Based on Network Pharmacology to Explore the Molecular Targets and Mechanisms of Gegen Qinlian Decoction for the Treatment of Ulcerative Colitis

Investigation on the Therapeutic Mechanism of Danbie Capsules for Endometriosis: A Network Pharmacology Approach

Objective

To explore the active substances and targets of Danbie Capsules in Endometriosis therapy.

Methods

This study was conducted through TCMSP and published literature screened and obtained 183 active substances of Danbie Capsules, combined and intersected with Endometriosis target genes collected and screened in the GEO database, obtained 24 target genes for Endometriosis treatment, and mapped the target network map of Danbie Capsules active substances against Endometriosis. The network was analyzed with the aid of Cytoscape version 3.9.1. With the aid of the platform of the STRING data analysis, PPI network analysis was conducted on 24 anti-Endometriosis targets of the Danbie Capsules.

Results

The research results obtained three critical active substances, namely, Quercetin, β-sitosterol, and Luteolin. Seven critical targets were identified, and two representative genes (TP53 and AKT1) have been verified in Macromolecular docking and immunohistochemical verification.

Conclusion

The active substances of Danbie Capsules in the treatment of Endometriosis are Quercetin, β-sitosterol and Luteolin, and the main targets are TP53 and AKT1.

The Mechanism of "Treating Different Diseases with the Same Treatment" by Qiangji Jianpi Decoction in Ankylosing Spondylitis Combined with Inflammatory Bowel Disease: A Comprehensive Analysis of Multiple Methods

Background

Ankylosing spondylitis (AS) and inflammatory bowel disease (IBD) are prevalent autoimmune disorders that often co-occur, posing significant treatment challenges. This investigation adopts a multidisciplinary strategy, integrating bioinformatics, network pharmacology, molecular docking, and Mendelian randomization, to elucidate the relationship between AS and IBD and to investigate the potential mechanisms of traditional Chinese medicine formulations, represented by Qiangji Jianpi (QJJP) decoction, in treating these comorbid conditions.

Methods

We utilized databases to pinpoint common targets among AS, IBD, and QJJP decoction's active compounds through intersection analysis. Through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, we mapped a network in Cytoscape, isolating critical targets. Molecular docking with AutoDock validated the affinity between targets and compounds. ROC analysis and dataset validation assessed diagnostic performance, while Gene Set Enrichment Analysis (GSEA) offered pathway insights. Mendelian randomization explored the AS-IBD causal relationship.

Results

Screening identified 105 targets for QJJP decoction, 414 for AS, and 2420 for IBD, with 85 overlapping. These targets predominantly participate in organismal responses and DNA transcription factor binding, with a significant cellular presence in the endoplasmic reticulum and vesicle lumen. Molecular docking, facilitated by Cytoscape, confirmed IL1A, IFNG, TGFB1, and EDN1 as critical targets, with IFNG demonstrating diagnostic potential through GEO dataset validation. The integration of GSEA with network pharmacology highlighted the therapeutic significance of the relaxin, osteoclast differentiation, HIF-1, and AGE-RAGE signaling pathways in QJJP decoction's action. Mendelian randomization analysis indicated a positive causal relationship between IBD and AS, pinpointing rs2193041 as a key SNP influencing IFNG.

Conclusion

Based on the principle of "treating different diseases with the same method" in traditional Chinese medicine theory, we explored the intricate mechanisms through which QJJP decoction addresses AS and IBD comorbidity. Our research spotlighted the pivotal role of the IFNG gene. IFNG emerges not only as a key therapeutic target but also assumes significance as a potential diagnostic biomarker through its genetic underpinnings. This investigation establishes a solid base for subsequent experimental inquiries. Our findings introduce novel approaches for incorporating traditional Chinese medicine into the treatment of AS-IBD comorbidity, setting the stage for groundbreaking research directions.

Paeoniflorin improves ulcerative colitis via regulation of PI3K‑AKT based on network pharmacology analysis

Paeoniflorin (PF) is the primary component derived from Paeonia lactiflora and white peony root and has been used widely for the treatment of ulcerative colitis (UC) in China. UC primarily manifests as a chronic inflammatory response in the intestine. In the present study, a network pharmacology approach was used to explore the specific effects and underlying mechanisms of action of PF in the treatment of UC. A research strategy based on network pharmacology, combining target prediction, network construction, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and molecular docking simulation was used to predict the targets of PF. A total of 288 potential targets of PF and 599 UC-related targets were identified. A total of 60 therapeutic targets of PF against UC were identified. Of these, 20 core targets were obtained by protein-protein interaction network construction. GO and KEGG pathway analyses showed that PF alleviated UC through EGFR tyrosine kinase inhibitor resistance, the IL-17 signaling pathway, and the PI3K/AKT signaling pathway. Molecular docking simulation showed that AKT1 and EGFR had good binding energy with PF. Animal-based experiments revealed that the administration of PF ameliorated the colonic pathological damage in a dextran sulfate sodium-induced mouse model, resulting in lower levels of proinflammatory cytokines including IL-1β, IL-6, and TNF-α, and higher levels of IL-10 and TGF-β. PF decreased the mRNA and protein expression levels of AKT1, EGFR, mTOR, and PI3K. These findings suggested that PF plays a therapeutic protective role in the treatment of UC by regulating the PI3K/AKT signaling pathway.

Berberine chloride suppresses pancreatic adenocarcinoma proliferation and growth by targeting inflammation-related genes: an in silico analysis with in vitro and vivo validation

PURPOSE

Targeting inflammatory crosstalk between tumors and their microenvironment has emerged as a crucial method for suppressing pancreatic adenocarcinoma (PAAD) progression. Berberine (BBR) is a natural pentacyclic isoquinoline alkaloid known for its anti-inflammatory and antitumor pharmacological effects; however, the mechanism underlying PAAD suppression remains unclear. We aim to investigate the effects of BBR on PAAD progression and their underlying mechanisms.

METHODS

The prognostic value of inflammation-related genes in PAAD was assessed using bioinformatics analyses, then the pharmacological effects and potential mechanisms of BBR on PAAD will be investigated in silico, in vitro, and in vivo.

RESULTS

Fifty-eight prognostic inflammation-related genes were identified in PAAD, which were shown to have good sensitivity and specificity using a novel inflammation-related gene risk-prognosis prediction model. Among these, four candidate genes (CAPS3, PTGS2, ICAM1, and CXCR4) were predicted as targets of BBR in PAAD in silico. Molecular docking simulations showed that the four key targets docked well with BBR. Further BBR treatment suppressed cell proliferation, colony formation, and induced cell cycle arrest in vitro. Moreover, BBR exhibited a significant tumor-suppressive effect in murine subcutaneous xenografts without macroscopic hepatic and renal toxicities. In addition, BBR downregulated CAPS3, PTGS2, ICAM1, and CXCR4 protein expression.

CONCLUSION

This study not only elucidated the prognostic value of inflammation-related genes in PAAD but also demonstrated the potential of BBR to inhibit PAAD by targeting these genes.

Identification of the therapeutic effect and molecular mechanism of Coptis chinensis Franch. and Magnolia officinalis var. biloba on chronic gastritis

ETHNOPHARMACOLOGICAL RELEVANCE

Traditional Chinese medicine (TCM) theory believes that clearing heat and promoting dampness is the main treatment method for chronic gastritis. Coptis chinensis Franch. has the effects of clearing heat, detoxifying, and anti-inflammatory; Magnolia officinalis var. biloba can be used to treat abdominal pain, cough, and asthma. Coptis chinensis Franch. and Magnolia officinalis var. biloba can regulate the balance of intestinal microbiota and inhibit inflammatory reactions.

AIM

This study will verify the therapeutic effect of Coptis chinensis Franch. and Magnolia officinalis var. biloba on chronic gastritis, and explore its mechanism through transcriptome sequencing.

METHODS

Firstly, a rat chronic gastritis model was established, and the anal temperature and body weight changes of the rats before and after modeling were observed. Next, H&E staining, TUNEL assay and ELISA assay were performed on rat gastric mucosal tissues. Subsequently, the key fractions of Coptis chinensis Franch. and Magnolia officinalis var. biloba were obtained by high performance liquid chromatography (HPLC), and a GES-1 cell inflammation model was constructed to select the optimal monomer. Finally, the mechanism of action of Coptis chinensis Franch. and Magnolia officinalis var. biloba was explored through RNA seq.

