2.7.2 Ligand preparation
The two-dimensional (2D) structures of all the isolated phytochemical
compounds were constructed using Marvin Sketch
(ChemAxon, 2013). The 2D structures were
then uploaded onto Avogadro software
(Hanwell et al., 2012) to generate the
three-dimensional (3D) coordinates of each compound. We used the
Avogadro software to minimize the energy and then optimized the
compounds using the UFF force field
(Rappé et al., 1992). Before molecular
docking, the final preparation of each of the compounds was carried out
on UCSF Chimera, whereby hydrogen atoms and corresponding Gasteiger
charges were added (Gasteiger and Marsili,
1978).