Targeting the Helicobacter pylori ClpX chaperone with 7,4′-Dihydroxy-8-methylflavone: a virtual screening and microsecond-scale triplicate molecular dynamics study

ClpX, a heat-shock protein 100 chaperone, is responsible for intracellular protein degradation and remodelling. It functions as the regulatory subunit of the ATP-dependent ClpXP protease, have demonstrated that some Clp family members contribute to the pathophysiology of several bacteria. Helicobacter pylori (H. pylori) ClpX exhibits chaperone activity through hydrophobic interactions with the substrate protein, and this activity depends on ATP hydrolysis. Researchers have identified numerous natural compounds with potential anti-H. pylori activity. H. pylori activity has been studied and reported because of its high levels of antibacterial activity and safety. In the current work, computational exploration screened 159 anti-H. pylori phytochemicals against ClpX (PDB: 1UM8), identifying 7,4-dihydroxy-8-methylflavone as a top binder via InstaDock (−8.3 kcal/mol), surpassing control Bismuth Subcitrate potassium. ADMET profiling confirmed the drug-likeness, high GI absorption, and low toxicity risks of the compound. Extended 1000 ns triplicate MD simulations revealed superior complex stability (RMSD ∼0.49 nm, Rg ∼2.39 nm), persistent H-bonds, rigidified PCA clusters, and MM-PBSA binding free energy of −11.16 kJ/mol driven by van der Waals forces. These computational findings suggest that this flavone may restrict ClpX to a more conformationally rigid, potentially inhibited state; experimental validation (e.g. ClpXP degradation, ATPase, or H. pylori growth-inhibition assays) is required to confirm functional inhibition, but the predicted binding profile paves the way for a natural-product lead against resistant gastric pathogens.