RESULTS

Compared with the control group, the rats in the administered group were in better condition, with higher anal temperature, reduced inflammatory response in gastric mucosal tissue and reduced apoptosis. The optimal fraction Coptisine was subsequently determined by HPLC and GES-1 cell model. RNA-seq analysis revealed that DEG was significantly enriched in ribosomes, NF-κB signaling pathway, etc. The key genes TPT1 and RPL37 were subsequently obtained.

CONCLUSIONS

This study verified the therapeutic effects of Coptis chinensis Franch. and Magnolia officinalis var. biloba on chronic gastritis by in vivo and in vitro experiments in rats, identified Coptisine as the optimal component, and obtained two potential target genes.

Tongmai Yangxin pill alleviates myocardial no-reflow by activating GPER to regulate HIF-1α signaling and downstream potassium channels

CONTEXT

The Tongmai Yangxin pill (TMYX) has potential clinical effects on no-reflow (NR); however, the effective substances and mechanisms remain unclear.

OBJECTIVE

This study evaluates the cardioprotective effects and molecular mechanisms of TMYX against NR.

MATERIALS AND METHODS

We used a myocardial NR rat model to confirm the effect and mechanism of action of TMYX in alleviating NR. Sprague-Dawley (SD) rats were divided into Control (Con), sham, NR, TMYX (4.0 g/kg), and sodium nitroprusside (SNP, 5.0 mg/kg), and received their treatments once a day for one week. In vitro studies in isolated coronary microvasculature of NR rats and in silico network pharmacology analyses were performed to reveal the underlying mechanisms of TMYX and determine the main components, targets, and pathways of TMYX, respectively.

RESULTS

TMYX (4.0 g/kg) showed therapeutic effects on NR by improving the cardiac structure and function, reducing NR, ischemic areas, and cardiomyocyte injury, and decreasing the expression of cardiac troponin I (cTnI). Moreover, the mechanism of TMYX predicted by network pharmacology is related to the HIF-1, NF-κB, and TNF signaling pathways. In vivo, TMYX decreased the expression of MPO, NF-κB, and TNF-α and increased the expression of GPER, p-ERK, and HIF-1α. In vitro, TMYX enhanced the diastolic function of coronary microvascular cells; however, this effect was inhibited by G-15, H-89, L-NAME, ODQ and four K⁺ channel inhibitors.

CONCLUSIONS

TMYX exerts its pharmacological effects in the treatment of NR via multiple targets. However, the contribution of each pathway was not detected, and the mechanisms should be further investigated.

Uncovering the anti-obesity constituents in Ginkgo biloba extract and deciphering their synergistic effects

Obesity has been recognized as a key risk factor for multiple metabolic disorders, including diabetes, cardiovascular diseases and many types of cancer. Herbal medicines have been frequently used for preventing and treating obesity in many countries, but in most cases, the key anti-obesity constituents in herbs and their anti-obesity mechanisms are poorly understood. This study demonstrated a case study for uncovering the anti-obesity constituents in an anti-obesity herbal medicine (Ginkgo biloba extract) and deciphering their synergistic effects via targeting human pancreatic lipase (hPL). Following screening the anti-hPL effects of eighty herbal medicines, Ginkgo biloba extract (GBE50) was found with the most potent anti-hPL activity. Global chemical profiling of herbal constituents coupling with hPL inhibition assay revealed that the bioflavonoids and several flavonoids in GBE50 were key anti-hPL constituents. Among all tested thirty-eight constituents, sciadopitysin, bilobetin, quercetin, isoginkgetin, and ginkgetin showed potent anti-hPL effects (IC50 values <2.5 μM). Inhibition kinetic analyses suggested that sciadopitysin, bilobetin, quercetin, isoginkgetin, and ginkgetin acted as non-competitive inhibitors of hPL, with the Ki values were <2 μM. Docking simulations revealed that four bioflavonoids (sciadopitysin, bilobetin, isoginkgetin, and ginkgetin) could tightly bind on hPL at cavity 2, which it is different from the binding cavity of quercetin on hPL. Further investigations demonstrated that the combinations of quercetin and one bioflavonoid-type hPL inhibitor (sciadopitysin or bilobetin) showed synergistic anti-hPL effects, suggesting that the multi-components in GBE50 may generate more potent anti-hPL effect. Collectively, our findings uncovered the anti-obesity constituents in GBE50, and explored their anti-hPL mechanisms as well as synergistic effects at molecular levels, which will be very helpful for further understanding the anti-obesity mechanisms of Ginkgo biloba.

Gegen-Qinlian decoction-A traditional Chinese medicine formula-Alleviates methamphetamine withdrawal induced anxiety by targeting GABAergic interneuron-pyramidal neuron pathway in mPFC

Methamphetamine (Meth) withdrawal elicits anxiety, which is a public health concern with limited therapeutic options. Previous studies implied a strong correlation between mPFC and Meth withdrawal. Here, we examined the role of Gegen-Qinlian decoction (GQD) in Meth withdrawal anxiety and explored potential therapeutic targets in mPFC. We found that intra-gastric administration of GQD during the withdrawal period efficiently alleviated anxiety-like behaviours in Meth-withdrawn mice. Further, GQD could restore Meth withdrawal-triggered pathway of GABAergic interneurons (GABA IN)-pyramidal neurons (PN) in the mPFC of Meth-withdrawn mice, especially the prelimbic cortex (PrL) sub-region and PV-positive GABA IN. While, GQD had no obvious effects on the glial cells in the mPFC of Meth-withdrawn mice. By transcriptomic analysis and validation of several gene candidates, we found that genes in the MAPK signalling pathway, especially those related to heat shock proteins, including Hspa1a, Hspa1b and Hspb1, might be GQD-targeting genes in mPFC to treat Meth withdrawal anxiety, as indicated that these genes were up-regulated by Meth withdrawal but rescued by GQD in mPFC. Collectively, our findings identified for the first time that GQD could efficiently alleviate Meth withdrawal anxiety, partially through regulating the local GABA IN-PN pathway and transcriptomic profile of mPFC. The present study confirms that TCM, such as GQD, will be a desirable therapeutic approach in the treatment of drug addiction and related emotional deficits.

Resveratrol plays an anti-fibrotic and anti-autophagy role by stimulating miR-192-5p expression in urethral fibrosis

BACKGROUND

Resveratrol (RSV) exerts anti-fibrotic effects on various fibrotic diseases. Whereas the biological role of RSV on urethral fibrosis remains to be elucidated. This study aimed to determine the mechanisms by which RSV affects urethral fibrosis and autophagy.

METHODS

Sprague‒Dawley rats and primary fibroblasts were treated with transforming growth factor-β1 (TGFβ1) to generate in vivo and in vitro fibrosis models. Then, those were treated with RSV, and autophagy and fibrosis-related indicators were tested.

RESULTS

Firstly, we found that RSV reversed the upregulation of indicators related to TGFβ1-induced fibrosis (TGFβ1, α-smooth muscle actin, collagen type I, and collagen type III), autophagy (TFEB and LC3), and TGFβR1/Smad4 pathway, as well as the downregulation of p62 and miR-192-5p expression both in vivo and in vitro. Overexpression of miR-192-5p suppressed the upregulation of fibrosis-related markers expression, as well as TFEB and LC3 expression, induced by TGFβ1, while the expression trend of p62 was the opposite. Inhibiting miR-192-5p reversed the effects of RSV on the model group cells. It was also shown that RSV combined with sh-Smad4 inhibited autophagy more effectively than RSV alone.

CONCLUSION

These results suggest that RSV inhibits urinary fibrosis and autophagy via the miR-192-5p/TGFβR1/Smad4 pathway. RAV may be a potential drug for alleviating urethral fibrosis.

Identification of kukoamine a as an anti-osteoporosis drug target using network pharmacology and experiment verification

BACKGROUND

Osteoporosis (OP) is a major and growing public health problem characterized by decreased bone mineral density and destroyed bone microarchitecture. Previous studies found that Lycium Chinense Mill (LC) has a potent role in inhibiting bone loss. Kukoamine A (KuA), a bioactive compound extract from LC was responsible for the anti-osteoporosis effect. This study aimed to investigate the anti-osteoporosis effect of KuA isolated from LC in treating OP and its potential molecular mechanism.

