Figure 8.

Molecular docking solution of berberine against CXR target obtained using AutoDock Vina. (A) Berberine (thick grey lines) in the ligand binding domain of CXR (ribbon representation), (B) Ligand interaction diagram of the berberine docking pose (dark green—conventional hydrogen bond; light green—carbon hydrogen bond; dark pink—pi-pi stacked interaction; light pink—pi-alkyl interaction; yellow—pi-sulfur interaction), (C) Berberine in the active sites delineated by the hydrophobic surface and surrounding residues which are labelled and represented as thin grey lines. Hydrogen atoms are not shown for clarity. (D) Dynamic nature of interactions represented by percentage of frames for which interactions was observed during 1 ns of molecular dynamics simulations of the fully solvated system.