Fig 1.
Flowchart depicting schematic strategy of in silico analysis.
Fig 2.
Structural details of target enzymes.
(a) Molecular structures of the indicated human target enzymes of 3-BP, except SDH, were retrieved from PDB data bank. Figure shows 3D ribbon structures along with topology of secondary structures. (b) The structure of SDH (i) was predicted by homology modelling as described in materials and methods, the quality of predicted SDH model was estimated by RMPAGE (ii) and PDBSum server (iii).
Table 1.
Details of structural elements of the target enzymes.
Fig 3.
3D structure of retrieved ligands.
Structure of 3-BP and its derivatives DBPA and PA were retrieved from PubChem compound database. The PubChem CIDs (Compound Identifier) are shown along with each ligands.
Fig 4.
Docking analysis of 3-BP and its derivatives by PatchDock and YASARA.
Docking properties analysis between indicated ligands and target enzymes was evaluated on various parameters including GSC score (a), AI area (b) by PatchDock server and binding energy (c) and dissociation constant (Kd) (d) by YASARA.
Fig 5.
Visualization of docked complexes.
Figure shows 3-D models of docked complexes as visualized by Discovery Studio 3.0, showing interactions of 3-BP and its derivatives with the target enzymes.
Table 2.
Docking calculations depicting interacting residues, binding site residues and atoms involved in H-bonding along with interacting residues common to reported active binding site residues.
Table 3.
The drug likeness of 3-BP and its derivatives.
Table 4.
FAF Drug3 analysis for ADME/tox properties of 3-BP and its derivatives.
Fig 6.
Figure presents summary of the binding of 3-BP to various target enzymes of glycolysis and TCA cycle, indicating the wide spectrum of its targets.