Discovery of a novel Keap1 inhibitor for neurodegeneration through virtual screening and molecular dynamics simulations

Oxidative stress is a key feature of Alzheimer's disease (AD) and other neurodegenerative disorders. The Kelch-like ECH-associated protein 1 (Keap1)-nuclear factor erythroid 2-related factor 2 (Nrf2) pathway controls redox balance, and disrupting the Keap1-Nrf2 protein-protein interaction (PPI) has become a promising therapeutic approach. Marine natural products (MNPs), because of their structural diversity and bioactivity, are an underexplored source of potential neuroprotective compounds. This study aimed to identify novel marine-derived inhibitors of the Keap1-Nrf2 interaction using a comprehensive in silico pipeline. A total of 14,492 compounds from an open-access MNP database were virtually screened against the Keap1 Kelch domain through molecular docking. The top 1,329 candidates exhibited strong binding affinities, with several reaching scores comparable to the co-crystallized reference ligand L5F. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling was employed to assess pharmacokinetic properties, brain penetration, and safety, leading to the identification of compound 145398-61-4 as the most promising hit. Molecular dynamics (MD) simulations verified the structural stability of the Keap1-145398-61-4 complex, while binding free energy calculations indicated energetically favorable interactions. Additional validation using principal component analysis (PCA) and highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energy analysis further confirmed the stability of this interaction. Overall, our in silico study identified compound 145398-61-4 as a novel Keap1-Nrf2 inhibitor, highlighting its potential as a lead candidate for developing treatments for Alzheimer's disease and other neurodegenerative disorders, such as amyotrophic lateral sclerosis and multiple sclerosis.