Fig. 3 | Scientific Reports

Fig. 3

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

Fig. 3

2D interaction maps of standard therapy, standard inhibitor, and best-performing ligands in the MMP2 ligand-binding domain (LBD). (a) Aspirin (a standard drug used in ischemic stroke therapy) bound to MMP2, forming hydrogen bonds with Leu83, Ala84, and His125. (b) TP0597850 (standard MMP2 antagonist) showing hydrogen bonding with Ala84, Ala86, Ala88, and Thr91. (c) Baicalin, a natural flavone glycoside, interacts with Ala84, Ala86, and Glu130. (d) DCP-sterol, a sterol-based compound, forms a single hydrogen bond with Pro141. (e) DMCG, the top-performing ligand, forms hydrogen bonds with Ala84, Ala86, and His125. The interaction types are color-coded as follows: hydrogen bonds (bright green), van der Waals interactions (pale green), Pi–Alkyl (pink), Pi–Sigma (purple), and Pi–Sulfur (orange). The figures were generated using BIOVIA Discovery Studio version 2025 (Dassault Systèmes BIOVIA, San Diego, USA; https://www.3ds.com/products/biovia/discovery-studio).

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