BACKGROUND
Huanglian Jiedu Decoction (HLJDD) is a classical herbal formula with potential efficacy in the treatment of sepsis. However, the main components and potential mechanisms of HLJDD remain unclear. This study aims to initially clarify the potential mechanism of HLJDD in the treatment of sepsis based on network pharmacology and molecular docking techniques.


METHODS
The principal components and corresponding protein targets of HLJDD were searched on TCMSP, BATMAN-TCM and ETCM and the compound-target network was constructed by Cytoscape3.8.2. Sepsis targets were searched on OMIM and DisGeNET databases. The intersection of compound target and disease target was obtained and the coincidence target was imported into STRING database to construct a PPI network. We further performed GO and KEGG enrichment analysis on the targets. Finally, molecular docking study was approved for the core target and the active compound.


RESULTS
There are 257 nodes and 792 edges in the component target network. The compounds with a higher degree value are quercetin, kaempferol, and wogonin. The protein with a higher degree in the PPI network is JUN, RELA, TNF. GO and KEGG analysis showed that HLJDD treatment of sepsis mainly involves positive regulation of transcription from RNA polymerase II promoter, negative regulation of apoptosis process, response to hypoxia and other biological processes. The signaling pathways mainly include PI3K-AKT, MAPK, TNF signaling pathway. The molecular docking results showed that quercetin, kaempferol and wogonin have higher affinity with JUN, RELA and TNF.


CONCLUSION
This study reveals the active ingredients and potential molecular mechanism of HLJDD in the treatment of sepsis, and provides a reference for subsequent basic research.

Network pharmacology prediction and molecular docking-based strategy to explore the potential mechanism of Huanglian Jiedu Decoction against sepsis

/pdf/network-pharmacology-and-experimental-validation-to-reveal-2nz1hqvye2.pdf

Network Pharmacology and Experimental Validation to Reveal the Pharmacological Mechanisms of Liuwei Dihuang Decoction Against Intervertebral Disc Degeneration

In this study, a novel peptide GPPGPA was screened from the collagen hydrolysates of Chinese giant salamander (Andrias davidianus) skin, and its anti-diabetes mechanism was predicted by network pharmacology, and an inhibitory effect on α-glycosidase and protective effect on IR (insulin resistance) and oxidative stress of IR-HepG2 cells were detected. Through network pharmacology screening, GPPGPA was found to have good drug-like properties, and 103 targets of GPPGPA overlap with T2DM targets. These targets were mainly enriched in the PI3K-Akt signaling pathway associated with T2DM, the AGE-RAGE signaling pathway in diabetic complications, the TNF signaling pathway, insulin resistance and so on. The core targets were identified as AKT1, MAPK8, MAPK10 and JUN by constructing a "peptide-target-pathway" network. The molecular docking results showed that GPPGPA was well bound to the core targets. These results suggested that GPPGPA had the potential to reduce T2DM. Further in vitro experiments showed that GPPGPA as a competitive inhibitor could effectively inhibit the activity of α-glucosidase. The results of the IR-HepG2 cell model experiments showed that GPPGPA was not toxic to HepG2 cells, and could reduce IR of HepG2 cells induced by high-glucose and high-insulin, improve glucose consumption, increase the activity of superoxide dismutase (SOD), and reduce the content of malondialdehyde (MDA). The above results suggested that GPPGPA could improve T2DM by reducing insulin resistance through a multi-target and multi-pathway mechanism. GPPGPA could be developed and utilized as a novel hyperglycemic inhibitor in functional food.

Screening and identification of a novel antidiabetic peptide from collagen hydrolysates of Chinese giant salamander skin: network pharmacology, inhibition kinetics and protection of IR-HepG2 cells.

Ulcerative colitis (UC) is a disease with complex pathological mechanisms. We explored the potential molecular mechanisms behind the therapeutic functions of Qingzi Zhitong decoction (QZZTD) in the treatment of UC by network pharmacology and molecular docking. QZZTD is a formula of Chinese traditional medicine consisting of 10 herbs. The potential active ingredients of QZZTD and their target genes were obtained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database, and UC-related target genes were obtained from GeneCards and OMIM databases. A total of 138 co-identified target genes were obtained by plotting the intersection target Venn diagram, and then the STRING database and Cytoscape software were used to establish protein–protein interaction networks and herb–ingredient–target networks. Four key active compounds and nine key proteins were identified. Then, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses showed that the biological functions of potential target genes were associated with DNA transcription, signaling receptor and ligand activity, cytokine activity, cellular autophagy, and antioxidant pathways, with related pathways involving the phosphatidylinositol 3-kinase (PI3K)–Akt signaling pathway, advanced glycosylation end product (AGE)–RAGE signaling pathway, tumor necrosis factor (TNF) signaling pathway, and IL-17 signaling pathway. Moreover, the binding activities of key target genes and essential active compounds of Chinese herbal medicines in QZZTD were further validated by molecular docking. This demonstrated that quercetin, luteolin, hyndarin, and beta-sitosterol had good binding to eight key proteins, and Akt1 was the target protein with the best binding activity, suggesting that Akt1 could be the essential mediator responsible for signaling transduction after QZZTD administration. The rat experiment verified that QZZTD inhibited PI3K-Akt pathway activation and reduced inflammation in UC. In conclusion, our study suggested four potential key active components, including quercetin, were identified in QZZTD, which could interact with Akt1 and modulate the activation of the PI3K-Akt pathway. The other three pathways may also be involved in the signaling transduction induced by QZZTD in the treatment of UC.

