Network pharmacology: Anti-obesity and insulin-sensitizing effects of Danggui-Huangjing herb-pair via epidermal growth factor receptor/phosphatidylinositol 3-kinase/protein kinase B pathway

Figure 4 Molecular dynamics simulation of the protein-ligand complexes. A: Root-mean-square deviation; B: Radius of gyration; C: Solvent-accessible surface area; D: Hydrogen bond count; E: Root-mean-square fluctuation; F: Free energy landscape. Receptors: AMBER14SB force field; ligands: GAFF2 (RESP charges); solvated in TIP3P water box (1 nm edge), 0.15 M NaCl; long-range electrostatics: Particle mesh Ewald method. Molecular dynamics results (GROMACS 2022, 100 nanoseconds, normal pressure and temperature: 310 K, 1 bar) of estrogen receptor 1/diosgenin-3-O-β-D-fructofuranosyl-α-L-rhamnopyranoside, epidermal growth factor receptor/zhonghualiaoine 1, signal transducer and activator of transcription 3/zhonghualiaoine 1 complexes. DFV: Diosgenin-3-O-β-D-fructofuranosyl-α-L-rhamnopyranoside; EGFR: Epidermal growth factor receptor; ESR1: Estrogen receptor 1; Rg: Radius of gyration; RMSD: Root-mean-square deviation; RMSF: Root-mean-square fluctuation; SASA: Solvent-accessible surface area; STAT3: Signal transducer and activator of transcription 3.