Integrative molecular simulations reveal NeuroAid II mechanisms in ischemic stroke through network pharmacology, molecular dynamics, and pharmacophore modeling.

Ischemic stroke remains a major health challenge with limited treatment options. NeuroAid II (MLC901), a multi-herbal remedy, has shown clinical promise in post-stroke recovery, though its molecular mechanisms are unclear. This study employed an integrative computational approach, including network pharmacology, molecular docking, molecular dynamics (MD) simulations, molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) free energy calculations, and pharmacophore modeling, to investigate NeuroAid II's neuroprotective mechanisms. Active compounds were screened for drug-likeness and matched to ischemic stroke-related targets via target prediction and protein-protein interaction analysis. Top ligands were docked to key targets, followed by 100 ns MD simulations and binding energy estimation. Network analysis identified MMP2 and SRC as critical targets. Docking and MD results showed baicalin, DCP-sterol, and DMCG formed stable, specific interactions with both proteins. DCP-sterol showed the strongest binding affinity to MMP2 (- 31.06 kcal/mol) and SRC (- 17.10 kcal/mol), outperforming standard inhibitors. DMCG and baicalin also displayed favorable binding to MMP2 (- 12.17 and - 13.54 kcal/mol, respectively) and SRC (- 16.19 and - 10.60 kcal/mol, respectively). Pharmacophore models revealed conserved hydrogen bonding (Ala86 in MMP2; Ala393/Ala296 in SRC) and key hydrophobic features. These findings provide molecular insights into NeuroAid II's multitarget effects and highlight promising lead compounds for further validation.