DOI: 10.57760/sciencedb.01889
title: Simulation analysis and physiological and biochemical evaluation of Sophora flavescens Alt. aboveground against aphid based on network pharmacology
title: Simulation analysis and physiological and biochemical evaluation of Sophora flavescens Alt. aboveground against aphid based on network pharmacology

description: First of all, for the Enzyme assays data: this is to determine the insect three Elisa kits (6-glucose-phospho-1-dehydrogenase;  Thymidylate synthase, translocation factor protein), we tested aphids on two host plants, datura (A) and Cabbages (B).  The alkaloids determined included matrine, oxymatrine, sophorine, and sophoridine.  The crude extract tested was the above-ground part of sophora flavescens.  SPSS software was used to conduct anOVA on the data. In ANOVA, 1 represented the administration group as blank control.  2 represents the concentration of administration of 100 micromol;  3 represents the dose concentration of 1 mM;  4 represents the administration concentration of 10 mM;  5 represents the dose concentration of 100 mM. For PPI in online pharmacological data: First, the compound names obtained by HIGH performance liquid chromatography-mass spectrometry/mass spectrometry (HPLC-MS/MS) before input on PubChem website were downloaded 2D structure and the formula was imported into SwissADME.  If the Druglikeness part contains three or more yes, the compound will be imported into swisStar Prediction to predict the possible target of its structure.  Download all relevant target information and compare it with aphid target information in uniprot database to find common target information.  Input the obtained common target protein into the string website, select the aphid species, and get the protein interaction diagram of sophora flavescens killing aphid.  The string system uses a scoring mechanism to give weight to the results, and finally gives an overall score. The interaction network of sophora flavescens killing aphid was constructed by setting the lowest correlation coefficient of the interacting proteins as 0.15.  Cytoscape software was used to obtain the core targets.For molecular docking data: download active ingredient formula from the PubChem database, with Swiss - model to predict the tertiary structure of large molecules aphids, when the target sequence and the template sequence &gt; consistency of 30%, PyMOL software was used to remove water and phosphate from the protein. AutoDockTools 1.5.6 software was used to convert the PDB format of drug active ingredients and core protein gene files to PDBQT format, and active pockets were retrieved. Finally, Vina script was used to calculate the molecular binding energy, and the results of molecular docking were shown.  For molecular dynamics data: with the help of molecular dynamics simulation software GROMACS 2019.6, using the complex (from docking analysis) as the initial conformation, all-atom molecular dynamics simulations of action and verify the reliability of the binding mode Amber 99SB-ILDN force field parameters were used for receptor protein, and the topology files of ligand molecules of GAFF2 type were generated by ACPYPE and Antechamber programs. The dodecahedral solvation box is selected, and the closest distance between the system boundary and the complex was seted to 1.1 nm. The TIP3P water model was selected and 15 Na+ were randomly added to the complex system according to the VERLET cut-off method to counteract the charge of the protein. Then, the system energy was minimized, the NVT temperature was controlled, and the NPT pressure was controlled to make the system temperature 300 K and the pressure constant at 101.325 kPa. Based on the above equilibrium system, a 0-100 ns free kinetic simulation was performed.The The binding free energy between protein and ligand by Molecular Mechanics-Poisson Bolzmann Surface Area (MM-PBSA) method. 
description: First of all, for the Enzyme assays data: this is to determine the insect three Elisa kits (6-glucose-phospho-1-dehydrogenase;  Thymidylate synthase, translocation factor protein), we tested aphids on two host plants, datura (A) and Cabbages (B).  The alkaloids determined included matrine, oxymatrine, sophorine, and sophoridine.  The crude extract tested was the above-ground part of sophora flavescens.  SPSS software was used to conduct anOVA on the data. In ANOVA, 1 represented the administration group as blank control.  2 represents the concentration of administration of 100 micromol;  3 represents the dose concentration of 1 mM;  4 represents the administration concentration of 10 mM;  5 represents the dose concentration of 100 mM. For PPI in online pharmacological data: First, the compound names obtained by HIGH performance liquid chromatography-mass spectrometry/mass spectrometry (HPLC-MS/MS) before input on PubChem website were downloaded 2D structure and the formula was imported into SwissADME.  If the Druglikeness part contains three or more yes, the compound will be imported into swisStar Prediction to predict the possible target of its structure.  Download all relevant target information and compare it with aphid target information in uniprot database to find common target information.  Input the obtained common target protein into the string website, select the aphid species, and get the protein interaction diagram of sophora flavescens killing aphid.  The string system uses a scoring mechanism to give weight to the results, and finally gives an overall score. The interaction network of sophora flavescens killing aphid was constructed by setting the lowest correlation coefficient of the interacting proteins as 0.15.  Cytoscape software was used to obtain the core targets.For molecular docking data: download active ingredient formula from the PubChem database, with Swiss - model to predict the tertiary structure of large molecules aphids, when the target sequence and the template sequence &gt; consistency of 30%, PyMOL software was used to remove water and phosphate from the protein. AutoDockTools 1.5.6 software was used to convert the PDB format of drug active ingredients and core protein gene files to PDBQT format, and active pockets were retrieved. Finally, Vina script was used to calculate the molecular binding energy, and the results of molecular docking were shown.  For molecular dynamics data: with the help of molecular dynamics simulation software GROMACS 2019.6, using the complex (from docking analysis) as the initial conformation, all-atom molecular dynamics simulations of action and verify the reliability of the binding mode Amber 99SB-ILDN force field parameters were used for receptor protein, and the topology files of ligand molecules of GAFF2 type were generated by ACPYPE and Antechamber programs. The dodecahedral solvation box is selected, and the closest distance between the system boundary and the complex was seted to 1.1 nm. The TIP3P water model was selected and 15 Na+ were randomly added to the complex system according to the VERLET cut-off method to counteract the charge of the protein. Then, the system energy was minimized, the NVT temperature was controlled, and the NPT pressure was controlled to make the system temperature 300 K and the pressure constant at 101.325 kPa. Based on the above equilibrium system, a 0-100 ns free kinetic simulation was performed.The The binding free energy between protein and ligand by Molecular Mechanics-Poisson Bolzmann Surface Area (MM-PBSA) method.