Integrated bioinformatics and network pharmacology to identify the therapeutic target and molecular mechanisms of Huangqin decoction on ulcerative Colitis

Abstract

Huangqin decoction (HQD) is a Traditional Chinese Medicine formula for ulcerative colitis. However, the pharmacology and molecular mechanism of HQD on ulcerative colitis is still unclear. Combined microarray analysis, network pharmacology, and molecular docking for revealing the therapeutic targets and molecular mechanism of HQD against ulcerative colitis. TCMSP, DrugBank, Swiss Target Prediction were utilized to search the active components and effective targets of HQD. Ulcerative colitis effective targets were obtained by microarray data from the GEO database (GSE107499). Co-targets between HQD and ulcerative colitis are obtained by Draw Venn Diagram. PPI (Protein–protein interaction) network was constructed by the STRING database. To obtain the core target, topological analysis is exploited by Cytoscape 3.7.2. GO and KEGG enrichment pathway analysis was performed to Metascape platform, and molecular docking through Autodock Vina 1.1.2 finished. 161 active components with 486 effective targets of HQD were screened. 1542 ulcerative colitis effective targets were obtained with |Log2FC|> 1 and adjusted P-value < 0.05. The Venn analysis was contained 79 co-targets. Enrichment analysis showed that HQD played a role in TNF signaling pathway, IL-17 signaling pathway, Th17 cell differentiation, etc. IL6, TNF, IL1B, PTGS2, ESR1, and PPARG with the highest degree from PPI network were successfully docked with 19 core components of HQD, respectively. According to ZINC15 database, quercetin (ZINC4175638), baicalein (ZINC3871633), and wogonin (ZINC899093) recognized as key compounds of HQD on ulcerative colitis. PTGS2, ESR1, and PPARG are potential therapeutic targets of HQD. HQD can act on multiple targets through multi-pathway, to carry out its therapeutic role in ulcerative colitis.

In Silico Identification of New Anti-SARS-CoV-2 Main Protease (Mpro) Molecules with Pharmacokinetic Properties from Natural Sources Using Molecular Dynamics (MD) Simulations and Hierarchical Virtual Screening

“…The ZINC15 database is a crucial computational tool when filtering specific molecules from a pool of different drug-like compounds. Al-Aziz et al [ 36 ], Susanti et al [ 37 ], and Wu et al [ 38 ] used ZINC15 to identify specific molecules of interest in their studies. Al-Aziz et al [ 36 ] leveraged the ZINC15 database to filter out 1,282 FDA and in-clinical approved drugs from approximately 0.5 million protomers of large compounds.…”

“…Al-Aziz et al [ 36 ] leveraged the ZINC15 database to filter out 1,282 FDA and in-clinical approved drugs from approximately 0.5 million protomers of large compounds. Wu et al [ 38 ] recognized vital compounds of Huangqin decoction (HQD) on ulcerative colitis using the ZINC15 database. Susanti et al [ 37 ] performed pharmacophore-based virtual screening of the ZINC15 database to identify CDK4/6 inhibitors.…”

Bioinformatics-Based Approach for Exploring the Immune Cell Infiltration Patterns in Alzheimer’s Disease and Determining the Intervention Mechanism of Liuwei Dihuang Pill

“…The DEGs of AD, immune-related genes, and target genes of LDP were uploaded to the Venn online mapping software to get the intersection targets. 26 The intersection targets were imported into the Cytoscape (v.3.8.0) software, 27 and the Bisogenet and CytoNCA plug-ins were used to construct a protein–protein interaction network; the core immune targets were screened according to the degree value of >61.…”

Mechanism of Zhinao Capsule in Treating Alzheimer’s Disease Based on Network Pharmacology Analysis and Molecular Docking Validation

“…Network pharmacology is a systematic analytical method based on systems biology that combines polypharmacology, molecular network data, bioinformatics, and computer simulations [ 10 ]. And it is a new method based on the multidisciplinary fusion theory of “active ingredient-target-disease” and interaction network [ 11 ].…”