Integrated In Silico Discovery of Thymoquinone Analogs Targeting the Keap1–Nrf2 Pathway for Amyotrophic Lateral Sclerosis Therapy

Abstract

Oxidative stress drives neuronal vulnerability in amyotrophic lateral sclerosis (ALS), making the Keap1–Nrf2 pathway a vital therapeutic target. While thymoquinone (TQ) modulates this axis, its efficacy is limited by low potency and poor drug-likeness. We utilized an integrated in silico workflow—including validated QSAR modeling (R² = 0.68, Q²_ext = 0.66), ADMET profiling, docking, 200 ns molecular dynamics, and MM–PBSA analysis—to identify improved TQ-derived Keap1 inhibitors. Screening 64 analogs prioritized three leads (CHEMBL3416163, CHEMBL4636830, and CHEMBL221598) with favorable safety and blood–brain barrier permeability. Docking and dynamics confirmed these analogs form stable interactions with Kelch domain hotspots. MM–PBSA calculations revealed significantly enhanced binding free energies (−75.10 to −93.79 kJ mol⁻¹) compared to parent TQ (−21.05 kJ mol⁻¹), driven primarily by van der Waals and hydrophobic forces. This study identifies structurally tractable TQ analogs with improved predicted potency and establishes a robust computational framework for neuroprotective discovery. The prioritized leads are compelling candidates for in vitro and in vivo validation as redox-modulating agents in ALS.