The Efficacy and Underlying Pathway Mechanisms of ShiDuGao Treatment for Anus Eczema Based on GEO Datasets and Network Pharmacology

This article evaluated the feasibility, target, and the mechanism of ShiDuGao in treating anus eczema. Network pharmacology and GEO database analysis confirms the multi-target nature of SDG in treating anal eczema, specifically by modulating TNIF, MAPK14, and the CASP3, which are crucial hard targets in the TNF and MAPK signaling pathways. These fundings provide a clear direction for further investigation into SDG's therapeutic mechanism for anal eczema, while highlighting its potential as an effective treatment approach for this debilitating condition.

Mechanism research is acknowledged as the most intricate aspect of herbal prescription investigation. Network pharmacology currently permits diverse aspect of the pharmaceutical field, making a paradigm shift from conventional to contemporary biomedicine and refining traditional Chinese medicine development. This research combined network pharmacology with GEO dataset to discern to topical drug mechanisms.

In this study, the pure data generation method was used to maximize data utilization by combining modified disease, especially for some diseases that are difficult to build animal models for. The online data are used primarily to predict and verify diseases and drug targets so as to gather research direction and lay a good foundation for subsequent experimental verification. To begin, turn on the computer system and launch the software.

Using anus eczema as the search term for disease target, access the GeneCards database and Online Mendelian Inheritance in Man database. Download the spreadsheets of the disease targets and delete the repeated targets to obtain the anus eczema targets. On the Traditional Chinese Medicine Systems Pharmacology database, search the keyword indigo naturalis, golden cypress, calcined gypsum, calamine, and Chinese gall to obtain the list of the candidate active ingredients and targets of ShiDuGao or SDG.

Entrust the component down to the Swiss ADME database. Extract the details for those exhibiting high GI absorption coupled with at least two yes DL values as active elements. In Venny 2.1, enter the targets of SDG and anus eczema into list one and list two respectively.

Once the visual representation of the intersection is generated, click on the shared area to reveal the common targets in the results section. Access the string database. In the list of names field, enter the targets, then select homo sapiens as the organism and proceed with search.

Then, click continue. Upon obtaining results, open settings. In the minimum required interaction score, set the highest confidence to 0.900.

In advanced settings, select the hide disconnected nodes in the network and click on update. Now, click on exports, then click download to download the text of the protein-protein interaction network in dot PNG and dot TSV format. The integration of target gene datasets revealed 149 frequently co-occurring target genes against anal eczema.

Subsequently, a pivotal target protein-protein interaction network was constructed. The top 10 genes with high degree scores were identified, and all were significant in relation to anal eczema drug targets. To begin, launch the Cytoscape 3.9.1 software on the desktop and import the dot TSV file containing core proteins of anus eczema.

Click on the style bar in the control panel to optimize the color, font, and size of the network nodes. For network topology analysis, employ the analyze network function. To obtain hub genes, use CytoHubba and establish the drug component disease target network.

Open the Metascape website. Select a file or paste a gene list into the dialog box and click the submit button, then select H sapiens in both input as species and analysis as species, and enable the custom analysis function. In the enrichment option, select GO molecular functions, GO biological processes, GO cellular components, and the KEGG pathway database.

Check pick selective GO clusters and click on the enrichment analysis button. Upon completion of the progress bar, initiate an analysis report page and click to retrieve the enrichment results. Open the GEO2R tool to search and analyze the GEO gene chip database.

Open the GEO database website, then enter the keyword or GEO accession and click on the search button. Select the best matching result and find the reference series. Now, on the GEO2R tool website, enter the reference series in the GEO accession box and click the set button.

Select atopic dermatitis as the experimental group and nonatopic control as the control group. Click the analyze button and wait for the results to appear. KEGG and GO enrichment analyses of 59 key targets identified 218 pathways and over 3, 000 biological processes, highlighting significant pathways in SDG and anal eczema.

GO analysis on biological processes, cell composition, and molecular function emphasized common targets in SDG and anal eczema. Relevant biological functions included peptidyl-tyrosine phosphorylation and regulation of cell-cell adhesion. To begin, open the Traditional Chinese Medicine Systems Pharmacology database.

Using the chemical name search box, search the selected ingredient names to download the corresponding 3D structure files in Mold2 format. To download the crystal structures of the key targets, open the RCSB protein database. In the search box, search the target names and download the corresponding crystal structure files in PDB format.

Import ingredients and target structure files in the analysis software. Click edit, then delete water to delete water molecules. To add hydrogens, click on edit, hydrogens, and add.

Set the ingredients as the ligand, select whole targets as the receptor, and perform blind docking. To determine the range of molecular docking, select the receptor and ligand in sequence. Click on grid, then grid box to adjust the grid box to include the entire model.

Click on file and close to save the current grid box status and save the files in GPF format. Now, click on run and run AutoGrid4. Click parameter file name and browse to select the GFP file, then click the launch button.

For molecular docking, open the AutoDock4 and click on docking, macromolecule, and set rigid file name to select the receptor. Then click on docking, ligand, and open or choose to select the ligand. Now, click on docking and search parameters to set operation algorithms, then click docking and docking parameters to set docking parameters.

Select the DPF file and click the launch button. Save files in the DPF format. Click on analyze, docking, and open to select the DLG file, then click on analyze and macromolecule to open the receptor.

Now, click on analyze, confirmations, and play ranked by energy to analyze the results. Finally, click set play, and write complex to save the results in PDBQT format. Import the docking files into PyMOL, then select the ligand and click on action, find, polar contracts, and to other atoms and object to display hydrogen bonds between ligands and the external environment.

Click on single letter C to change color. Click action and extract object. Click show, then sticks to show the stick structure of the receptor.

Identify the residuals connected to ligands and show the stick structure. Then, click wizard and measurement and click on two atoms in sequence. Click label, then residue to show the label of the residues.

If necessary, adjust the background color and transparency. Finally, click file, then export image as to save the picture. In the atopic dermatitis group, GEO database analysis revealed upregulation of PPARG, EGFR, TNF, and PTPRC, MMP9, MAPK14, and CAPS3 were downregulated.

Docking analysis confirmed the interaction between active SDG components and potential target proteins, indicating their significant role in anal eczema treatment. Indigo and berberrubine demonstrated strong binding activity with energies less than minus five kilo calories per mole, emphasizing their therapeutic potential.