To offer rationalizations of SAR trends, select synthesized molecules were analyzed by molecular docking using AutoDock Vina 1.5.6.50 (link) The PDB file of DHODH (1D3G) was downloaded from the Protein Data Bank and was prepared for docking by fixing missing bonds or atoms, adding polar hydrogens and Kollman charges, and removing water molecules. The protein was validated by first removing the cocrystallized brequinar analogue followed by docking it in the same binding site. The coordinates to be used as the center of the grid box were determined by calculating the centroid of the brequinar analogue using BIOVIA Discovery Studio Visualizer.51 The compounds were drawn using ChemDraw Ultra and converted to 3D structures, with their geometries optimized by the semiemperical MM2 method, and were converted to pdbqt files using AutoDock Tools.
Discovery studio visualizer
Manufactured by Revvity Signals Software
Sourced in United States
Discovery Studio Visualizer is a software tool that enables the visualization and analysis of molecular structures and data. It provides a comprehensive set of tools for tasks such as protein structure visualization, ligand-binding site analysis, and molecular dynamics simulation analysis.
Automatically generated - may contain errors
2 protocols using discovery studio visualizer
1
Molecular Docking Analysis of DHODH
2
Jengkol Metabolite Profiling and Molecular Modeling
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Samples of jengkol were obtained from several markets in West Java, using the cluster sampling method. The stationary phase used for HPLC was column C18 (250 × 4.6 mm, 5 µm) and for that of LC-MS was column C18 1.7 µm (2.1 × 100 mm). Chemical materials include 2,3-diaminonaphthalene (Sigma-Aldrich®, St. Louis, MO, USA), sodium selenite (Na2SeO3; Sigma-Aldrich®), acetonitrile (ACN; Merck® (St. Louis, MO, USA) HPLC grade)), methanol (Merck® HPLC Grade), cyclohexane (Merck® Analysis Grade), nitric acid (Merck® Analysis Grade), perchloric acid (Merck® Analysis Grade), hydrochloric acid (HCl; Merck® Analysis Grade), and Na-EDTA (Merck® Analysis Grade). The analysis of molecular docking was performed using Auto dock 1.2.6, BIOVIA Discovery Studio Visualizer® (San Diego, CA, USA), ChemDraw 8.0. The molecular dynamic simulation was performed using GROMACS 2016.3.
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