Journal Article

Elucidating the isorhamnetin-3-O-glucoside-iNOS interaction via molecular dynamics and Hirshfeld surface analyses

Merzouki, Mohammed, Bouammali, Haytham, Khibech, Oussama, Al-zharani, Mohammed, Nasr, Fahd A., Qurtam, Ashraf Ahmed, Abadi, Said, Bouammalli, Boufelja, Hammouti, Yousra, bouhrim, Mohamed, Challioui, Allal

2025

Overview

Inducible nitric oxide synthase (iNOS) remains a demanding metallo-enzyme target because the catalytic heme shapes both geometry and electrostatics at the binding site. We evaluated the dietary flavonol glycoside isorhamnetin-3-O-glucoside (I3OG) against mouse (3E6T) and human (3E7G) iNOS oxygenase domains using a heme-aware, auditably validated docking workflow. we centered the docking grids at the crystallographic Fe position and validated the protocol by re-docking the native co-crystallized inhibitors (3E6T: AR-C118901/1A2; 3E7G: AR-C95791/AT2), reproducing the crystal poses with heavy-atom RMSD = 1.093 Å and 0.327 Å, respectively (≤ 2.0 Å criterion). Explicit-solvent 100-ns MD confirmed stable complexes for both systems; 3E6T showed tighter ligand RMSD, lower pocket Cα-RMSF, and a more persistent H-bond network. MM/GBSA over equilibrated frames (60−100 ns) yielded ΔG_bind ≈ −44.9 ± 3.9 kcal·mol −1 (3E6T) vs −36.1 ± 3.7 kcal·mol −1 (3E7G), with per-residue hot spots matching docking contacts. Principal-component free-energy maps indicated more focused minima for 3E6T and a broader low-energy valley for 3E7G, consistent with the MD metrics. we performed an apo-form heme-cavity test (heme removed, grid kept at Fe; proximal Cys re-protonated) to probe pocket occupancy/flexibility without claiming a catalytic model. Collectively, the heme-centred, co-crystal-validated protocol plus the apo-cavity readout support I3OG as a plausible scaffold for iNOS engagement and provide a transparent template for future metallo-enzyme docking studies.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Analysis / Animals / Binding Sites / Bioflavonoids / Crystallization / Crystallography / Electrostatic properties / Electrostatics / Enzymes / Flavones / Flavonoids / Flavonols / Free energy / Glucosides / Glucosides - chemistry / Glucosides - metabolism / Glycosides / Heme / Humans / Hydrogen Bonding / Hydrogen bonds / Ligands / Metallography / Mice / Molecular Docking Simulation / Molecular dynamics / Molecular Dynamics Simulation / Natural products / Nitric oxide / Nitric Oxide Synthase Type II - antagonists & inhibitors / Nitric Oxide Synthase Type II - chemistry / Nitric Oxide Synthase Type II - metabolism / Nitric-oxide synthase / Protein Binding / Proteins / Quercetin - analogs & derivatives / Quercetin - chemistry / Quercetin - metabolism / Simulation / Systems stability / Trends