The commonly used pyrethroid compound, permethrin, was chosen for the present study. The three-dimensional structure of permethrin was downloaded from the PubChem compound database (https://pubchem.ncbi.nlm.nih.gov/ ; accessed on 20 December 2020). All four possible stereoisomers were generated from the given structure and were subjected to structural binding studies using the Schrodinger 2017 suite with Maestro 11.4 as a graphical user interface (Schrodinger, LLC, New York, NY, USA, 2017). The detailed methodology was already described in our previous study [36 (link)].
2017 suite
Manufactured by Schrödinger
Sourced in United States
The 2017 suite is a collection of software tools developed by Schrödinger to aid in computational chemistry and drug discovery research. The suite includes a range of applications that can be used for tasks such as molecular modeling, simulation, and analysis. The core functionality of the suite is to provide a comprehensive set of tools for researchers working in these fields.
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Lab products found in correlation
4 protocols using 2017 suite
1
Structural Binding Analysis of Permethrin Stereoisomers
2
Structural Characterization of PBDE Flame Retardants
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The three-dimensional structural coordinates of PBDE flame retardants: BDE-28, BDE-100, BDE-153, and BDE-154, were downloaded from the PubChem compound database (https://pubchem.ncbi.nlm.nih.gov/ ) on 10 June 2021. The aforementioned ligands were chosen as they are very commonly used PBDEs and are detected in a large section of the population [92 ]. It was followed by structural binding characterization of these ligands using Schrodinger 2017 suite with Maestro 11.4 as a graphical user interface (Schrodinger, LLC, New York, NY, USA, 2017). The detailed methodology is described in our previous studies [93 (link),94 (link)].
3
In Silico Docking of Acetylshikonin with TOPK
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To further confirm that acetylshikonin can bind with TOPK, we performed in silico docking using the Schrödinger Suite 2017 software programs (Schrödinger, 2017 ). The sequence of TOPK was downloaded from the National Center for Biotechnology Information (GI: 83305809). The TOPK crystal structure was built with prime followed by refining and minimizing loops in the binding site, and then it was prepared under the standard procedures of the Protein Preparation Wizard. Hydrogen atoms were added consistent with a pH of 7, and all water molecules were removed. The TOPK ATP‐binding site‐based receptor grid was generated for docking. Acetylshikonin was prepared for docking by default parameters using the LigPrep program. Then, the docking of acetylshikonin with TOPK was accomplished with default parameters under the extra precision (XP) mode using the program Glide. Then, TOPK modelling structure was refining and minimizing loops in the binding site. When the docking was performed, usually several docking models were generated. Herein, we based on the docking score and ligand interaction diagram to choosing best docked representative structure for our final docking model.
4
Molecular Docking and Binding Analysis
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Protein coordinates were downloaded from the Protein Data Bank, accession code 5ZUN. The Schrödinger suite 2017 (Schrödinger, Cambridge, MA, USA) was used for all the computational procedures, and, unless otherwise stated, default settings were applied. The protein was prepared using Protein Preparation Wizard; tetraethylene glycol (PG4), 1,2 ethanediol (EDO), chloride ion (CL), and water molecules (except water molecules HOH542 and HOH585) were removed. Cognate ligand (1-(2-chlorobiphenyl-3-yl)-4-[4-(1,3-thiazol-2-ylcarbonyl)-piperazin-1-yl]pyrrolidin-2-one) and ArLuc-1 were built using the Maestro Build Toolbar and prepared for docking by Schrödinger Ligand Preparation. The receptor grid was created by the Receptor Grid Generation, the box was centered on the cognate ligand of 5ZUN, and the size of the ligand diameter midpoint cubic box was set to 14 Å. The docking was run with Glide Docking using the extra precision (XP) mode, keeping at most 20 poses per ligand and 200 poses to include in the minimization. The top poses were refined using MM–GBSA (molecular mechanics with generalized Born surface area), as implemented in Prime. Residues at a distance of 12 Å from the ligand were considered as a flexible region in the refinement.
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