METHOD

In this study, network pharmacology and molecular docking were investigated firstly to find the active ingredients of LC such as KuA, and the target genes of OP by the TCMSP platform. The LC-OP-potential Target gene network was constructed by the STRING database and network maps were built by Cytoscape software. And then, the anti-osteoporotic effect of KuA in OVX-induced osteoporosis mice and MC3T3-E1 cell lines were investigated and the potential molecular mechanism including inflammation level, cell apoptosis, and oxidative stress was analyzed by dual-energy X-ray absorptiometry (DXA), micro-CT, ELISA, RT-PCR, and Western Blotting.

RESULT

A total of 22 active compounds were screened, and we found KuA was identified as the highest active ingredient. Glycogen Phosphorylase (PYGM) was the target gene associated with a maximum number of active ingredients of LC and regulated KuA. In vivo, KuA treatment significantly increased the bone mineral density and improve bone microarchitecture for example increased BV/TV, Tb.N and Tb.Th but reduced Tb.Sp in tibia and lumber 4. Furthermore, KuA increased mRNA expression of osteoblastic differentiation-related genes in OVX mice and protects against OVX-induced cell apoptosis, oxidative stress level and inflammation level. In vitro, KuA significantly improves osteogenic differentiation and mineralization in cells experiment. In addition, KuA also attenuated inflammation levels, cell apoptosis, and oxidative stress level.

CONCLUSION

The results suggest that KuA could protect against the development of OP in osteoblast cells and ovariectomized OP model mice and these found to provide a better understanding of the pharmacological activities of KuA again bone loss.

Network pharmacology, molecular docking, and experimental validation to explore the potential mechanism of Long Mu Qing Xin mixture for the treatment of attention deficit hyperactivity disorder

Background: Long Mu Qing Xin Mixture (LMQXM) has shown potentially positive effects in alleviating attention deficit hyperactivity disorder (ADHD); however, the action mechanism is still not fully understood. This study aimed to predict the potential mechanism of LMQXM for ADHD using network pharmacology and molecular docking, which were then validated using animal experiments.

Methods: Network pharmacology and molecular docking techniques were used to predict the core targets and potential pathways of LMQXMQ for ADHD, and KEGG pathway enrichment analysis revealed the potential significance of dopamine (DA) and cyclic adenosine monophosphate (cAMP) signaling pathways. To verify the hypothesis, we conducted an animal experiment. In the animal experiment, the young spontaneously hypertensive rats (SHRs) were randomly divided into the model group (SHR), the methylphenidate hydrochloride group (MPH, 4.22 mg/kg), and 3 LMQXM groups (low-dose (LD) group, 5.28 ml/kg; medium-dose (MD) group, 10.56 ml/kg; and high-dose (HD) group, 21.12 ml/kg), and administered by gavage for 4 weeks; the WKY rats were set as the control group. The open field test and Morris water maze test were used to evaluate the behavioral performance of rats, high performance liquid chromatography mass spectrometry (LC-MS) was used to analyze DA levels in the prefrontal cortex (PFC) and striatum of rats, ELISA was used to detect cAMP concentrations in the PFC and striatum, and immunohistochemistry and qPCR were used to analyze positive cell expression and mRNA expression for indicators related to DA and cAMP pathways.

Results: The results showed that beta-sitosterol, stigmasterol, rhynchophylline, baicalein, and formononetin might be key components of LMQXM for ADHD and that these components bind well to the core targets, DA receptors (DRD1 and DRD2). Furthermore, LMQXM might act through the DA and cAMP signaling pathways. In the animal experiment, we found that MPH and LMQXM-MD controlled hyperactivity and improved learning and memory in SHRs, while LMQXM-HD only controlled hyperactivity in SHRs; meanwhile, MPH and LMQXM-MD upregulated DA and cAMP levels, mean optical density (MOD) of cAMP, and MOD and mRNA expression of DRD1 and PKA in the prefrontal cortex (PFC) and striatum of SHRs, while LMQXM-LD and LMQXM-HD upregulated DA and cAMP levels in the striatum, MOD of cAMP in the PFC, and mRNA expression of PKA in the PFC. However, we did not find a significant regulatory effect of LMQXM on DRD2.

Conclusion: To sum up, this study demonstrated that LMQXM may increase DA levels mainly by activating the cAMP/PKA signaling pathway through DRD1, thereby controlling the behavioral disorders of SHRs, which is most effective at moderate doses, and this may be a key mechanism for LMQXM in the treatment of ADHD.

Wumei Wan attenuates angiogenesis and inflammation by modulating RAGE signaling pathway in IBD: Network pharmacology analysis and experimental evidence

BACKGROUND

Wumei Wan (WMW) has been used to address digestive disorder for centuries in traditional Chinese medicine. Previous studies have demonstrated its anti-colitis efficacy, but the underlying mechanism of its action remains to be further clarified.

PURPOSE

To investigate the underlying mechanisms of WMW in the treatment of chronic ulcerative colitis (UC) through network pharmacology and experimental validation.

METHODS

Traditional Chinese Medicine Systems Pharmacology (TCMSP) platform were used to identify the ingredients and potential targets of WMW. The microarray gene data GSE75214 datasets from GEO database was used to define UC-associated targets. Cytoscape3.7.2 was employed to construct the protein-protein interaction (PPI) network and compounds-disease targets network. GO enrichment analysis and KEGG pathway analysis were performed by R software for functional annotation. UPLC-TOF-MS/MS method was used to quantitatively analyze the active ingredients of WMW. For experimental validation, three cycles of 2% dextran sulfate sodium salt (DSS) were used to construct chronic colitis model. The hub targets and signal pathway were detected by qPCR, ELISA, western blotting , immunohistochemical and immunofluorescence.

RESULTS

Through network analysis, 104 active ingredients were obtained from WMW, and 47 of these ingredients had potential targets for UC. A total of 41 potential targets of WMW and 13 hub targets were identified. KEGG analysis showed that WMW involved in advanced glycation end products-receptor of advanced glycation end products (AGE-RAGE) signaling pathway. Taxifolin, rutaecarpine, kaempferol, quercetin, and luteolin of WMW were the more highly predictive components related to the AGE-RAGE signaling pathway. In vivo validation, WMW improved DSS-induced colitis, reduced the expression of inflammatory cytokines and chemokines. Notably, it significantly decreased the mRNA expression of Spp1, Serpine1, Mmp2, Mmp9, Ptgs2, Nos2, Kdr and Icam1, which were associated with angiogenesis. In addition, we confirmed WMW inhibited RAGE expression and diminished DSS-induced epithelial barrier alterations CONCLUSION: Our results initially demonstrated the effective components and the strong anti-angiogenic activity of WMW in experimental chronic colitis. Sufficient evidence of the satisfactory anti-colitis action of WMW was verified in this study, suggesting its potential as a quite prospective agent for the therapy of UC.

Gegen Qinlian decoction activates AhR/IL-22 to repair intestinal barrier by modulating gut microbiota-related tryptophan metabolism in ulcerative colitis mice

ETHNOPHARMACOLOGICAL RELEVANCE

Gegen Qinlian decoction (GQD) is a traditional Chinese medicine derived from Treatise on febrile diseases and is clinically used for the treatment of acute ulcerative colitis (UC). However, the potential mechanism of GQD treatment for UC remains elusive.

AIM OF STUDY

In this study, we aimed to explore the involvement of gut microbiota-related tryptophan metabolism in mediating protective effects of GQD against intestinal barrier damage.

MATERIALS AND METHODS

Mice with colitis were treated with 3% dextran sulfate sodium (DSS) for 6 days. The therapeutic effects of GQD in UC mice were examined based on body weight, disease activity index (DAI), organ index, length and pathological changes in the colon. The distribution of fluorescein isothiocyanate dextran (FITC-dextran) in the intestinal tract was observed using small animal imaging, while concentration of FITC-dextran in serum was detected using a fluorescein microplate analyser. Bacterial infiltration in colon tissues was observed by fluorescence in situ hybridisation (FISH), and the bacterial load in mesenteric lymph nodes (MLNs) was further examined through bacterial culture. Subsequently, colonic goblet cells were detected using Alcian blue staining. The tight junctions of the colonic epithelium were observed using transmission electron microscopy, and the expression of tight junction proteins was detected by immunofluorescence (IF) and western blot. In addition, flow cytometry was used to analyse the proportion of interleukin-22-positive (IL-22⁺) ILC3 cells in lamina propria lymphocytes, and the content of IL-22 in colon homogenates was determined using an ELISA kit. In addition, targeted tryptophan metabolomics was used to detect the concentration of indole derivatives produced by tryptophan metabolism in faeces, and 16S rDNA was used to investigate the composition and abundance of gut microbiota-related tryptophan metabolism.

