproducibly retained and coptisine was consistently displaced. Global Keap1 conformational sampling remained compact, and the dominant cross-correlation patterns were shared across retained and non-retained complexes; without an apo control, these patterns do not support ligand-specific allosteric inference. The preliminary prioritisation of morroniside was therefore not reproduced. These findings identify catalpol and geniposide as computational candidates, not experimentally established Keap1 binders or Nrf2 activators through pocket competition. Direct-binding and ETGE-peptide competition assays, followed by cellular target-engagement and pathway studies, are required to test the proposed mechanism and its neuroprotective relevance.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40203-026-00724-2.