In the molecular docking study, hCA I (PDB: 2FOY) (29) and hCA II (PDB: 1IF7) (29), as well as AChE and BChE (30), were retrieved from the Protein Data Bank in pdb format. Ions, water molecules, and ligands were removed from the downloaded proteins, and polar hydrogens and Gasteiger charges were added to the proteins. The proteins were saved in pdbqt format using AutoDockTools 1. 5.6 (31) . Ligands were drawn in ChemDraw3D 19.0, minimized, and saved in pdb format. After conversion to pdbqt format using AutoDockTools 1.5.6, molecular docking was carried out using the latest AutoDock Vina program (32). The results were visualized in 2D and 3D using PyMOL (33) and the Discovery Studio Visualizer (34).
Vina program
Manufactured by AutoDock
17 citations
About the product
AutoDock Vina is a molecular docking software program. It is designed to predict the binding affinity and conformation of small molecules to target proteins. The program uses a scoring function to evaluate the interactions between the ligand and the receptor, and then generates a set of possible binding modes. AutoDock Vina is a free, open-source software available for academic and non-commercial use.
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17 protocols using «vina program»
1
Molecular Docking Study of Enzymes
2
Antibacterial and Molecular Docking
The antibacterial activities of isoliquiritigenin, biochanin A, and isorhamnetin were evaluated by filter paper diffusion (5 mg/mL). On the basis of antibacterial activity, the UCSF Chimera software was used for the molecular docking of filamenting temperature-sensitive mutant Z (FtsZ: 4XSG) protein with isoliquiritigenin to predict its interaction force. First, FtsZ protein and isoliquiritigenin were pretreated, which included removing water molecules, adding hydrogen atoms, adding electrons, and minimizing energy. Second, the molecular docking of FtsZ and isoliquiritigenin was performed using the AutoDock Vina program to predict their affinity. The grid box with dimensions of 50 points × 55 points × 55 points was centered on the active site of the protein. Finally, the stability of FtsZ–isoliquiritigenin binding was evaluated with reference to the binding energy. A low score corresponded to high stability.
Corresponding organizations : Shanxi Agricultural University
3
Homology Modeling and Molecular Docking of PKCδ
Since the structure of human PKCδ has not been characterized, homology modeling was performed to generate the human PKCδ protein structure for molecular docking simulations [23 (link)]. The structures of each of the six iridoid compounds were obtained from PubChem (https://pubchem.ncbi.nlm.nih.gov/ accessed on 7 January 2021) and determined using the Marvin program (https://www.chemaxon.com accessed on 10 January 2021). As previously described, the docking simulation between PKCδ and each compound was performed using the Autodock Vina program (http://vina.scripps.edu accessed on 6 February 2021), as presented in Table S1 and Supplementary Figure S5 [23 (link)].
Corresponding organizations : Korea Research Institute of Bioscience and Biotechnology, Chungnam National University, Korea University of Science and Technology
4
Molecular Docking for Network Pharmacology Validation
In this study, molecular docking method was preliminarily utilized to validate the results of network pharmacology. Through the RCSB Protein Data Bank (PDB, http://www.rcsb.org/pdb ), protein receptors of hub genes were selected according to the following criteria: (1) the structure of protein receptors was identified by X-ray diffraction, (2) X-ray resolution < 3 as the first choice, and (3) protein structures containing original ligands (e.g., inhibitors) were preferred. By using AutoDockTools1.5.6 (http://autodock.scripps.edu ), the original ligands (if any), excess protein chains, and water molecules of the protein receptor were removed, then hydrogen was added to the protein receptors, and possible docking coordinates were searched. The structure (“mol2” format) of the corresponding bioactive ingredients of the target protein was obtained by TCMSP database. Subsequently, the file format of protein receptor or bioactive ingredient was converted to “PDBQT” using AutoDockTools, and molecular docking was performed using AutoDock Vina program (http://vina.scripps.edu/ ). Finally, the results were analyzed and visualized using PyMOL (http://www.pymol.org/ ) and Discovery Studio 2016.
Corresponding organizations : Guangzhou University of Chinese Medicine, Shenzhen Pingle Orthopedic Hospital, Shenzhen Nanshan Center for Chronic Disease Control
5
Computational Docking of c-MYC G4 Ligands
The NMR structure of a mutated c-MYC G-quadruplex (PDB 2MGN) was used to perform docking study on ligands 2 and 3 . The three-dimensional structure of small molecules was sketched with DS viewer 3.5. Autodock Tools (version 1.5.6) was used for converting structure files to pdbqt format (49 (link)). The docking study was carried out by using AutoDock Vina program (50 (link)). The dimensions of the active site box were chosen to be large enough to encompass the entire G4 structures. An exhaustiveness of 100 was used and other parameters were left as default.