RESULTS

Administration of GQD significantly alleviated the pathological symptoms, including weight loss, increased DAI score, changes in organ index, colon shortening, and colon pathological injury in UC mice. In addition, GQD reduced the diffusion of FITC-dextran in the intestinal tract, the content of FITC-dextran in serum, and bacterial infiltration in MLNs and colon tissues. Additionally, GQD significantly increased the number of colonic goblet cells, repaired the structure of epithelial tight junctions and increased the expression of tight junction proteins. Furthermore, GQD significantly increased the proportion of IL-22⁺ ILC3 in the lamina propria, the expression of CYP1A1 protein in colon tissue, and the level of IL-22 in colon homogenates. However, the above protective effects of GQD were inhibited by co-administration of GQD and aryl hydrocarbon receptor (AhR) antagonist. Additionally, GQD restored the content of indole derivatives generated by tryptophan metabolism, regulated the diversity of the gut microbiota, and significantly increased the abundance of genes related to tryptophan metabolism.

CONCLUSION

Our results confirmed that GQD repaired the damaged intestinal barrier in UC mice by regulating gut microbiota-related tryptophan metabolism and restoring the generation of indole derivatives to activate AhR-mediated IL-22 production.

Mechanism of andrographis paniculata on lung cancer by network pharmacology and molecular docking

BACKGROUND

Traditional Chinese medicine (TCM) has been widely recognized and accepted worldwide to provide favorable therapeutic effects for cancer patients. As Andrographis paniculata has an anti-tumor effect, it might inhibit lung cancer.

OBJECTIVE

The drug targets and related pathways involved in the action of Andrographis paniculata against lung cancer were predicted using network pharmacology, and its mechanism was further explored at the molecular level.

METHODS

This work selected the effective components and targets of Andrographis paniculata against the Traditional Chinese Medicine System Pharmacology (TCMSP) database. Targets related to lung cancer were searched for in the GEO database (accession number GSE136043). The volcanic and thermal maps of differential expression genes were produced using the software R. Then, the target genes were analyzed by GO and KEGG analysis using the software R. This also utilized the AutoDock tool to study the molecular docking of the active component structures downloaded from the PubChem database and the key target structures downloaded from the PDB database, and the docking results were visualized using the software PyMol.

RESULTS

The results of molecular docking show that wogonin, Mono-O-methylwightin, Deoxycamptothecine, andrographidine F_qt, Quercetin tetramethyl (3',4',5,7) ether, 14-deoxyandrographolide, andrographolide-19-β-D-glucoside_qt and 14-deoxy-11-oxo-andrographolide were potential active components, while AKT1, MAPK14, RELA and NCOA1 were key targets.

CONCLUSION

This study showed the main candidate components, targets, and pathways involved in the action of Andrographis paniculata against lung cancer.

Exploring the Targets and Molecular Mechanisms of Thalidomide in the Treatment of Ulcerative Colitis: Network Pharmacology and Experimental Validation

BACKGROUND

Ulcerative colitis (UC) is a chronic, nonspecific, inflammatory disease of the intestine with an unknown cause. Thalidomide (THA) has been shown to be an effective drug for the treatment of UC. However, the molecular targets and mechanism of action of THA for the treatment of UC are not yet clear.

OBJECTIVES

Combining network pharmacology with in vitro experiments, this study aimed to investigate the potential targets and molecular mechanisms of THA for the treatment of UC.

METHODS

Firstly, relevant targets of THA against UC were obtained from public databases. Then, the top 10 hub targets and key molecular mechanisms of THA for UC were screened based on the network pharmacology approach and bioinformatics method. Finally, an in vitro cellular inflammation model was constructed using lipopolysaccharide (LPS) induced intestinal epithelial cells (NCM460) to validate the top 10 hub targets and key signaling pathways.

RESULTS

A total of 121 relevant targets of THA against UC were obtained, of which the top 10 hub targets were SRC, LCK, MAPK1, HSP90AA1, EGFR, HRAS, JAK2, RAC1, STAT1, and MAP2K1. The PI3K-Akt pathway was significantly associated with THA treatment of UC. In vitro experiments revealed that THA treatment reversed the expression of HSP90AA1, EGFR, STAT1, and JAK2 differential genes. THA was able to up- regulate the mRNA expression of pro-inflammatory factor IL-10 and decrease the mRNA levels of anti-inflammatory factors IL-6, IL-1β, and TNF-α. Furthermore, THA also exerted anti-inflammatory effects by inhibiting the activation of the PI3K/Akt pathway.

CONCLUSION

THA may play a therapeutic role in UC by inhibiting the PI3K-Akt pathway. HSP90AA1, EGFR, STAT1, and JAK2 may be the most relevant potential therapeutic targets for THA in the treatment of UC.

Efficacy and Mechanism of Quercetin in the Treatment of Experimental Colitis Using Network Pharmacology Analysis

Quercetin, a flavonoid that is present in vegetables and fruits, has been found to have anti-inflammatory effects. However, the mechanism by which it inhibits colitis is uncertain. This study aimed to explore the effect and pharmacological mechanism of quercetin on dextran sodium sulfate (DSS)-induced ulcerative colitis (UC). Mice were given a 4% (w/v) DSS solution to drink for 7 days, followed by regular water for the following 5 days. Pharmacological mechanisms were predicted by network pharmacology. High-throughput 16S rDNA sequencing was performed to detect changes in the intestinal microbiota composition. Enzyme-linked immunosorbent assay and western blotting were performed to examine the anti-inflammatory role of quercetin in the colon. Quercetin attenuated DSS-induced body weight loss, colon length shortening, and pathological damage to the colon. Quercetin administration modulated the composition of the intestinal microbiota in DSS-induced mice and inhibited the growth of harmful bacteria. Network pharmacology revealed that quercetin target genes were enriched in inflammatory and neoplastic processes. Quercetin dramatically inhibited the expression of phosphorylated protein kinase B (AKT) and phosphatidylinositol 3-kinase (PI3K). Quercetin has a role in the treatment of UC, with pharmacological mechanisms that involve regulation of the intestinal microbiota, re-establishment of healthy microbiomes that favor mucosal healing, and the inhibition of PI3K/AKT signaling.

Qingchang Wenzhong Decoction reduce ulcerative colitis in mice by inhibiting Th17 lymphocyte differentiation

BACKGROUND

Qingchang Wenzhong Decoction (QCWZD), a chinese herbal prescription, is widely used for ulcerative colitis (UC). Nevertheless, the active ingredients and mechanism of QCWZD in UC have not yet been explained clearly.

PURPOSE

This research focuses on the identification of the effective ingredients of QCWZD and the prediction and verification of their potential targets.

METHODS

The UC mice were established by adding 3.0% dextran sulfate sodium (DSS) to sterile water for one week. Concurrently, mice in the treatment group were gavage QCWZD or mesalazine. LC-MS analyzed the main components absorbed after QCWZD treatment, and network pharmacology predicted their possible targets. ELISA, qPCR, immunohistochemistry and immunofluorescence experiments were used to evaluate the colonic inflammation level and the intestinal barrier completeness. The percentage of Th17 and Treg lymphocytes was detected by flow cytometry.

RESULTS

After QCWZD treatment, twenty-seven compounds were identified from the serum. In addition, QCWZD treatment significantly reduced the increased myeloperoxidase (MPO) and inflammatory cell infiltration caused by DSS in the colonic. In addition, QCWZD can reduce the secretion of inflammatory factors in serum and promote the expression of mRNAs and proteins of occludin and ZO-1. Network pharmacology analysis indicated that inhibiting IL-6-STAT3 pathway may be necessary for QCWZD to treat UC. Flow cytometry analysis showed that QCWZD can restore the normal proportion of Th17 lymphocytes in UC mice. Mechanistically, QCWZD inhibited the phosphorylation of JAK2-STAT3 pathway, reducing the transcriptional activation of RORγT and IL-17A.

