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AutoDock Tools v1.5.6

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AutoDock Tools v1.5.6 is a molecular docking software package that allows users to predict the binding of small molecules to protein targets. The software provides a graphical user interface for preparing input files, running docking calculations, and analyzing the results.

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67 protocols using AutoDock Tools v1.5.6

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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The potential binding modes and the main interactions of compounds 5b, 6a and 9g with the AChE were determined using AutoDock Vina (version 1.1.2). The crystal structure of AChE (PDB ID: 6WVO) was obtained from Protein Data Bank (https://www.rcsb.org). After water and other irrelevant small molecules were removed by Pymol 2.1 software, the AChE structure was pretreated and converted into pdbqt format using AutoDockTools v.1.5.6. The size of the grid box was set to 60 × 70 × 80 Å with a grid spacing 0.375 Å, and the grid was centered at −17.222, −38.784, and 28.591 (in x, y, and z dimensions, respectively). The optimized 5b, 6a and 9g at the DFT/B3LYP/6-31G(d) level was also pretreated and converted into pdbqt format using AutoDockTools v.1.5.6.
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Protein processing consisted of binding polar hydrogens, merging nonpolar hydrogens, and calculating Kollman’s charge with AutoDock Tools v.1.5.6 (Morris et al., 2009 (link)). Ligand preparation consisted of adding hydrogens under pH 7.4, minimizing their energies under an MMFF94 force field employing Avogadro v.1.2.0 software; subsequently, Gaisteiger charges were calculated with AutoDock Tools v.1.5.6. With the DoGSiteScorer tool of the ProteinPlus server (Schöning-Stierand et al., 2020 (link)) the protein binding regions were predicted, only those regions with a druggability score greater than or equal to 0.75 were evaluated. Molecular docking was performed using AutoDock v.4.2 software; 64 X 64 X 64 boxes were used, covering individually the previously predicted regions.
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We selected the crystallographic structures of β-ketoacyl-acyl carrier protein synthase (β-ketoacyl-ACP synthase) and tyrosyl-tRNA synthetase (TyrRS) with Protein Data Bank IDs 1FJ4 and 1JIJ [36 (link),37 (link)]. Water molecules and bound ligands were removed from the enzymes. In AutoDock Tools v1.5.6, the target protein was protonated by adding polar hydrogen atoms and Kollman charges [38 (link)]. Meanwhile, the structures of the isolated compound and ciprofloxacin (ligand) were drawn using ChemDraw and optimized in HyperChem with AM1 methods. Lastly, hydrogen atoms were added to the ligand structures, and the Gasteiger charges were adjusted using AutoDock Tools v1.5.6 [39 (link)].
The binding affinity and interactions of the isolated compounds in S. trifasciata were determined using AutoDock. The native ligands (TLM and 629) were redocked to the β-ketoacyl-ACP synthase and TyrRS, respectively, to validate the docking parameters. The validated procedures were identified with a root mean square deviation (RMSD) below 2 Å [40 (link)]. The binding site of β-ketoacyl-ACP synthase and TyrRS were set according to their native ligand positions and calculated using a cubic shape with a grid area of 40 × 40 × 40 Å. The proteins’ and ligands’ hydrogen bonding and hydrophobic interactions were analyzed and visualized employing Discovery Studio Visualizer v.17.2.0.16349 software.
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The Alphafold software tool was used to generate the predicted structure of SEMA3C and its interaction with possible ligands.70 (link),71 (link) The X-ray crystal structure of RAGE (RCSB entry: 4IM8) was obtained from the Protein Data Bank. To ensure the accuracy of the docking results, the protein was prepared using AutoDock Tools v1.5.7,71 and water molecules were manually removed from the protein-protein docking structure.72 (link),73 (link) The resulting protein-protein complex was also manually optimized by removing water and adding polar hydrogen using AutoDock Tools v1.5.7. Finally, the protein-protein interactions were predicted and visualized using PyMOL (The PyMOL Molecular Graphics System, Version 1.3, Schrödinger, LLC). The SEMA3C protein was represented as a purple-colored cartoon model, while the RAGE protein was represented as a cyan-colored cartoon model. Their binding sites are presented as stick structures, respectively colored purple for SEMA3C and cyan for RAGE. When focusing on the binding region, the binding site is then shown as a representation of the protein to which it belongs.
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Compound 5 was sketched using the Maestro GUI (Schrödinger Release 2018-4: Maestro, Schrödinger, LLC, New York, NY, USA, 2018) and its ionization states were predicted using Epik [73 (link)] at a pH range of 7 ± 1; the state with the lowest ionization penalty was chosen for the following docking studies. The docking target structure 5DCG was downloaded from the Protein Data Bank and prepared, analogously to previously reported studies [74 (link),75 (link)], using the Protein Preparation Wizard [76 (link)]. AutoDockTools v1.5.6 [77 (link)] was used to prepare ligand and protein input files for the docking simulations. Molecular docking simulations were performed using AutoDock Vina [54 (link)]. The search space was set as a cube (62.5 Å side) centered on the protein and including both chain A and B. Considering the pretty big search space, exhaustiveness was set to 1000. The best scoring pose (−7.7 kcal/mol) was considered as the predicted bound conformation. Molecular modeling pictures were generated using open source PyMol (The PyMOL Molecular Graphics System, Version 1.7.0.0-1, Schrödinger, LLC., New York city, NY, USA)
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According to the sequence numbers of key targets identified in the UniProt database, three-dimensional images were downloaded from the PDB database and saved in the PDB format. Subsequently, the file was imported into Pymol, wherein non-polar hydrogens were introduced and water molecules and small molecular ligands were deleted to obtain the intended receptors. The three-dimensional structural diagrams of the main active components of PDB were downloaded from the TCMSP database and saved in mol2 format. The ligands and receptors were then imported into AutoDockTools V1.5.6 for molecular docking analysis and visual presentation.
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The crystal structure of TOP1 and 22 base pair DNA duplex (PDB ID: 1T8I) was used in order to perform molecular docking analysis. The energy minimization run of TOP1/DNA duplex was performed by the steepest descent algorithm with a maximum number of minimization steps of 50,000. The complex was centered in a dodecahedron box with a minimal distance of 1.0 nm to the edge of the box, and the TIP3P water model was used to solvate the system by adding 18 sodium ions [88 (link)]. Both the receptor and the ligands were prepared for the docking analysis using Autodocktools v. 1.5.6 [89 (link)]. The receptor was prepared by removing crystal ligands, adding polar hydrogens and Kollman charges as partial charges. 3D coordinates of 8a, 8b, 4a, and 4b, provided in smile format, were generated by using Open Babel software v. 2.3.2 [90 (link)]. Polar hydrogens were added to each ligand, and Gasteiger charges were added as partial charges.
AutoDock Vina software [91 (link)] was used to perform docking experiments between the selected compound and TOP1/DNA duplex. A grid box with size 10 × 10 × 10 and centered at X = 94.906 Y = 95.914 Z = 32.500 was used as search space. AutoDock Vina provided the best binding affinity rank for each ligand.
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9

