The active site of enzymatic proteins contains a catalytic site, where the substrate binds, and the reaction is catalysed forming the product. Mammalian PKM2 is a tetrameric protein with identical subunits. Each monomer contains one active site and is composed of three main domains—designated A, B, and C—plus a small N-terminal domain. Molecular docking is a well-known screening tool that can analyse the best binding mode of a ligand to a targeted macromolecule. The molecular docking was performed using AutoDock-Vina software (La Jolla, CA, USA) [27 (link)]. The receptor molecule (PKM2) was cleaned before preparation. The non-polar hydrogen was added and then Kollman charges were added. The spacing of the grid was set to 1 Å. The size of the grid was 60 × 72 × 92 with centre as x = 3.580, y = −18.461, and z = 27.361. The receptor was finally saved into PDBQT format using MGLTools 1.5.6. The ligand molecules were made flexible by detecting the roots to obtain the best possible conformation. The ligands were saved in PDBQT format. The analysis of molecular docking was performed using LigPlot+ (Cambridge, UK), Discovery Studio 2021, AutoDock Tools (La Jolla, CA, USA), and PyMOL [28 (link),29 (link),30 ].
Discovery studio 2021
Manufactured by AutoDock
Sourced in United Kingdom
Discovery Studio 2021 is a comprehensive software suite designed for molecular modeling, simulation, and visualization. It provides a range of tools for structure-based drug design, protein structure prediction, and other computational chemistry applications.
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Lab products found in correlation
3 protocols using discovery studio 2021
1
Molecular Docking of Mammalian PKM2 Active Site
2
Molecular Docking and Virtual Screening Protocol
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The Autodock4 tools was used to generate the ‘pdbqt’ file of the proteins and ligands.32 (link) The grid coordinates for the site-specific and random docking are given in Table S2 . The molecular docking is performed using the AutoDock Vina 1.1.2 scoring function, whereas the strawberry-pearl 5.32.1.1 script was used to perform virtual screening.33 (link) The Lamarckian genetic algorithm (LGA) was used for the molecular docking studies. The docked structures were analysed by using Biovia Discovery studio 2021.
The free energy of the protein-ligand interaction was computed by AutoDock 4.2. The free energy of binding is calculated as ΔG (bind) = ΔH - TΔS, where the ΔH represents the enthalpic, and TΔS the entropic contribution (only a negative ΔG value is energetically favourable). The energy of ligand and protein in the unbound state was estimated first, and then the energy of the protein-ligand complex was computed. The difference was used to estimate ΔG by following equation.34 (link),35 (link)
The free energy of the protein-ligand interaction was computed by AutoDock 4.2. The free energy of binding is calculated as ΔG (bind) = ΔH - TΔS, where the ΔH represents the enthalpic, and TΔS the entropic contribution (only a negative ΔG value is energetically favourable). The energy of ligand and protein in the unbound state was estimated first, and then the energy of the protein-ligand complex was computed. The difference was used to estimate ΔG by following equation.34 (link),35 (link)
3
Molecular Docking of Petroselinum crispum Compounds
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To investigate the inhibition mechanism of molecules extracted from Petroselinum crispum essential oil towards the protein targets, the molecular docking technique was performed using Discovery Studio 2021 [27 ] and Autodock 4.2 software [28 (link)], based on the standard protocol of (ligand-protein) complex preparation as clearly stated and recognized in the literature [29 (link)], in which the major compounds of PC-Eo were docked to NADPH oxidase from Lactobacillus Sanfranciscensis [30 (link)], sterol 14-alpha demethylase (CYP51) from Candida Albicans [31 (link)], and DNA Gyrase-B from Escherichia-Coli [32 (link)], as targeted receptors coded in proteins data bank (PDB) basis by 2CDU.pdb, 5TZ1.pdb, and 6F86.pdb, which were extracted by X-ray diffraction method with good resolutions of 1.80 Å, 2.00 Å, and 1.90 Å, respectively.
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