CONCLUSIONS

Overall, for the first time, our work revealed the components of QCWZD absorbed into blood, indicated that the effective ingredients of QCWZD may inhibit IL-6-STAT3 pathway and inhibit the differentiation of Th17 lymphocytes to reduce colon inflammation.

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

Background

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.

Materials and Methods

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.

Results

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.

Conclusion

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.

Application of network pharmacology in the study of mechanism of Chinese medicine in the treatment of ulcerative colitis: A review

Network pharmacology is a research method based on a multidisciplinary holistic analysis of biological systems, which coincides with the idea of the holistic view of traditional Chinese medicine. In this review, we summarized the use of network pharmacology technology through studying Chinese medicine single medicine or Chinese medicine compound research ideas and methods for the treatment of ulcerative colitis, based on the application of the current network pharmacology in Chinese medicine research, including the important role in the mechanism of the prediction and verification, to search for new ideas for disease diagnosis and treatment, this study summarizes the application of network pharmacology in the treatment of ulcerative colitis in traditional Chinese medicine, including monotherapy and compound therapy, and considers that relevant research studies have fully demonstrated the function characteristics of the multi-component, multi-target, and multi-pathway of traditional Chinese medicine, and can also explain the connotation of “selecting appropriate treatment methods according to the differences and similarities of pathogenesis” of traditional Chinese medicine. Finally, we raised important questions about the prospects and limitations of network pharmacology, such as differences caused by different data collection methods, a considerable lag, and so on.

Efficacy of the Panax Notoginseng Ejiao Suppository in the Treatment of Patients with Ulcerative Proctitis and Its Effect on Inflammatory Response and Immune Function

Objective. To investigate the efficacy of the Panax notoginseng Ejiao suppository in patients with ulcerative proctitis and its effect on inflammatory response and immune function. Methods. This study recruited 100 patients with ulcerative proctitis who were hospitalized to our hospital’s anorectal outpatient department between May 2015 and October 2020. They were randomly separated into either a control or a study group, with 50 cases in each. The control group received the mesalazine suppository, whereas the study group received the Panax notoginseng Ejiao suppository. Outcome measures included clinical effectiveness, inflammatory response, and immunological state of patients. Results. The total efficiency in the study group was significantly higher than that in the control group ( $P=0.019$ ). The Mayo score and Baron endoscopic score between the two groups were significantly decreased after treatment, with lower results in the study group ( $P<0.05$ ). The inflammatory variables were dramatically reduced following therapy, with the study group doing worse. Following treatment, the number of Th 17 cells declined dramatically in both groups, while the proportion of Treg cells increased significantly, with greater alterations of Th17 cells and Treg cells observed in the study group than those in the control group ( $P<0.05$ ). The Panax notoginseng Ejiao suppository resulted in significantly shorter time lapses before symptom alleviation and a lower incidence of recurrence at 6 months after treatment versus mesalazine suppository ( $P<0.05$ ). Conclusion. In patients with ulcerative proctitis, the Panax notoginseng Ejiao suppository significantly improves clinical efficacy, reduces the incidence of recurrence, mitigates inflammatory response, and improves immune function.

Research into the mechanism of intervention of SanQi in endometriosis based on network pharmacology and molecular docking technology

BACKGROUND

By using network pharmacology and molecular docking technology, we have explored the mechanism of action of Sanqi in the treatment of endometriosis (EMS), in order to provide reference for clinical studies of Chinese medicine treatment of Ems and Chinese medicine pharmacology.

METHODS

There are 123 intersecting targets between the active ingredients of Sanqi and disease targets. In the Protein-Protein Interaction network, Jun proto-oncogene, AP-1 transcription factor subunit, tumor necrosis factor, interleukin 6, etc., are the core proteins. The top 20 genes ranked by degree have been analyzed according to the Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology analysis, and 20 pathways have been identified.

RESULTS

On the Kyoto Encyclopedia of Genes and Genomes pathway, the most important part is the phosphatidylinositol 3'-kinase-Akt signaling pathway, and on the Gene Ontology pathway, it is the Heme binding. The top 3 targets docked to quercetin have a certain affinity when it is docked to their degree value. Among the chemical components of Sanqi, quercetin has the most targets, suggesting that it may play a major role in the treatment of EMS.

CONCLUSION

The results of molecular docking provide further evidence of the potential role of Sanqi for EMS. Overall, our study provides a new direction for the treatment of EMS and provides the basis for Sanqi as a drug for the treatment of EMS.

Study on the effect of Pogostemon cablin Benth on skin aging based on network pharmacology

BACKGROUND

At present, there is still little research on the anti-aging effect of Pogostemon cablin Benth (PCB) on human skin. In this paper, the mechanism of anti-aging effect of PCB on human skin was studied by using network pharmacology and molecular docking methods.

OBJECTIVE

To analyze the pharmacological mechanism of PCB in the treatment of skin aging, so as to provide reference for new drug development and clinical application.

METHODS

Active ingredients and related targets of PCB and skin aging-related disease targets are obtained through public databases, and the "drug-disease-target" and protein-protein interaction (PPI) network diagrams were constructed with the help of software to screen the core targets; Then GO analysis and KEGG pathway analysis were performed on the target; Finally, the molecular docking between the components and the targets were verified.

RESULTS

After screening, 112 intersection targets of active compounds of skin aging and PCB were obtained. Through GO and KEGG enrichment analysis, it is found that these biological processes mainly focus on epithelial cell proliferation, aging, growth factors, longevity regulation pathway, cancer pathway, AGE-RAGE signal pathway, PI3K Akt signal pathway and IL-17 signal pathway. The molecular docking results showed that quercetin, apigenin, irisnepalensis isoflavone, 3,23-dihydroxy-12-oleorene-28-oleic acid, 5-hydroxy-7,4'- dimethoxyflavone and other major compounds were connected with TP53, JUN, HSP90AAL, AKT1 and MAPK1 through hydrogen bonds, and there was high binding energy between them.

CONCLUSION

Through multi-target prediction and molecular docking verification, it shows that PCB provides a strong effect in the treatment of skin aging, which provides a reference for its further research.

A Discovery Strategy for Active Compounds of Chinese Medicine Based on the Prediction Model of Compound-Disease Relationship

An accurate characterization of diseases and compounds is the key to predicting the compound-disease relationship (CDR). However, due to the difficulty of a comprehensive description of CDR, the accuracy of traditional drug development models for large-scale CDR prediction is usually unsatisfactory. In order to solve this problem, we propose a new method that integrates the molecular descriptors of compounds and the symptom descriptors of diseases to build a CDR two-dimensional matrix to predict candidate active compounds. The Matlab software draws grayscale images of CDRs, which are used as a benchmark dataset for training convolutional neural network (CNN) models. The trained model is used to predict candidate antitumor active compounds. Among the AlexNet and GoogLeNet models, we selected the GoogLeNet model for the prediction of active compounds in Chinese medicine, and its Acc, Sen, Pre, F-measure, MCC, and AUC are 0.960, 0.956, 0.965, 0.960, 0.920, and 0.964, respectively. In the prediction results of compounds, 1624 candidate CDRs were found in 124 Chinese medicines. Among them, we obtained 31 features of candidate antitumor active compounds. This method provides new insights for the discovery of candidate active compounds in Chinese medicine.

Gene Network Mechanism of Zhilong Huoxue Tongyu Capsule in Treating Cerebral Ischemia–Reperfusion

Objective: To investigate the effect of Zhilong Huoxue Tongyu capsule (ZLH) in the treatment of cerebral ischemia–reperfusion injury and determine the underlying molecular network mechanism.

Methods: The treatment effect of Zhilong Huoxue Tongyu capsule (ZLH) was evaluated for cerebral ischemia–reperfusion injury in middle cerebral artery occlusion (MACO) rat, and the underlying molecular network mechanism was explored by using molecular network analysis based on network pharmacology, bioinformatics including protein–protein interaction (PPI) network, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG), as well as molecular docking.

