Table 1.
Energy calculations for top models of MtTPS generated by SWISS-MODEL and ESyPred3D.
Table 2.
Evaluation of MtTPS homology model by using PROCHECK, PROSA, PRO-Q, VERIFY3D and ERRAT online protein structure evaluation tools.
Figure 1.
Comparative homology modeling based three-dimensional structure of MtTPS.
(a) The overall structure of MtTPS showing the characteristic triosephosphate isomerase fold. The binding site groove of MtTPS (b) and PfTPS (c) is shown and the depth of the binding site groove is encircled. The structure is shown from a side view rotated 90 degrees along the vertical axis with respect to the top view. The figures were prepared by using Pymol Molecular viewer [56].
Figure 2.
Verification of the docking procedures of Autodock4 and DOCK6.
(a) A Ribbon representation of MtTPS structure is shown in a side view rotated 90 degrees along the vertical axis with respect to the top view. The grid used for the docking of ligands is shown in a box representation. (b) The ligand CF3HMP-PP bound at the active site of BsTPS in the X-ray crystal structure (PDB ID- 1G4P). Ligand docked by Autodock4 (c) and DOCK6 (d) at the active site of MtTPS. The ligand is shown in orange stick model. Figure (a) was prepared by software Autodock4 while the rest of the figures were prepared by using Pymol Molecular viewer [56].
Figure 3.
Evaluation of the compounds for their potential to inhibit the activity of MtTPS.
Bar diagram represents percent inhibition of MtTPS activity in the presence of compounds at a concentration of 100 µg/ml. The data depicts the values as mean ± S.E. of two separate experiments carried out in duplicates.
Table 3.
IC50 and MIC99 values of the top seven compounds.
Figure 4.
Effect of compounds on the viability of M.smegmatis and M.tuberculosis.
The data depicts the values as mean ± S.E. of two separate experiments.
Figure 5.
Evaluation of compound 9 for its cytotoxic effect on various cell lines.
Cell viability of THP-1, HeLa, HepG2 and HuH cells in the presence of varying concentrations of compound 9.
Figure 6.
Differences in the binding site of MtTPS.
(a) Comparison of the residues at the binding site groove. The structures of MtTPS and PfTPS are superimposed (wheat colour), CF3HMP-PP is bound at the binding site (yellow colour), residues Cys139, Phe174 and Arg194 of MtTPS (red) and corresponding Gly125 ,Val158, Gly178 of PfTPS (blue) are shown in stick model. (b) Molecular surface representation of the mutated MtTPS structure. In-silico substitutions of Cys139, Phe174 and Arg194 in the MtTPS structure by Gly, Val and Gly resulted in a much deeper active-site groove than in the original structure. (c) Molecular surface representation of the original MtTPS structure. The depth of the groove is encircled. The figures were prepared by using Pymol Molecular viewer [56].
Figure 7.
Interaction of compound 9 with the active site of MtTPS and its mode of action.
(a) Binding mode of compound 9 (NSC33472) at the active site of MtTPS. The figure was prepared by using Pymol Molecular viewer [56]. (b) Inhibition of MtTPS activity by compound 9 in the presence of varying concentrations of HMP-PP.