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73 protocols using vina v1

1

Molecular Docking of COVID-19 Targets

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Through the above-mentioned cytoHubba analysis, the hub genes for the treatment of COVID-19 were obtained. The top hub gene and other key genes with the more connected active component in herbs were linked by molecular docking. The structural formula (SDF format) of the compounds were downloaded from the PubChem database and converted to PDB format with Open babel v.2.4.1 [37 (link)] from the RCSB Protein Data Bank (PDB, https://www.rcsb.org/) to obtain the crystal structure of the core target [38 ]. The targets were processed by removing water, adding hydrogen, optimising amino acids, and selecting the magnetic field, and the pdbqt format was saved as a pair acceptor. Atomic charges and assigned atom types were added to compounds in the PDB format, and the pdbqt format was saved as a docked ligand. The active site for molecular docking was determined and size was set. Finally, Autodock Vina v.1.1.2 was run to perform molecular docking [39 (link)]. PyMOL v.2.3 software [40 (link)], and Molecular Operating Environment v.2.2 (MOE) software [41 ] were used to visualize the docking results, and based on the binding conformations of the docking results of each compound, the docking results with lower binding energy and better conformation were selected.
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2

Molecular Docking of C. perfringens ColA

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A molecular docking experiment was carried out to investigate the binding energies of the screened compounds and the potential binding poses that could explain the biological activity. Since there is no readily available crystal structure of C. perfringens ColA, in our study, we used a validated homology model of the target protein that we reported in a previous paper [29 (link)]. The docking experiment was carried out using the AutoDock Vina v1.1.2 [30 (link)] algorithm within YASARA Structure [31 ]. The docking search space was established around the peptidase domain, the active site including the catalytic Zn2+, which is complexed by histidine residues 502 and 506, and histidine-stabilizing glutamate residues 503 and 534.
Protein and ligand structures were protonated according to the physiological pH (7.4). Conformations of the screened ligands were generated using DataWarrior 5.2.1 [32 (link)] and were minimized with MMFF94s+ forcefield. A total of 12 docking runs was performed for each compound and the results were retrieved as the binding energy (ΔG, kcal/mol) and ligand efficiency (ΔG\no. of heavy atoms). Molecular interactions and binding poses were analyzed using BIOVIA Discovery Studio Visualizer (BIOVIA, Discovery Studio Visualizer, Version 17.2.0, Dassault Systèmes, 2016, San Diego, CA, USA).
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3

Molecular Docking of Emodin with SARS-CoV-2 Targets

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The three-dimensional structure of emodin was downloaded from the PubChem database [22 (link)]. Subsequently, the MOL2 file was transformed into a PDB format using Open Babel 2.4.1 software. Then, we converted the PDB file into a pdbqt format using the AutoDock Tools v.1.5.6 software. The receptor proteins, including 3CL (PDB ID: 6LU7) and ACE2 (PDB ID:2AJF), were obtained from RCSB Protein Data Bank (PDB, http://www.rcsb.org/) database [23 (link)]. During the docking process, the proteins were imported into PyMOL 2.3.2 software to remove water molecules, and the AutoDock Tools v.1.5.6 software was used to conduct hydrogenation and to calculate Gasteiger charges; these results were subsequently saved as the pdbqt format. The parameters of the receptor protein docking sites were set to cover those active pocket sites in which small molecular ligands complex might bind. In addition, the ligand compound (emodin) was set to flexibility and the receptor to rigidity. Furthermore, AutoDock Vina v.1.1.2 [24 (link)] was used to dock the compound and core targets or proteins, including the proteins of 3CL and ACE2 in SARS-CoV-2. The visualization of the docking results with the lowest binding energy was presented using PyMOL 2.3.2 software and LigPlot +v2.2.
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4

Molecular Docking of Imidazole and Sfβgly

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Sfβgly initial coordinates were taken from the PDB entry 5CG0. The imidazole 3D coordinates were generated in Gabedit v. 2.5.1 [30 (link)]. The addition of hydrogen atoms, and deletion of water molecules, ions, and other molecules from the protein initial structure were carried out using Chimera v. 1.14 [31 (link)], as well as the grid box coordinates covering all protein atoms, as previously described [32 ]. Docking of imidazole and Sfβgly was performed using AutoDock Vina v. 1.1.2 [33 (link)] launched from Chimera searching the 10 best models. The imidazole was docked in the mono‐protonated (+1 charge) state. The Sfβgly–imidazole complexes representing the different docking solutions were visualized by using the pymol v 0.99 software (Schrödinger LLC, New York, NY, USA).
The crystallographic structures of the β‐glucosidases from Neotermes koshunensis and Paenibacillus polymyxa (PDB ID 3AI0, 2O9R, 2Z1S, respectively) containing the substrates NPbglc, thiocellobiose and C4 were structurally superposed to the Sfβgly (PDB ID 5CG0). Next, the structure of the β‐glucosidases from N. koshunensis and P. polymyxa were removed leaving only the substrate overlaid on the Sfβgly active site niche. The superimpositions were prepared and visualized using the pymol v 0.99 software.
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5