Results: The neurological function of rats in the ZLH group was significantly improved compared to those in the NS group (p = 0.000), confirming the positive effect of ZLH for the treatment of brain ischemia. There were 126 intersecting genes screened in ischemia–reperfusion cerebrum that are associated with several important biological processes, such as lipopolysaccharide, and the most important cell component, such as raft, as well as the most important molecular function pointed as cytokine receptor binding. The most important KEGG signaling pathway was the AGE-RAGE signaling pathway in diabetic complications. Moreover, according to the STRING interaction in the PPI network, 10 hub genes including MAPK14, FOS, MAPK1, JUN, MYC, RELA, ESR1, STAT1, AKT1, and IL6 were selected and exhibited in Cytoscape and molecular docking. Lastly, the relation between PPI, GO, and KEGG was analyzed. These findings indicated that multiple hub network genes have been involved in behavior improvement in cerebral ischemia–reperfusion rats subjected to ZLH treatment.

Conclusion: Zhilong Huoxue Tongyu capsule improves cerebral ischemia–reperfusion and is associated with multiple network gene expressions.

Identifying the Mechanism of Polygoni Cuspidati Rhizoma et Radix in Treating Acute Liver Failure Based on Network Pharmacology and Molecular Docking

Materials and Methods

The potential bioactive compounds of PCRR and their targets were collected from TCMSP, TCMID, and BATMAN-TCM databases with absorption, distribution, metabolism, and excretion protocols (oral bioavailability ≥30% and drug-likeness ≥0.18). The ALF-related target genes were identified using the GeneCards and OMIM databases. A protein-protein interaction (PPI) network among these targets was constructed using the Cytoscape software to obtain the core targets. The genes associated with ALF were analyzed via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to identify the signaling pathways related to the therapeutic effect of PCRR in ALF.

Results

In total, 10 bioactive compounds of PCRR and 200 targets related to them were obtained, and 2913 ALF-related target genes were identified. PPI network analysis pinpointed 15 core targets, namely, TP53, AKT1, JUN, HSP90AA1, MAPK1, RELA, TNF, ESR1, IL6, MYC, MAPK14, FOS, RB1, CDKN1A, and EGFR. GO enrichment and KEGG pathway analyses revealed that the therapeutic mechanisms of PCRR in ALF are related to cell metabolism, oxidative stress, inflammation, and hepatocyte apoptosis.

Conclusion

This is the first study to explore the therapeutic mechanisms of PCRR in ALF via network pharmacology and molecular docking. This study provides a research platform with candidate ALF-related targets of PRCC for the development of therapeutics against ALF.

A Network Pharmacology-Based Study on Vital Pharmacological Pathways and Targets of Eucommiae Cortex Acting on Osteoporosis

Background

Eucommiae Cortex is a Chinese herbal medicine with bone protective effects and treats osteoporosis. This study aimed to explore the pharmacological mechanisms of this complex mixture.

Methods

The active compounds and disease targets involved in the study were obtained from publicly available websites and databases. Core target genes were identified by protein-protein interaction (PPI) network and topology analysis and mapped to critical components by a “component-target” regulatory network. Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway analysis and Gene Ontology (GO)analysis were performed to analyze the biological processes of target genes. Moreover, we carried out molecular docking, cell experiments, and quantitative real-time PCR to propel the research forward.

Results

Eucommiae Cortex contained 28 active ingredients and 85 potential targets for antiosteoporosis. PPI networks and topology analysis screened 17 core target genes. The therapeutic mechanism involves a series of biological reactions, including host-virus response, chemical stress, oxidative stress, and cell cycle control. The KEGG enrichment illustrated that the MAPK signaling pathway might play a significant role. The final experiment detected ten genes (EGF, AKT1, JUN, MAPK8, MAPK1, CASP3, FOS, VEGFA, EGFR, and MYC) and three compounds (quercetin, kaempferol, and beta- carotene) in the MAPK pathway. Firstly, the CCK-8 and ALP activity test results showed that three compounds could enhance the proliferation and differentiation of osteoblast-like MC3T3-E1 cells. Secondly, molecular docking confirmed the favorable binding potential. Subsequently, we observed that adding 1∗10⁻⁶ mol/L quercetin, 1∗10⁻⁵  mol/L kaempferol, and 1∗10⁻⁵  mol/L beta-carotene activated the ERK/JNK cascades and the heterodimer complex AP-1(Fos/Jun) in the MAPK pathway.

Conclusion

MAPK pathway might provide an essential mechanism for the antiosteoporosis effect of Eucommiae Cortex. Eucommiae Cortex and its active ingredients have the potential to treat osteoporosis.

The Integrated Study on the Chemical Profiling to Explore the Constituents and Mechanism of Traditional Chinese Medicine Preparation Huatuo Jiuxin Pills Based on UPLC-Q-TOF/MSE and Network Pharmacology

Huatuo Jiuxin Pills (HJP), a traditional Chinese medicine (TCM) preparation, has been widely used to treat Cardiovascular Diseases (CVDs) for more than 20 years. However, there were still gaps in the study of chemical components and potential pharmacological effects in the HJP. In this study, ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MSE) combined with network pharmacology was used to comprehensively explore the chemical components in HJP and explore its potential active compounds and the mechanism for the treatment of CVDs. A total of 117 compounds, mainly including saponins, cholic acids, and bufadienolides, were rapidly identified and characterized. Simultaneously, the fragmentation mode and characteristic ion analysis of different types of representative compounds were carried out. Network pharmacology results showed that the more important active ingredients mainly include 5β‐hydroxybufotalin, 19 oxo‐cinobufagin, bufarenogin, etc. While, the main targets were PIK3CA, MAPK1, VEGFA and so on. Importantly, HJP has therapeutic effects on CVDs by acting on endocrine resistance, PI3K-Akt signaling pathway, HIF-1 signaling pathway, etc. In addition, molecular docking results showed that the core active ingredients with higher degrees in HJP have a strong affinity with the core targets of CVDs. The current work fills the gap in the chemical substance basis of HJP, and also facilitates a better understanding of the effective components, therapeutic targets, and signaling pathways of HJP in the treatment of CVDs.

Mass Spectrometric Behavior and Molecular Mechanisms of Fermented Deoxyanthocyanidins to Alleviate Ulcerative Colitis Based on Network Pharmacology

Aims. Ulcerative colitis (UC) is a type of chronic idiopathic inflammatory bowel disease with a multifactorial pathogenesis and limited treatment options. The aim of the present study is to investigate the hydrogen deuterium exchange mass spectrometry (HDX-MS) behaviors of fermented deoxyanthocyanidins and their molecular mechanisms to alleviate UC by using quantum chemistry and network pharmacology. Methods. Tandem MS indicated at least two fragmentation pathways through which deuterated vinylphenol-deoxyanthocyanidins could generate different product ions. Quantum calculations were conducted to determine the transition states of the relevant molecules and analyze their optimized configuration, vibrational characteristics, intrinsic reaction coordinates, and corresponding energies. The potential targets of deoxyanthocyanidins in UC were screened from a public database. The R package was used for Gene Ontology (GO) and KEGG pathway analyses, and the protein–protein interactions (PPIs) of the targets were assessed using Search Tool for the Retrieval of Interacting Genes (STRING). Finally, molecular docking was implemented to analyze the binding energies and action modes of the target compounds through the online tool CB-Dock. Results. Quantum calculations indicated two potential fragmentation pathways involving the six-membered ring and dihydrogen cooperative transfer reactions of the vinylphenol-deoxyanthocyanidins. A total of 146 and 57 intersecting targets of natural and fermented deoxyanthocyanidins were separately screened out from the UC database and significant overlaps in GO terms and KEGG pathways were noted. Three shared hub targets (i.e., PTGS2, ESR1, and EGFR) were selected from the two PPI networks by STRING. Molecular docking results showed that all deoxyanthocyanidins have a good binding potential with the hub target proteins and that fermented deoxyanthocyanidins have lower binding energies and more stable conformations compared with natural ones. Conclusions. Deoxyanthocyanidins may provide anti-inflammatory, antioxidative, and immune system regulatory effects to suppress UC progression. It is proposed for the first time that fermentation of deoxyanthocyanidins can help adjust the structure of the intestinal microbiota and increase the biological activity of the natural compounds against UC. Furthermore, HDX-MS is a helpful strategy to analyze deoxyanthocyanidin metabolites with unknown structures.

