Naringenin as a dual-target modulator of RAGE–NF-κB signaling and Aβ fibrillization in Alzheimer’s disease: integrated computational and experimental analyses
Alzheimer’s disease (AD) is a complex neurodegenerative disorder characterized by the accumulation and aggregation of β-amyloid (Aβ) and chronic neuroinflammation mediated by the receptor for advanced glycation end products (RAGE). Current therapeutic candidates targeting RAGE signaling or Aβ aggregation continue to face challenges, including off-target toxicity, poor blood-brain barrier (BBB) penetration, and limited multi-target efficacy. Naringenin (NAR), a naturally occurring flavanone polyphenol prioritized through structure-based virtual screening and preliminary biological evaluation, was selected for further mechanistic investigation as a potential dual-target modulator of RAGE-associated inflammatory signaling and Aβ42 fibrillization. Molecular docking analyses showed that NAR interacts with the RAGE interface (PDB: 6XQ3) via π-cation interactions with ARG_98 and LYS_110 (docking score: −5.072 kcal/mol). At the Aβ fibril (PDB: 2MXU), NAR showed a superior docking score than ALZ-801 (valiltramiprosate), involving hydrogen bonding and π–π stacking with HIS_A14 (docking score: −8.098 kcal/mol). 100 ns molecular dynamics simulations supported the stability of these binding modes, with RMSD and RMSF values within acceptable ranges. MM-GBSA rescoring indicated competitive predicted binding free energies (ΔGBind: −30.260 kcal/mol at RAGE; −220.162 kcal/mol at the fibril, compared to ALZ- 801’s −214.482 kcal/mol), influenced by electrostatic and hydrophobic interactions. Per-residue energy decomposition indicated PHE_20 (−9.10 kcal/ mol) as the dominant hotspot residue, alongside ARG_98 (−4.71 kcal/mol) and LYS_52 (−3.96 kcal/mol) as key RAGE anchors. In silico ADMET profiling suggested favorable predicted BBB accessibility (score: 0.001), Caco-2 permeability, Lipinski compliance, and a more favorable predicted cardiac safety profile (hERG: 0.145) relative to V6Y. Experimentally, NAR reduced Aβ42-induced NF-κB activation in RAGE-positive C6 cells, protected SH-SY5Y neurons from Aβ42 toxicity, and inhibited Aβ42 fibrillization in vitro , producing non-seeding aggregates consistent with impaired fibril formation, and attenuated rotenone-induced α-synuclein-associated cellular stress. Collectively, these findings support further investigation of NAR as a mechanistically plausible multi-target candidate for protein aggregation and RAGE-associated inflammatory signaling in neurodegenerative disease models.