2.2 Preparation of 3D structure of 2-DG and 2-DG derivative as ligands
The structure of 2-deoxy-D-glucose and 2-DG derivative (1, 3, 4, 6-Tetra-O-acetyl-2-deoxy-D-glucopyranose) were downloaded in xml format from PubChem database and structures were validated (Butkiewicz et al., 2013). Hydrogen atoms were introduced into the ligands structure using Argus lab (4.0.1), so as to customize them for rigid docking. The hydrogenated ligand molecules were then converted into pdb format using Open Babel (2.4) interface (openbabel.org/docs/dev/OpenBabel.pdf), as required for rigid docking. Similarly, 3D structures of standard chemotherapeutic agents (lopinavir, favipiravir, hydroxychloroquine) were also customized for docking.