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.