Corresponding organizations : Guangdong University of Technology, Thunder Bay Regional Research Institute, Lakehead University, Sun Yat-sen University, Hong Kong Polytechnic University, Wuyi University
Top 5 most cited protocols using «vina program»
1
Molecular Docking of HIV-1 Protease and Reverse Transcriptase
HIV-1 protease (PDB: 5KR0) [48 (link)] and HIV-1 RT (PDB: 3QIP) [49 (link)] were obtained from the Protein Data Bank. The proteins were prepared using AutoDockTools-1.5.6. The water molecules and the original ligands: Amprenavir, Nevirapine, and 5,6-dihydroxy-2-[(2-phenyl-1H-indol-3-yl) methyl] pyrimidine-4-carboxylic acid (P4Y) were removed. Moreover, all missing hydrogen atoms were added in the protein structures. Then the file format was converted to PDBQT before molecular docking analysis. Energy minimization for the ligands was done using BIOVIA Discovery Studio 2020 software. All candidate ligands were docked against HIV-1 PR and RT by using AutoDock 4.2 [13 (link)]. For HIV-1 PR, the grid box was set to 60 × 60 × 60 xyz points of size and 0.375 Å of spacing at the center of HIV-1 PR. Moreover, two active sites of HIV-1 RT, including polymerase and RNase H active sites, were studied. The parameters of grid boxes for polymerase and RNase H active sites were set to 40 × 40 × 40 xyz points of size, 0.375 Å of spacing, and grid center at 9.831 × 13.983 × 17.1 xyz; and 35 × 35 × 35 xyz points of size, 0.375 Å of spacing, and grid center at 0.144 × 74.854 × 34.626 xyz, respectively. The top 10 compounds provided the highest binding affinity were further run on another molecular docking platform, AutoDock Vina program [42 (link)] to support the AutoDock 4.2 results. Hydrogen bond interactions of the docked structures were further analyzed using the Discovery Studio Visualizer.
Corresponding organizations : Chulalongkorn University
2
Molecular Docking of Ginsenoside Rh1 with ROCK1 and RhoA
The ROCK1 protein [PDB ID: 5WNE] and RhoA protein [PDB ID: 4D0N] 3D structure was retrieved from the Protein Data Bank (PDB) [92 (link),93 (link)] along with the co-crystalized ligand of fasudil and GDP. To perform the docking studies, the ROCK and RhoA structure was prepared by Autodock tool graphical interface (GUI) [94 (link)]. A known inhibitor fasudil and GDP along with the water molecules were removed from the original structure and made as a free receptor [58 (link)]. Further, Kollman charges and polar hydrogens were added to the receptors. The fasudil and GDP binding sites are the most likely active sites. Further, fasudil is involved in two hydrogen bond interactions with the M156 and D160 residues and other studies have shown that these residues play a role in ROCK1 inhibition [95 (link)].
The energy-minimized ginsenoside Rh1 with ROCK1 and RhoA protein structures were used to perform docking simulations by the Autodock Vina program [89 (link)]. The fasudil and GDP compound was used as a control for this study. The detailed docking procedures were followed according to our previous study [96 (link),97 (link)]. The potential binding interaction was identified based on binding affinity scores and hydrogen bond interactions between ROCK1 and RhoA with ginsenoside Rh1. The results of each complex were saved from the graphical interface of Autodock tools and imported to DS.3.5 visualizer to analyze their interactions at the molecular level.
The energy-minimized ginsenoside Rh1 with ROCK1 and RhoA protein structures were used to perform docking simulations by the Autodock Vina program [89 (link)]. The fasudil and GDP compound was used as a control for this study. The detailed docking procedures were followed according to our previous study [96 (link),97 (link)]. The potential binding interaction was identified based on binding affinity scores and hydrogen bond interactions between ROCK1 and RhoA with ginsenoside Rh1. The results of each complex were saved from the graphical interface of Autodock tools and imported to DS.3.5 visualizer to analyze their interactions at the molecular level.
Corresponding organizations : Kyung Hee University
3
Molecular Docking of G-Quadruplex Ligands
Molecular docking study was performed using the solution structure of anti-parallel human telomeric DNA G-quadruplex (PDBID: 2mb3) [45] . The first two thymine residues at the 5' end and the last residue adenine at the 3' end were deleted to produce 21-mer G-quadruplex. The 3D structures of the small molecules were generated with DS viewer 3.5. Autodock Tools (ver. 1.5.6) was used to convert the structure files to pdbqt format. [54] Docking was performed using the AUTODOCK vina program. [55] The dimensions of the active site box were chosen to be large enough to encompass the entire G-quadruplex structures. An exhaustiveness of 20 was used and other parameters were left as default.
Corresponding organizations : Guangdong University of Technology, Wuyi University, Thunder Bay Regional Research Institute, Lakehead University, Hong Kong Polytechnic University
4
Identifying SARS-CoV-2 Main Protease Inhibitors
Out of 1,275 similar compounds of boceprevir available in PubChem database [13] (link), we retrieved a total of 180 compounds having molecular weight less than 519.68 g/mol with available 3D conformers. Compounds having a Tanimoto score of 0.9 or greater were considered as similar compounds based on 2D similarity[14] (link). The Mpro structure at room temperature (PDB ID: 6WQF) [9] (link) was selected for docking since it had the suggested protonation states of histidine residues, and the structure was solved at room temperature. It has been suggested that this structure solved at room temperature is more appropriate for molecular docking studies as it provides more relevant information at physiological temperatures [9] (link). The compounds were energy minimized with the steepest descent algorithm prior to docking using UCSF Chimera [15] (link). The selected compounds, along with boceprevir as control were docked by centering the grid box centered on the substrate-binding site of Mpro (x, y and z center coordinates :36.56, 46.43 and 56.04) with the AutoDock vina program [16] (link). The screening was performed with a exhaustiveness value of 8 and ten runs for each compound, and the best pose was selected based on the lowest binding free energy (kcal/mol). The 2D ligand interactions were visualized with the Discovery studio visualizer [17] .
Corresponding organizations : Indian Institute of Technology BHU, Banaras Hindu University, Indian Institute of Technology Delhi
5
Docking Studies of FtsZ Inhibitors
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Corresponding organizations : Rutgers, The State University of New Jersey
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