Science Evidence of Chinese Herbal Medicine (Gegen Qinlian Decoction) in the Treatment of Ulcerative Colitis

Objectives. Gegen Qinlian decoction (GQD), a Chinese herbal compound, has been widely used in the treatment of ulcerative colitis (UC) in China. However, evidence from systematic reviews (SRs)/meta-analyses (MAs) of GQD in UC remains highly controversial. To collate, evaluate, and synthesize the current evidence, we carried out this study. Methods. SRs/MAs of GQD for UC were obtained from eight databases. Methodological Quality of Systematic Reviews 2 (AMSTAR-2) was utilized to appraise the methodological quality, Preferred Reporting Item for Systematic Reviews and Meta-Analyses (PRISMA) for reporting quality, and Grading of Recommendations Assessment, Development, and Evaluation (GRADE) for evidence quality. Results. Four eligible SRs/MAs were obtained. According to AMSTAR 2, all SRs/MAs were graded as critically low quality. According to PRISMA checklist, all SRs/MAs failed to report the information of protocol and registration. With GRADE, no outcome measure with high-quality evidence was found, and the evidence quality for outcome measures was in the moderate to critically low levels. Conclusions. GQD with conventional medicine (CM) seems to be more effective in UC than CM alone. This finding provides a new alternative strategy for the treatment of UC. However, owing to the limitations of the evidence provided by the included SRs/MAs, this conclusion must be treated with caution.

Mechanism of Gegen Qinlian Decoction Regulating ABTB1 Expression in Colorectal Cancer Metastasis Based on PI3K/AKT/FOXO1 Pathway

It was to investigate the role of Gegen Qinlian decoction (GQD) in the regulation of ABTB1 gene based on PI3K/AKT/FOXO1 signaling pathway in colorectal cancer (CRC) metastasis. In this study, 10 cases of the CRC mouse model were established by inoculating CT26 cells into the spleen of mice, which were divided into the experimental group and the control group, 5 cases in each group; the control group was intragastrically administered with normal saline 0.3 mL/d, and the experimental group was intragastrically administered with GQD 0.2 mL/d at a ratio of 0.2 g medicinal materials/10 g for 10 days and sacrificed, and pathological sections were made. The expression density of signaling pathway PI3K/AKT/FOXO1 as well as gene ABTB1 was detected in the sections of the two groups, and the mechanism of action of this gene in the two groups of mice was studied. It was found that the densities of p-PI3K, p-AKT, and p-FOXO1 in the experimental group of mice were 26.55 g/cm³, 70.2 g/cm³, and 24.36 g/cm³, respectively, which were significantly increased compared with the control group, P < 0.05; the density of ABTB1 was 35.4 g/cm³, which was significantly increased compared with the control group, P < 0.05; the proliferation and migration ability of CRC cells in the experimental group were significantly decreased, P < 0.05. GQD can promote the expression of ABTB1 by activating the PI3K/AKT/FOXO1 signaling pathway, in order to inhibit the proliferation and growth ability of CRC cells.

Current Advances in Coptidis Rhizoma for Gastrointestinal and Other Cancers

Cancer is a serious disease with an increasing number of reported cases and high mortality worldwide. Gastrointestinal cancer defines a group of cancers in the digestive system, e.g., liver cancer, colorectal cancer, and gastric cancer. Coptidis Rhizoma (C. Rhizoma; Huanglian, in Chinese) is a classical Chinese medicinal botanical drug for the treatment of gastrointestinal disorders and has been shown to have a wide variety of pharmacological activity, including antifungal, antivirus, anticancer, antidiabetic, hypoglycemic, and cardioprotective effects. Recent studies on C. Rhizoma present significant progress on its anticancer effects and the corresponding mechanisms as well as its clinical applications. Herein, keywords related to C. Rhizoma, cancer, gastrointestinal cancer, and omics were searched in PubMed and the Web of Science databases, and more than three hundred recent publications were reviewed and discussed. C. Rhizoma extract along with its main components, berberine, palmatine, coptisine, magnoflorine, jatrorrhizine, epiberberine, oxyepiberberine, oxyberberine, dihydroberberine, columbamine, limonin, and derivatives, are reviewed. We describe novel and classic anticancer mechanisms from various perspectives of pharmacology, pharmaceutical chemistry, and pharmaceutics. Researchers have transformed the chemical structures and drug delivery systems of these components to obtain better efficacy and bioavailability of C. Rhizoma. Furthermore, C. Rhizoma in combination with other drugs and their clinical application are also summarized. Taken together, C. Rhizoma has broad prospects as a potential adjuvant candidate against cancers, making it reasonable to conduct additional preclinical studies and clinical trials in gastrointestinal cancer in the future.

Analysis of the Efficacy and Pharmacological Mechanisms of Action of Zhenren Yangzang Decoction on Ulcerative Colitis Using Meta-Analysis and Network Pharmacology

OBJECTIVE

We analyzed the efficacy and pharmacological mechanisms of action of Zhen Ren Yang Zang decoction (ZRYZD) on ulcerative colitis (UC) using meta-analysis and network pharmacology.

METHODS

The major databases were searched for randomized controlled trials of ZRYZD for the treatment of UC. Meta-analysis of the efficacy of ZRYZD on UC was conducted using RevMan software. Active compounds and target genes were acquired using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. UC-related genes were searched using the GeneCards database. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using RGUI. A compound-target network was constructed using Cytoscape software, and a protein-protein interaction network was constructed using the STRING database. Molecular docking simulations of the macromolecular protein targets and their corresponding ligand compounds were performed using the AutoDock tool and AutoDock Vina software.

RESULTS

Meta-analysis revealed that the total effective rate and recovery rate of clinical efficacy were significantly higher in the experimental group than those of the control group. The screening identified 169 active compounds and 277 active target genes for ZRYZD. The 277 active target genes were compared with the 4,798 UC-related genes. This identified 187 active target genes of ZRYZD for UC that correlated with 138 active compounds. GO functional enrichment and KEGG pathway enrichment analyses were performed, and compound-target and protein-protein interaction networks were constructed. The key compounds and key target proteins were then selected. Finally, target protein binding with the corresponding compound was analyzed using molecular docking.

CONCLUSION

Our findings demonstrate the effectiveness and safety of ZRYZD for the treatment of UC and provide insight into the underlying pharmacological mechanisms of action. Furthermore, key compounds were identified, laying the foundation for future studies on ZRYZD for the treatment of UC.

Network Pharmacology and Molecular Docking-Based Investigation: Prunus mume Against Colorectal Cancer via Silencing RelA Expression

Colorectal cancer (CRC) is one of the most pervasive cancers in the human disease spectrum worldwide, ranked the second most common cause of cancer death by the end of 2020. Prunus mume (PM) is an essential traditional Chinese medicine for the adjuvant treatment of solid tumors, including CRC. In the current study, we utilize means of network pharmacology, molecular docking, and multilayer experimental verification to research mechanism. The five bioactive compounds and a total of eight critical differentially expressed genes are screened out using the bioinformatics approaches of Cytoscape software, String database, Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes pathways, and molecular docking. RelA has been proven to be highly expressed in CRC. Experiments in vitro have shown that kaempferol, the main active component of PM, dramatically inhibited the growth, migration, and invasion of CRC cells, and experiments in vivo have shown that PM effectively delays CRC formation and improves the survival cycle of mice. Further analysis shows that PM inhibits the CRC progression by down-regulating the expression level of RelA, Bax, caspase 3, caspase 9, and EGFR in CRC. PM and its extract are potentially effective therapeutics for the treatment of CRC via the RelA/nuclear factor κB signaling pathway.

Stigmasterol Restores the Balance of Treg/Th17 Cells by Activating the Butyrate-PPARγ Axis in Colitis

Inflammatory bowel disease (IBD) is a chronic inflammatory disorder with gut microbiota disequilibrium and regulatory T (Treg)/T helper 17 (Th17) immune imbalance. Stigmasterol, a plant-derived sterol, has shown anti-inflammatory effects. Our study aimed to identify the effects of stigmasterol on experimental colitis and the related mechanisms. Stigmasterol treatment restored the Treg/Th17 balance and altered the gut microbiota in a dextran sodium sulfate (DSS)-induced colitis model. Transplantation of the faecal microbiota of stigmasterol-treated mice significantly alleviated inflammation. Additionally, stigmasterol treatment enhanced the production of gut microbiota-derived short-chain fatty acids (SCFAs), particularly butyrate. Next, human naïve CD4+ T cells sorted from IBD patients were cultured under Treg- or Th17-polarizing conditions; butyrate supplementation increased the differentiation of Tregs and decreased Th17 cell differentiation. Mechanistically, butyrate activated peroxisome proliferator-activated receptor gamma (PPARγ) and reprogrammed energy metabolism, thereby promoting Treg differentiation and inhibiting Th17 differentiation. Our results demonstrate that butyrate-mediated PPARγ activation restores the balance of Treg/Th17 cells, and this may be a possible mechanism, by which stigmasterol attenuates IBD.

