Structures of the 12 ginger compounds with proven in vitro and/or in vivo activity against various central nervous system insults were retrieved from the literature.26 (link) The structures of the ligands were drawn in ChemDraw 8.0 (PerkinElmer Informatics, Waltham, MA, USA) and converted to their three-dimensional structures in Chem3D 8.0 (PerkinElmer Informatics). Geometry optimization was done using PM3 method by MOPAC program (http://OpenMOPAC.net ). Finally, all the compounds were saved in pdb format for further docking studies.
Chemdraw 8
Manufactured by PerkinElmer
Sourced in United States
ChemDraw 8.0 is a software application for chemical structure drawing and editing. It provides a set of tools for creating, modifying, and visualizing chemical structures and diagrams. The software supports various file formats and can be used for a range of applications in the field of chemistry and related disciplines.
Automatically generated - may contain errors
Lab products found in correlation
4 protocols using chemdraw 8
1
Ginger Compounds for Neurological Modeling
2
Molecular Optimization and Docking
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The two-dimensional structures of 6-gingerol, 6-shogaol, and the other redox molecules were elaborated using ChemDraw 8.0 (PerkinElmer Informatics, Waltham, MA, USA), and were imported into Avogadro (https://avogadro.cc accessed on 20 April 2022) to optimize the geometry using the force field function MMFF94. All compounds were saved as mol2 files for subsequent docking studies [19 (link),22 (link),23 (link)].
3
Designing Novel Tps1 Inhibitors
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Compounds with highest binding affinities were selected and their structures analyzed in terms of suitability for further modification, with H-bonding being one criteria. Finally, Compound 24789937 was chosen as the template, and 26 modifications were performed using ChemDraw® 8.0 and Chem3D® 8.0 (CambridgeSoft, Cambridge, MA). Each of the 26 compounds was docked into Tps1 to assess the binding affinity. SYBYL-X2.0 (Tripos, St. Louis, MO) was used to plot the electrostatic potential of the compounds.
4
Molecular Docking and Computational Analysis
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Molecular modelling and docking analysis study was carried out using AutoDock 4.2 MGL Tools (The Scripps Research Institute, USA) and Pymol Molecular Visualization package (Schrödinger).[4 (link)5 ] Computed Atlas of Surface Topography of Protein (CastP) and FT site open source servers were used to determine the possible binding sites and pocket occupancy of the target protein respectively.[6 (link)7 (link)] The polyphenolic ligands were filtered from Pubchem Database.[8 ] The selected ligands were sketched and converted to their three-dimensional formats using Chemdraw 8.0 and Chemdraw three-dimensional (Cambridge soft. Comp.).[9 (link)] SWISS-MODEL server was used to generate the homology model of target protein.[10 (link)] BLAST server was used to validate the query sequence of the protein.[11 (link)] Procheck server was used to validate the protein by generating Procheck Ramachandran plot (European Bioinformatics Institute, UK).[12 ] DruLiO tool has been used to calculate the drug-likeness of the molecule set.[13 (link)]
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