Data analysis was performed in Origin Pro 9. Chemical structures were drawn using ChemDraw Professional 17.1. All schematics were created in Adobe Illustrator CC 22.1 and ChemDraw Professional 17.1 using included copyright-free templates.
Chemdraw professional 17
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ChemDraw Professional 17.0 is a software tool designed for creating high-quality chemical structures, diagrams, and illustrations. It offers a range of drawing and editing tools to assist scientists, researchers, and professionals in the fields of chemistry, biology, and related disciplines.
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Lab products found in correlation
5 protocols using chemdraw professional 17
1
Analytical Pipeline for Chemical Structures
2
Structural Preparation and Docking of SARS-CoV-2 Mpro Inhibitors
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The ChemDraw professional 17.0 was used to sketch the 2D chemical structures of the selected pederin, mycalamide, onnamide, and theopederin compounds (1–34) which were copied to the MOE window individually. Each transferred compound was converted to its 3D form, energy minimized after the adjustment of its partial charges as well, and saved as (.moe) extension to be ready for the docking step as described earlier.65–67 Moreover, the co-crystallized inhibitors of both the used dimeric SARS-CoV-2 Mpro (6Y2G ) besides that of the monomeric form (6LU7) (35 and 36, respectively) were extracted and saved separately to be used as reference standards. Finally, all the aforementioned prepared compounds (1–36) were inserted in one database file and saved as (.mdb) extension to be uploaded to the ligand site during the docking process.
3
Molecular Docking of BAP 16 with Proteins
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The PDB files for the crystal structures of Bcl-2, NF-κB/p65, and p38 were obtained using the protein data bank codes 1YSW, 1MY5, and 4FA2, respectively. The molecular docking procedure was performed under the C-DOCKER protocol of Accelry’s Discovery Studio 2017R2 software. For ligand preparation, the structure of BAP 16 was constructed using ChemDraw Professional 17.0 software, saved in SDF file format and minimised using Accelry’s Discovery Studio 2017R2 software. The protein structures were cleaned and inspected for errors, hydrogens were added, and the water molecules were deleted. For Bcl-2 protein as a receptor, the centroid of the binding site was defined based on the ligand in the cocrystal structure. Then removed the original ligand and placed the molecule of BAP 16 in the sphere position to carry out molecular docking. Subsequently, p65 and P38 proteins were defined as receptors and docked in a similar process. For energy minimisation, the CHARMM force field was utilised within Accelry’s Discovery Studio 2017R2 software. Finally, types of interactions between the docked proteins and BAP 16 were analysed.
4
Structural Analysis of Carbonic Anhydrase Enzymes
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hCA I (PDB code: 6Y00, resolution 1.37 Å) [35 (link)], hCA II (PDB code: 4BF1, resolution 1.35 Å) and hCA IX (PDB code: 4ZWX, resolution 1.70 Å) [36 (link)] crystal structures were retrieved from the Protein Data Bank (www.pdb.org , accessed on 19 February 2022). The downloaded crystal structures were prepared employing the preparation wizard of the Schrodinger 2021 suite package under the default settings with the pH value set at a value of 7.4. All ligands were first sketched via ChemDraw Professional 17.0, then exported as a structure data file format and sent to the Ligprep module. Ligand preparation was achieved utilizing the Schrodinger Ligprep module to optimize the geometry of the studied ligands. Glide’s standard precision module was employed to dock the minimized ligands into the appropriate crystal structure binding site, yielding 10 poses for each docked ligand.
5
Structural Analysis of Human Carbonic Anhydrase Isoforms
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The crystal structures of carbonic anhydrase isoforms hCA I (PDB code: 6Y00, resolution 1.37 Å)39 , hCA II (PDB ID: 4BF1, resolution 1.35 Å)40 (link), hCA IX (PDB code: 4Z0Q, resolution 1.45 Å)41 (link) and hCA XII (PDB code: 1JD0, resolution 1.50 Å)42 (link) were obtained from the Protein Data Bank (www.pdb.org ). The downloaded crystal structure was prepared using the Schrodinger 2021 suite package’s preparation wizard with the default settings and pH value of 7.4. ChemDraw Professional 17.0 was employed to sketch the ligands, which were then exported in the structure data file format (SDF) and sent to the Ligprep module. The Schrodinger Ligprep module was then utilised in the ligand preparation process to further optimise the geometry. Glide’s extra precision module was used to dock the minimised ligands inside the binding cavity of the appropriate crystal structure, generating 10 poses per docked ligand. The pose with the most negative docking score was chosen to display.
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