2.7 In-silico molecular docking
In-silico molecular docking of OST was performed using catalytic
subunits, STT3A and STT3B. The AlphaFold structures of STT3A
(AF-P46977-F1) and STT3B (AF-Q8TCJ2-F1) were retrieved from UniProt
(24). A library of 89 potential FDA approved drug candidates was
prepared by downloading their 3D structure for PubChem database (25).
NGI-1, a known OST inhibitor was used as control to set the threshold
for the binding energy and to determine the active sites of the
proteins. Energy minimization of ligands was performed using open babel
and Autodock Vina (Version 1.1.2) (26) of PyRx software was used to
perform docking with exhaustiveness value set to 50. The out.pdbqt files
generated after the molecular docking were split into individual poses
using vina split command and the pose with lowest binding energy was
used for post docking analysis. PyMOL (Version 2.5.4) and Discovery
Studio Visualizer Software (Version 4.0) was used to visualize the
docked structures and binding interactions were identified using
protein-ligand interaction profiler (PLIP) server (27).