Molecular docking studies were performed using X-ray crystal structures of COX-1 (PDB code: 1EQH) [60 (link)] and COX-2 (PDB code: 1PXX) [61 (link)] with bound inhibitors obtained from the Protein Data Bank (PDB) via AutoDock 4.2 program [62 (link)]. For the docking, the grid size was set to 50 × 50 × 50 xyz points with grid spacing of 0.375Å. For the preparation of ligand structures, 2D structure was sketched in chemdraw12.0, hydrogens were added and converted to mol2 format. For the docking simulation, default values of quaternation, translation and torsion steps were applied. The Lamarckian Genetic Algorithm with default parameters was applied for minimization. The number of docking runs was 100. The graphical depictions of all ligand-protein complexes were achieved by Discovery Studio Visualizer version 4.0 (BIOVIA, San Diego, CA, USA).
Discovery studio visualizer version 4
Manufactured by Dassault Systèmes
Sourced in United States
Discovery Studio Visualizer version 4.0 is a molecular visualization software tool. It provides a platform for the interactive display and analysis of molecular structures, proteins, and other biological macromolecules.
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Lab products found in correlation
4 protocols using discovery studio visualizer version 4
1
Molecular Docking of COX Inhibitors
2
Molecular Modeling of COX and 5-LOX Inhibitors
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Molecular modeling studies were performed using the AutoDock 4.2 software [33 ]. X-ray crystal structures of COX-1 (PDB code: 1EQG) [34 (link)], COX-2 (PDB code: 1CX2) [6 (link)] with bound inhibitors and the human 5-LOX (PDB ID: 6N2W) [23 (link)] bound to NDGA, were retrieved from Brookhaven Protein Data Bank (PDB). The resulting poses and potential interactions were visualized using the Discovery studio visualizer version 4.0 (BIOVIA, San Diego, CA, USA). Moreover, in order to validate the accuracy of the docking program AutoDock 4.2, the co-crystallized ligands, ibuprofen, SC-558, and NDGA were docked into the active site of COX-1, COX-2, and 5-LOX enzymes respectively. The results revealed that the docked ligands ibuprofen (S), SC-558, and NDGA were exactly superimposed on the co-crystallized bound ones with a root mean square deviation value (RMSD) of 0.93 Å and 0.35 Å and 0.67 Å respectively. All the procedures were carried out as described in our previous work [35 ].
3
Homology Modeling of HCV NS3 Helicase
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PDB and UniProt databases were searched for the available genotype-specific NS3 helicase structures and crystal structures were only found for genotypes 1a and 1b. These structures (genotype 1a: PDBid:1A1V and genotype 1b: PDBid:1CU1) were downloaded on .pdb format. For genotypes 2b and 3a, the Homology Modeling approach was adopted for the generation of 3D protein structures10 (link),42 (link). For accuracy and reliability, 3D models of NS3 were generated using three different homology modeling tools, namely the CPH model, the Swiss model and Phyre 243 (link)–45 (link). The structures were visually inspected in Discovery Studio Visualizer version 4.0 (DSV4.0; Dassault Systèmes BIOVIA, Discovery Studio Visualizer, version 4.0, San Diego: Dassault Systèmes, 2016; Retrieved from http://accelrys.com/products/discovery-studio/ ), and thereafter saved in PDB format. Subsequently, the structures were verified using the Verify 3D tool, while the energy minimization and validation were performed using the GROMACS tool46 (link) and Ramachandran plot analysis implemented in DSV4.0.
4
SARS-CoV-2 Helicase Structure and Docking
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The protonation state of SARS-CoV-2 helicase was first investigated using the H++ server32 (link). In H++ calculations, the following physical conditions were employed: pH = 6.5, internal dielectric = 10, external dielectric = 80 and salinity = 0.15. The SARS-CoV-2 helicase was then prepared based on the AutoDock protocol33 (link). The preparation involved merging of nonpolar hydrogens, addition of polar hydrogens, and generation of PDBQT files using AutoDock Tools34 (link). Subsequently, molecular docking calculations were performed to predict and analyze the drug-helicase interactions using AutoDock Vina software35 (link). The Vina parameters were kept to the default, except the exhaustiveness parameter was set to 200. Blind docking was employed in which the binding site was realized by a docking box around the whole protein. The grid spacing value was set to 1.0 Å. Visualization of docking poses and analysis of drug-protein interactions was performed using Discovery Studio Visualizer version 4.0 (DSV4.0; Dassault Systèmes BIOVIA, Discovery Studio Visualizer).
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