Chem. Biodiversity 2021, 18, e2000832
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Molecular Docking Studies
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The 3D structures of compounds were generated by
HyperChem software (version 8.0). The initial struc-
tures were energy minimized using molecular mechan-
ics MM+ force field (ref) followed by fully optimization
via AM1 semi-empirical method available in Hyper-
Chem. The optimized structures were converted to
SYBYL mol2 file format using OpenBabel 2.0.2 version
to be used as an acceptable format for docking
procedure. Flexible docking of the studied compounds
into the active site of the COX-2 isoenzyme was
performed using GOLD program (version 5.0) running
under LINUX operating system. For this purpose, the
crystal structure of COX-2 (PDB code: 5KIR) was
obtained from Protein Data Bank. Prior to molecular
docking, hydrogen atoms were added to the protein
in GOLD program. The active site of the enzyme was
determined based on the position of rofecoxib co-
crystallized with COX-2. To this end, geometric center
of the residues involved in the binding to the co-
crystallized inhibitor molecule (i.e., rofecoxib) was
calculated and set as the center of the binding site.
Following the optimization of the docking parameters
by re-docking the rofecoxib into the active site of the
enzyme, the optimized structures were docked into
the COX-2. The best solutions in terms of scoring
function were selected and used for analysis of
interactions using LigPlot+ and PyMOL program.
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Acknowledgment
The authors would like to thank Biotechnology
Research Center, School of Pharmacy, and Research
Deputy at Tabriz University of Medical Sciences for
providing research facilities and financial support
under the Postgraduate Research Scheme toward the
Ph.D. thesis of TV (Grant number 49292).
Author Contribution Statement
T.V. performed all the experiments. J.K. performed the
COX inhibition assays. S.H. supervised the synthetic
procedure. M.H. helped in molecular docking and data
analysis. A.A.A. assisted in MTT assay. F.W. helped in
COX inhibition assay and data analysis. S.D. designed
and supervised this project. All authors have contrib-
uted to the final version and approved the final
manuscript.
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