Computational protocol: Molecular docking studies on InhA, MabA and PanK enzymes from Mycobacterium tuberculosis of ellagic acid derivatives from Ludwigia adscendens and Trewia nudiflora

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Protocol publication

[…] ChemBio3D Ultra 12.0 ( was used to draw the structures of compounds 1 and 2 (Fig. ), optimise ligand geometry and run MM2 energy minimisation of the 3D structures (Allinger ). The structures of the experimental inhibitors, isonicotinic-acyl-NADH for InhA and MabA, and triazole inhibitory compound for PanK, were retrieved from the respective protein crystal structures (PDB ID: 1ZID and PDB ID: 4BFT, respectively). All file conversions required for the docking study were performed using the open source chemical toolbox Open Babel version 2.3.2 ( (O’Boyle et al. ). All rotatable bonds present on the ligands were treated as non-rotatable to perform the rigid docking. The Gasteiger charge calculation method was used and partial charges were added to the ligand atoms prior to docking (Gasteiger and Marsili ). The crystal structures of InhA (PDB ID: 1BVR), MabA (PDB ID: 1UZN) and PanK (PDB ID: 3AF3) were retrieved from the RCSB Protein Data Bank (PDB) ( All water molecules and hetero atoms were removed from the crystal structures by using PyMOL molecular graphic system, version ( 1 [...] Docking experiments were performed with compound 1, 2 and the experimental control inhibitors against InhA, MabA and PanK proteins. Grid box parameters (Table ) were set by using AutoDock Tools (ADT), a free graphic user interface of MGL software packages (version 1.5.6rc3) (Morris et al. ). The molecular docking program AutoDock Vina (version 1.1.2) (Trott and Olson ) was employed to perform the docking experiment. The Lamarckian Genetic Algorithm was used during the docking process to explore the best conformational space for the ligand with a population size of 150 individuals. The maximum numbers of generation and evaluation were set at 27,000 and 2,500,000, respectively. Other parameters were set as default (Table ). […]

Pipeline specifications

Software tools Open Babel, PyMOL, AutoDock, AutoDock Vina
Applications Drug design, Protein interaction analysis
Organisms Homo sapiens
Diseases Protein Deficiency, Tuberculosis
Chemicals Ellagic Acid