Molecular Docking of Bio-Active Compounds

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Three dimensional (3D) shapes of the bio-active compounds were constructed using the ChemOffice v.17.1 software (PerkinElmer, CA, USA) and then converted into mol2 format. The 3D shapes of the core targets with PDB format were downloaded from RCSB Protein Data Bank (PDB) (http://www.rcsb.org/) [37 (link),38 (link)]. Protein pre-processing operations including dehydrating and hydrogenation were performed using PyMOL v2.4 software (Palo Alto, CA, USA); then, the format of bio-active compounds and core targets were converted into PDBQT format using AutoDock v.4.2.6 software [39 (link)]. Subsequently, the molecular docking was performed using AutoDock Vina v. 1.1.2 software [40 ]. The binding energy below −20 kJ/mol was used as the screening threshold [41 (link)].
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6

Molecular Docking Analysis of MtGST Proteins

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The 3D structure of the above MtGST proteins was used as a receptor to check the binding potential with two well-characterized substrates- reduced glutathione (GSH) and 1-Chloro-2,4-dinitrobenzene (CDNB). Three-dimensional chemical structures of these two ligands were retrieved from the PUBCHEM compound database (http://www.pubchem.ncbi.nlm.nih.gov) as SDF file. The ligand file conversions required for the docking study were performed using the open-source chemical toolbox Open Babel v. 2.3.2. [52 (link)]. Grid box parameters were set to accommodate each compound within the binding site of each protein and determined using AutoDock Tools v. 1.5.6rc3 [53 (link)]. Molecular docking calculations for two ligands with each of the proteins were performed using AutoDock Vina v. 1.1.2. [54 (link)] and the PDBQT files were generated using the MGL tools.
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7

Docking Simulation of cAMP-bound SmPDE4A_CD

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The ligand and the cAMP-liganded SmPDE4A_CD structure (PDB code: 6EZU [30 (link)]) were obtained from the PDEStrIAn database [35 (link)]. The protein, ligand and 3D grid were prepared with AutoDockTools v1.5.6. The coordinates of the center of the 3D grid were defined as: center_x = 17.609, center_y = 13.197, center_z = 47.972. The dimensions of the grid were: 26, 24 and 28 (for x, y and z, respectively). The docking was performed with AutoDock Vina v1.1.2 [36 (link)] using the default settings. The residues M614 (MS.40) and N578 (NHC1.25) were kept flexible.
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8

Zebrafish BMP1 Docking Study

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First, the structure of zebrafish BMP1 (BMP1_DANRE) for the docking study was modeled using the SWISS-MODEL server with the human BMP1 structure as the template (PDB: 6BSL). Then, hydrogen atoms were added and subjected to further docking experiments with AutoDock Vina v1.1.2 according to the instructions [53 (link)]. The grid box size was defined around a known BMP1 inhibitor (hydroximate Compound 22) binding site with dimensions of 40 × 40 × 40 Å grid points. Ligand conformations of NPL1010 and NPL3008 were obtained from the virtual screening database LIGANDBOX (version 1306) [54 (link)]. Molecules were docked using AutoDock Vina with exhaustiveness grade 8 and a maximum of 100 poses searched per molecule. The lowest energy conformations for NPL1010 and the second-lowest energy conformation for NPL3008, which exhibited good agreement with NPL1010 binding, were selected. The results were visualized using PyMOL (opensource version, Schroedinger).
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9

Structural Modeling of LMO4-Peptide Complexes

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Structures of LMO4:peptide complexes were modeled using coordinates of LMO4:Ldb1 complex (PDBId: 1RUT) using Swiss‐PDB Viewer v4.1 (Guex & Peitsch, 1997 (link); Johansson et al, 2012 (link)). Positional refinement and calculation of free binding energy ΔΔG of LMO4:peptide complexes were performed by FoldX v5 (Schymkowitz et al, 2005 (link)). Donor and acceptor atoms of LMO4 LI1:Jacob peptide complexes were identified using ZINCPharmer and ZINC15 (11/20) (Koes & Camacho, 2012 (link)). Nitarsone (4‐Nitrophenylarsonic acid) has been geometrically optimized and generated in PDB format by Avogadro v1.2 (Hanwell et al, 2012 ) and used as ligand for LMO4 LIM1 by molecular docking program AutoDock Vina v1.1.2 (Eberhardt et al, 2021 (link)). Secondary structures of full‐length hJacob and hCreb were predicted with PsiPred v1.1.2 (McGuffin et al, 2000 (link)). RaptorX (12/20) (Källberg et al, 2012 (link)) was used to predict the structure of Jacob C‐terminus. Structures were visualized using Open‐source PyMol v2.5 (pymol.org).
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10

Computational Docking of Inflammatory Targets

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The open-source software, Auto Dock Vina v1.1.2.26 (link),27 (link) was used for carrying out the docking study. The 3D protein structures were downloaded from the protein data bank.27 (link) (https://www.rcsb.org/) as pdb format for tumor necrosis factor-alpha “TNF-α” (ID: 2AZ5), interleukin-1β “IL-1β” (ID: 6Y8M), glycogen synthase kinase 3-β “GSK3-β” (ID: 3F88), matrix metalloproteinases-8 “MMP-8” (ID: 5H8X) and nitric oxide synthase “iNOS” (ID: 3N2R). Protein and ligand preparations were performed by MGL tools 1.5.7. and both files were saved as pdbqt which is the required format needed in Auto Dock Vina docking procedure. The protein-ligand interaction patterns were visualized by the BIOVIA Discovery Studio Visualizer v21.1.0.20298.27 (link)
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