The major identified compounds by GC-MS analysis in the highest yield (winter) oil of C. subulatus leaves (eucalyptol, α-pinene and α-phellandrene) were docked into the active sites of elastase and acetylcholinestrase (AChE) enzymes. The software implicated was autodock Vina. Docking was done as per reported methodology29 (link),30 (link). The crystal structures of both enzymes co-crystallized with ligands were downloaded from the protein data bank with PDB-IDs as follows (6qeo for elastase and 7d9o for acetylcholinesterase). The compound structures were drawn using ChemDraw Ultra 8.0 and Amber12: EHT force field was applied for energy minimisation. Conformers of lowest energies are saved by the program. Docking validation was carried out by re-docking the co-crystallized ligands into the active sites of their respective enzymes. Following revealing of the active sites, the identified compounds of the oil were docked separately into them and their docking was analysed by Biovia Discovery Studio visualiser to show their binding interaction diagrams.
Discovery studio visualiser
Manufactured by Dassault Systèmes
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Discovery Studio Visualiser is a software tool developed by Dassault Systèmes for the visualization and analysis of molecular structures and simulations. It provides users with a range of tools for exploring and interpreting 3D molecular data.
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Lab products found in correlation
6 protocols using discovery studio visualiser
1
Molecular Docking of Eucalyptus Compounds
2
Molecular Dynamics of Influenza Hemagglutinin Fusion Peptide
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We considered a 23-residue long HAfps: wt GLFGAIAGFIEGGWQGMVDGWYG and E11A and and W14A mutants. The N-terminus was modeled as a charged amino group, and the C-terminus was amidated. For most cases, we simulated E11 in protonated (neutral) state; however, a peptide with its charged version, denoted as wt , was considered as well for membrane-spanning configurations. Simulated systems included one peptide, 162 POPC molecules (81 per leaflet) and 9337 TIP3P [32 (link)] water molecules together with sodium and chloride ions necessary to construct a neutral system consisting of a membrane slab with ∼20 Å of 0.15 mol/L NaCl solution margins on both sides. Peptides and lipids were modeled with Amber99SB-ILDNP* [33 (link)] and Amber Lipid14 [34 (link)] force fields, respectively. In addition, we considered wt HAfp simulations in transmembrane hairpin configuration using Charmm36 force field [35 (link)]. Starting geometries for surface bound and transmembrane peptides were taken from our previous runs [20 (link)]. Necessary mutations were introduced with Discovery Studio Visualiser (Biovia).
3
Conformational Analysis of Ligand-Protein Interactions
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We chose the best conformation of the ligands based on lower binding energy and orientation of the ligand within our specified grid for further analysis using various softwares. We employed BIOVIA Discovery Studio Visualiser to generate 2D diagrams depicting the interactions between the ligand (Drug) and the protein models, both wild type and alpha strain models. All the settings used were set at default. We further used Protein-Ligand Interaction Profiler (PLIP) available online for analysing the hydrophobic contacts between the ligands and the protein [37 , 38 (link)]. The 3D coordinates of the spike protein model of the alpha strain were superimposed with the spike protein (PDB ID: 7DDN) using the “super” command available in PyMol [39 (link)]. The docked structure from the ClusPro 2.2 webserver was also analysed using PyMol.
4
Molecular Docking of Inhibitors for Soluble Epoxide Hydrolase
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Molecular docking of the compounds was carried out in a 3D model of the sEH – t-AUCB (1a ) complex (PDB: 5AM3) (substances used for protein X-ray diffraction analysis and t-AUCB molecule were preliminarily removed from the model). The protein atoms were charged according to the standard Kollman method using the AutoDock Tools 1.5.6 program. The 2D structures of the ligands were transformed into 3D ones, and the geometry was optimised by molecular mechanics in the Amber ff14SB force field using the Gasteiger charge model in the USCF Chimera 1.15 program.40 (link) The docking procedure was carried out using the AutoDock Vina 1.1.2 program41 (link) (grid box size: 12.75 Å × 15.0 Å × 21.75 Å, coordinates of the centre: x = 16.111 Å, y = 9.722 Å, z = 13.582 Å, exhaustiveness: = 20, energy range: = 4). The ligand – protein complexes with the best values of the scoring functions were selected. The structures of the complexes were visualised using the UCSF Chimaera 1.15 program.40 (link)
2D interaction plots were obtained using Discovery studio visualiser (BIOVIA, San Diego, CA, USA).42
2D interaction plots were obtained using Discovery studio visualiser (BIOVIA, San Diego, CA, USA).42
5
Molecular Docking of PDC-Piperacillin Interactions
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To elucidate the molecular interactions between the structural models of PDC and piperacillin, docking simulations were performed using AutoDock Vina 1.1.2 [33 (link)]. Prior to docking simulation, polar hydrogen atoms and Gasteiger charges were added to PDC models using AutoDockTools 1.5.6. The grid box size was set to include all proteins. After the 20 docking models were generated using AutoDock Vina, 3D molecular interactions and conformations were visualized using PyMOL 2.3.4. Docking models with root mean square deviation ≥2, relative to the values obtained prior to docking simulation, were omitted. The optimal models in each cluster were determined from the docking models using AutoDock Vina based on the binding energy. The molecular interactions were analyzed in a 2D diagram using the BIOVIA Discovery Studio Visualiser.
6
Docking of IL-6R Inhibitors
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The 3D structural model of the human interleukin 6 receptor (IL-6R) was generated from the crystallographic structure of the complex between IL-6 and its receptor (IL-6R-α and IL-6R-β, PDB id 1P9M) by editing out the coordinates of the IL-6 molecule. All bound water molecules and ligands were removed.
Bis-PMSs5 and 6 and a mono penthamethinium salt with a phenyl group in the γ-position were docked to the IL-6R using the CB-Dock web server [38 (link)]. All docking poses from this cavity (binding site) were visually inspected with BIOVIA Discovery Studio Visualiser [39 ], and 2D interaction diagrams and 3D visualizations of the protein–ligand complex were generated and are presented.
Bis-PMSs
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