3.5 Docking studies
Docking studies were carried out to understand the possible binding sites and thus the mechanism of action of Phormidin against bacterial FAS II and human FAS I. Crystal structure of Bacillus subtilisFAS II with inhibitor Cerulenin bonded at beta-ketoacyl-ACP synthase II domain and human FAS IKS-MAT di-domain were considered as a model for the studies. Binding results were interpreted based on the scores obtained in docking studies, as well as the theoretical binding energies calculated from the docked poses. Possible amino acid residues involved in binding and the type of interactions made by Phormidin with active site residues are shown in Figure 4a. for FAS II and in Figure 4b. in the case of FAS I. As seen from the Table 3, for both FAS II and FAS I, the glide scores as well as the theoretically calculated binding energies are better for Phormidin compared to that of both the other inhibitors, Cerulenin and C75. Glide score is calculated based on different parameters of ligand-protein interactions and it represents the overall affinity of ligand-protein binding. MMGBSA simulates binding free energy of ligand-protein interaction; more negative values represent tighter binders. Parameters like number of H-bonds between ligand atoms and active site residues, ligand interaction with number of hydrophobic residues and the total number of van der Waals contacts involved in ligand binding indicates the affinity and strength of ligand enzyme interactions. Table 4 gives a comparison of total number of these parameters with respect to Phormidin and other two FAS inhibitors in FAS II and FAS I. It can be clearly seen that Phormidin has stronger interaction with both FAS II and FAS I enzymes when compared to the other known inhibitors. Also, the results of ADME prediction have been summarized in Table 5.