/pdf/network-pharmacology-and-molecular-docking-analysis-on-20hur00w.pdf

Network Pharmacology and Molecular Docking Analysis on Molecular Mechanism of Qingzi Zhitong Decoction in the Treatment of Ulcerative Colitis

Traditional Chinese medicine (TCM) has the advantage of multi-component and multi-target, which becomes a hot spot in the treatment of numerous diseases. Shaoyao decoction (SYD) is a TCM prescription, which is mainly used to treat damp-heat dysentery clinically, with small side effects and low cost. However, its mechanism remains elusive. The purpose of this study is to explore the mechanism of SYD in the treatment of mice with ulcerative colitis (UC) induced by dextran sulfate sodium (DSS) through metabolomics and network pharmacology, and verify through molecular docking and immunohistochemistry, so as to provide a scientific basis for the role of SYD in the treatment of UC.Firstly, DSS-induced UC models were established and then untargeted metabolomics analysis of feces, livers, serum and urine was performed to determine biomarkers and metabolic pathways closely related to the role of SYD. Besides, network pharmacology was applied to screen the active components and UC-related targets, which was verified by molecular docking. Finally, metabonomics and network pharmacology were combined to draw the metabolite-pathway-target network and verified by immunohistochemistry.Metabolomics results showed that a total of 61 differential metabolites were discovered in SYD-treated UC with 3 main metabolic pathways containing glycerophospholipid metabolism, sphingolipid metabolism and biosynthesis of unsaturated fatty acids, as well as 8 core targets involving STAT3, IL1B, IL6, IL2, AKT1, IL4, ICAM1 and CCND1. Molecular docking demonstrated that the first five targets had strong affinity with quercetin, wogonin, kaempferol and baicalein. Combined with metabolomics and network pharmacology, sphingolipid signaling pathway, PI3K/AKT-mTOR signaling pathway and S1P3 pathway were identified as the main pathways.SYD can effectively ameliorate various symptoms and alleviate intestinal mucosal damage and metabolic disorder in DSS induced UC mice. Its effect is mainly related to sphingolipid metabolism, PI3K/AKT-mTOR signaling pathway and S1P3 pathway. 

Integrated Metabonomics and Network Pharmacology to Reveal the Action Mechanism Effect of Shaoyao Decoction on Ulcerative Colitis

Background Huai Hua San (HHS), a famous Traditional Chinese Medicine (TCM) formula, has been widely applied in treating ulcerative colitis (UC). However, the interaction of bioactives from HHS with the targets involved in UC has not been elucidated yet. Aim A network pharmacology-based approach combined with molecular docking and in vitro validation was performed to determine the bioactives, key targets, and potential pharmacological mechanism of HHS against UC. Materials and methods Bioactives and potential targets of HHS, as well as UC-related targets, were retrieved from public databases. Crucial bioactive ingredients, potential targets, and signaling pathways were acquired through bioinformatics analysis, including protein-protein interaction (PPI), as well as the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Subsequently, molecular docking was carried out to predict the combination of active compounds with core targets. Lastly, in vitro experiments were conducted to further verify the findings. Results A total of 28 bioactive ingredients of HHS and 421 HHS-UC-related targets were screened. Bioinformatics analysis revealed that quercetin, luteolin, and nobiletin may be potential candidate agents. JUN, TP53, and ESR1 could become potential therapeutic targets. PI3K-AKT signaling pathway might play an important role in HHS against UC. Moreover, molecular docking suggested that quercetin, luteolin, and nobiletin combined well with JUN, TP53, and ESR1, respectively. Cell experiments showed that the most important ingredient of HHS, quercetin, could inhibit the levels of inflammatory factors and phosphorylated c-Jun, as well as PI3K-Akt signaling pathway in LPS-induced RAW264.7 cells, which further confirmed the prediction by network pharmacology strategy and molecular docking. Conclusion Our results comprehensively illustrated the bioactives, potential targets, and molecular mechanism of HHS against UC. It also provided a promising strategy to uncover the scientific basis and therapeutic mechanism of TCM formulae in treating diseases.

/pdf/network-pharmacology-prediction-and-molecular-docking-based-58cgneu5ii.pdf

Network Pharmacology Prediction and Molecular Docking-Based Strategy to Discover the Potential Pharmacological Mechanism of Huai Hua San Against Ulcerative Colitis.

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Network Pharmacology Prediction and Molecular Docking-Based Strategy to Discover the Potential Pharmacological Mechanism of Huai Hua San Against Ulcerative Colitis.