Exploring the Potential Mechanism of Xiaokui Jiedu Decoction for Ulcerative Colitis Based on Network Pharmacology and Molecular Docking

Introduction

Network pharmacology is in line with the holistic characteristics of TCM and can be used to elucidate the complex network of interactions between disease-specific genes and compounds in TCM herbal medicines. Here, we investigate the pharmacological mechanism of Xiaokui Jiedu decoction (XJD) for the treatment of ulcerative colitis (UC).

Methods

The Computational Systems Biology Laboratory Platform (TCMSP) database was searched and screened for the active ingredients of all drugs in XJD. The Uniport database was used to retrieve possible gene targets for the therapeutic effects of XJD. GeneCards, PharmGKB, TTD, and OMIM databases were used to retrieve XJD-related gene targets. A herb-compound-protein network and a protein-protein interaction (PPI) network were constructed, and hub genes were screened for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Finally, molecular docking was performed to validate the interrelationship between disease target proteins and active drug components.

Results

A total of 135 XJD potential action targets, 5097 UC-related gene targets, and 103 XJD-UC intersection gene targets were screened. The hub gene targets of XJD that exert therapeutic effects on UC are RB1, MAPK1, TP53, JUN, NR3C1, MAPK3, and ESR1. GO enrichment analysis showed 741 biofunctional enrichments, and KEGG enrichment analysis showed 124 related pathway enrichments. Molecular docking showed that the active components of XJD (β-sitosterol, kaempferol, formononetin, quercetin, and luteolin) showed good binding activities to five of the six hub gene targets. Discussion. The active ingredients of XJD (β-sitosterol, kaempferol, formononetin, quercetin, and luteolin) may regulate the inflammatory and oxidative stress-related pathways of colon cells during the course of UC by binding to the hub gene targets. This may be a potential mechanism of XJD in the treatment of UC.

A network pharmacology study with molecular docking to investigate the possibility of licorice against posttraumatic stress disorder

Post traumatic stress disorder (PTSD) is a mental health condition that has a debilitating effect on a person's quality of life and leads to a high socioeconomic burden. Licorice has been demonstrated to have neuroprotective and antidepressant-like effects, but little is known about its effects for the treatment of PTSD. The present study aimed to explore the potential of licorice for PTSD therapy using a network pharmacology approach with molecular docking studies. The compounds of licorice were obtained from databases with screening by absorption, distribution, metabolism and excretion (ADME) evaluation. Genes associated with compounds or PTSD were obtained from public databases, and the genes overlapping between licorice compounds and PTSD were compared by Venn diagram. A network of medicine-ingredients-targets-disease was constructed, visualized, and analyzed using cytoscape software. Protein-protein interactions, gene ontology, pathway enrichment and molecular docking were performed to evaluate the effect of licorice for the treatment of PTSD. 69 potential compounds were screened after ADME evaluation. A total of 81 compound-related genes and 566 PTSD-related genes were identified in the databases with 27 overlapping genes. Licorice compounds (e.g., medicarpin, 7-methoxy-2-methyl isoflavone, shinpterocarpin, formononetin, licochalcone a) and target proteins (e.g., ESR1, PTGS2, NOS2, and ADRB2) with high degree in the network were involved in G protein-coupled receptor signaling pathways at the postsynaptic/synaptic membrane. Moreover, neuroactive ligand-receptor interactions, calcium signaling, cholinergic synapse, serotonergic synapse and adrenergic signaling in cardiomyocytes may play important roles in the treatment of PTSD by licorice. This study provides molecular evidence of the beneficial effects of licorice for the treatment of PTSD.

Molecular Mechanism of Jinchan Oral Liquid in the Treatment of Children with Respiratory Syncytial Virus Pneumonia Based on Network Pharmacology and Molecular Docking Technology

Objective

Exploration of the underlying molecular mechanism of Jinchan Oral Liquid (JOL) in treating children with the respiratory syncytial virus (RSV) pneumonia to provide new evidence for the clinical application.

Methods

The active components and target genes of JOL were screened by the TCMSP database. The targets of RSV pneumonia were obtained from the GeneCards, OMIM, DrugBank, and PharmGKB database. Then, we constructed the active component-target network and screened the core genes. The overlaps were screened for PPI network analysis, GO analysis, and KEGG analysis. Finally, result validation was performed by molecular docking.

Results

According to the screening criteria of the ADME, 74 active compounds of JOL were obtained; after removing redundant targets, we selected 180 potential targets. By screening the online database, 893 RSV pneumonia-related targets were obtained. A total of 82 overlapping genes were chosen by looking for the intersection. The STRING online database was used to acquire PPI relationships, and 16 core genes were obtained. GO and KEGG analyses showed that the main pathways of JOL in treating RSV pneumonia include TNF signaling pathway and IL17 signaling pathway. The molecular docking results showed that the active compounds of JOL had a good affinity with the core genes.

Conclusion

In this study, we preliminarily discussed the main active ingredients, related targets, and pathways of JOL and predicted the pharmacodynamic basis and the potential therapeutic mechanisms of RSV pneumonia. In summary, the network pharmacology strategy may be helpful for the discovery of multitarget drugs against complex diseases.

Molecular Targets and Mechanisms of Scutellariae radix-Coptidis rhizoma Drug Pair for the Treatment of Ulcerative Colitis Based on Network Pharmacology and Molecular Docking

This study aims to analyze the targets of the effective active ingredients of Scutellariae radix-Coptidis rhizoma drug pair (SCDP) in ulcerative colitis (UC) by network pharmacology and molecular docking and to explore the associated therapeutic mechanism. The effective active ingredients and targets of SCDP were determined from the TCMSP database, and the drug ingredient-target network was constructed using the Cytoscape software. The disease targets related to UC were searched in GeneCards, DisGeNET, OMIM, and DrugBank databases. Then, the drug ingredient and disease targets were intersected to construct a protein-protein interaction network through the STRING database. The Metascape database was used for the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of the predicted targets of SCDP for UC. The Autodock software was used for molecular docking between the main active ingredient and the core target to evaluate the binding ability. SCDP has 43 effective active ingredients and 134 intersection targets. Core targets included AKT1, TP53, IL-6, VEGFA, CASP3, JUN, TNF, MYC, EGFR, and PTGS2. GO functional enrichment analysis showed that biological process was mainly associated with a cytokine-mediated signaling pathway, response to an inorganic substance, response to a toxic substance, response to lipopolysaccharide, reactive oxygen species metabolic process, positive regulation of cell death, apoptotic signaling pathway, and response to wounding. KEGG enrichment analysis showed main pathway concentrations were related to pathways in cancer, AGE-RAGE signaling pathway in diabetic complications, bladder cancer, IL-17 signaling pathway, apoptosis, p53 signaling pathway, and PI3K-Akt signaling pathway. The drug active ingredient-core target-key pathway network contains 41 nodes and 108 edges, of which quercetin, wogonin, baicalein, acacetin, oroxylin A, and beta-sitosterol are important active ingredients; PTGS2, CASP3, TP53, IL-6, TNF, and AKT1 are important targets; and the pathways involved in UC treatment include pathways in cancer, PI3K-Akt signaling pathway, AGE-RAGE signaling pathway in diabetic, apoptosis, IL-17 signaling pathway and herpes simplex infection. The active ingredient has a good binding capacity to the core target. SCDP key active ingredients are mainly quercetin, wogonin, baicalein, acacetin, oroxylin A, and beta-sitosterol, which function mainly by regulating targets, such as PTGS2, CASP3, TP53, IL-6, TNF, and AKT1, and are associated with multiple signaling pathways as pathways in cancer, PI3K-Akt signaling pathway, apoptosis, IL-17 signaling pathways.