An investigation on the molecular structure, interaction with metal clusters, anti-Covid-19 ability of 2-deoxy-D-glucose: DFT calculations, MD and docking simulations

Studies of the geometrical, vibration, absorption and physicochemical properties of 2-deoxy-D-glucose with and without metal clusters are reported using the DFT method. 2-Deoxy-D-glucose forms stable clusters with transition metal clusters of copper, silver and gold. Frontier molecular orbitals and molecular electrostatic potential of 2-deoxy-D-glucose and associated metal clusters (Cu₆, Au₆, Ag₆, 2-DGCu₆, 2-DGCu₅Au, 2-DGCu₅Ag, 2-DGAu₆, 2-DGAu₅Ag, 2-DGAu₅Cu, 2 -DGAg₆, 2-DGAg₅Au, 2-DGAg₅Cu) are examined with the B3LYP / LANL2DZ basis set. It is observed that the stability and chemical properties of 2-deoxy-D-glucose strongly depends on the cluster size. The molecular electrostatic potential maps were developed to provide information about the chemical reactivity of the molecules to explain intermolecular interactions. Then, to explore the ligand-protein recognition properties molecular docking and molecular dynamic (MD) simulation analyses have shown that the compound under consideration possesses potential activity as anti-cancer, anti-SARS-CoV-2, anti-SARS-CoV. Each of these analyzes contributes significantly to our understanding of the biological effects of the molecules outlined.