2.4. Molecular Docking Method

The 3D structure of the α-glucosidase from Saccharomyces cerevisiae (PDB, 3A4A) was downloaded from the RSCB protein databank (http://www.rcsb.org). Before docking, the structure of the α-glucosidase was prepared by removing the water and ligands, adding polar hydrogen and charge, and repairing residues. The chemical structures of myricetin and dihydromyricetin were established and optimized using MOPAC 2016 and employing a semiempirical PM6 method [23]. By using Autodock 4.2 software [24], myricetin and dihydromyricetin were docked into the active site based on the binding mode of maltose to the enzyme by the Lamarckian genetic algorithm method. The grid spacing was set at 0.375 Å, and all of the points of the grid box in the x, y, and z directions were 60. During docking, the rigid structure of the α-glucosidase was maintained while the structure of the flavonoid was regarded as fully flexible. Then, the complex with the lowest binding energy was selected and analyzed to obtain a schematic diagram of the interaction between the flavonoid and α-glucosidase by using LigPlot+ v.2.1 software [25].