Molecular Docking and QM/MM Optimization of Natural Product Inhibitors Against SARS-CoV-2 Proteases

Molecular structures of the natural product ligands were optimized by B3LYP/6-311G(d) method25 , 26 , 27 . The crystal structure of 3CLpro (PDB ID: 6LZE)6 (link) and PLpro (7CJM)10 (link) were used as a reference for protein–ligand system. Docking calculations were performed by AutoDock Vina and AutoDocktools v1.5.6 software28 (link). The extracted complex of the ligand and amino acid residues from molecular docking was optimized by QM/MM simulations. The QM atoms from schaftoside, H41, G143, C145, R188 and Q192 of 3CLpro, and K157, E167, A246 and Y268 of PLpro were described by DFT method B3LYP at 6-311G basis set, while the MM atoms from T25, T26, M49, M162, H163, F140, N142, H164, M165, E166, P168, D187 and Q189 of 3CLpro, and D164, P247, P248, Y264, Q269, Y273 and T301 of PLpro were simulated by the UFF force field29 . The calculations were performed using the Gaussian16 suite of codes30 .
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According to the CAS number of the small molecule, we downloaded the 3D structure of small molecules in mol2 format from ZINC (chttp://zinc.docking.org/) [20 (link)]. We then imported it into ChemBio3D ultra 14.0 for energy minimization, set the minimum RMS gradient to 0.001, and saved the small molecules in “mol2” format. The optimized small molecules were imported into AutodockTools v1.5.6 for hydrogenation, charged calculation, charged distribution, set the rotatable key, and saved in “pdbqt” format.
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