A Network Pharmacology Approach to Uncover the Pharmacological Mechanism of XuanHuSuo Powder on Osteoarthritis

Integration of proteomics and network toxicology reveals the mechanism of mercury chloride induced hepatotoxicity, in mice and HepG2 cells

Mercury is one heavy metal toxin that could cause severe health impairments. Mercury exposure has become a global environmental issue. Mercury chloride (HgCl₂) is one of mercury's main chemical forms, but it lacks detailed hepatotoxicity data. The present study aimed to investigate the mechanism of hepatotoxicity induced by HgCl₂ through proteomics and network toxicology at the animal and cellular levels. HgCl₂ showed apparent hepatotoxicity after being administrated with C57BL/6 mice (16 mg/kg.bw, oral once a day, 28 days) and HepG2 cells (100 μmol/L, 12 h). Otherwise, oxidative stress, mitochondrial dysfunction and inflammatory infiltration play an important role in HgCl₂-induced hepatotoxicity. The differentially expressed proteins (DEPs) after HgCl₂ treatment and enriched pathways were obtained through proteomics and network toxicology. Western blot and RT-qPCR results showed Acyl-CoA thioesterase 1 (ACOT1), Acyl-CoA synthetase short chain family member 3 (ACSS3), Epidermal growth factor receptor (EGFR), Apolipoprotein B (APOB), Signal transducer and activator of transcription 3 (STAT3), Alanine--glyoxylate aminotransferase (AGXT), cytochrome P450 3A5(CYP3A5), CYP2E1 and CYP1A2 may be the major biomarkers for HgCl₂-induced hepatotoxicity, which involved chemical carcinogenesis, fatty acid metabolism, CYPs-mediated metabolism, GSH metabolism and others. Therefore, this study can provide scientific evidence for the biomarkers and mechanism of HgCl₂-induced hepatotoxicity.

Protective Effect of Bojungikki-Tang against Radiation-Induced Intestinal Injury in Mice: Experimental Verification and Compound-Target Prediction

Bojungikki-tang (BJIT) is a traditional herbal medicine used in Korea, Japan, and China to treat gastrointestinal disorders. In this study, we aimed to investigate whether BJIT has protective effects against radiation-induced intestinal injury and to predict the underlying therapeutic mechanisms and related pathways via network pharmacological analyses. BJIT was injected intraperitoneally (50 mg/kg body weight) to C₃H/HeN mice at 36 and 12 h before exposure to partial abdominal irradiation (5 Gy and 13 Gy) to evaluate the apoptotic changes and the histological changes and variations in inflammatory cytokine mRNA levels in the jejunum, respectively. Through in silico network analysis, we predicted the mechanisms underlying BJIT-mediated regulation of radiation-induced intestinal injury. BJIT reduced the level of apoptosis in the jejunal crypts 12 h post 5-Gy irradiation. Histological assessment revealed intestinal morphological changes in irradiated mice 3.5 days post 13-Gy irradiation. Furthermore, BJIT decreased inflammatory cytokine levels following radiation exposure. Apoptosis, TNF, p53, VEGF, toll-like receptor, PPAR, PI3K-Akt, and MAPK signaling pathways, as well as inflammatory bowel disease (IBD), were found to be linked to the radioprotective effects of BJIT against intestinal injury. According to our results, BJIT exerted its potential protective effects by attenuating histopathological changes in jejunal crypts and suppressing inflammatory mediator levels. Therefore, BJIT is a potential therapeutic agent that can treat radiation-induced intestinal injury and its associated symptoms.

Two Novel Sesquiterpenoid Glycosides from the Rhizomes of Atractylodes lancea

Secoatractylohexone A (1), an unprecedented secoguaiane lactone glycoside featuring 6/7 cores and dihydroxy-9-guaine-3-one 11-O-β-d-glucopyranoside (2), a 9,10-unsaturated guaiene-type glycoside possessing an uncommon scaffold, were isolated from the water-soluble portion of the ethanolic extract of Atractylodes lancea rhizomes together with five known compounds (3–7). The structures of 1 and 2 were elucidated on the basis of extensive spectroscopic data and application of the CD technique. The potential biological activities of secoatractylohexone A were predicted by network pharmacology in silico, the result of which indicated that secoatractylohexone A may be used to treat type II diabetes.

Deciphering the Underlying Mechanisms of Formula Le-Cao-Shi Against Liver Injuries by Integrating Network Pharmacology, Metabonomics, and Experimental Validation

Le-Cao-Shi (LCS) has long been used as a folk traditional Chinese medicine formula against liver injuries, whereas its pharmacological mechanisms remain elusive. Our study aims to investigate the underlying mechanism of LCS in treating liver injuries via integrated network pharmacology, metabonomics, and experimental validation. By network pharmacology, 57 compounds were screened as candidate compounds based on ADME parameters from the LCS compound bank (213 compounds collected from the literature of three single herbs). According to online compound–target databases, the aforementioned candidate compounds were predicted to target 87 potential targets related to liver injuries. More than 15 pathways connected with these potential targets were considered vital pathways in collectively modulating liver injuries, which were found to be relevant to cancer, xenobiotic metabolism by cytochrome P450 enzymes, bile secretion, inflammation, and antioxidation. Metabonomics analysis by using the supernatant of the rat liver homogenate with UPLC-Q-TOF/MS demonstrated that 18 potential biomarkers could be regulated by LCS, which was closely related to linoleic acid metabolism, glutathione metabolism, cysteine and methionine metabolism, and glycerophospholipid metabolism pathways. Linoleic acid metabolism and glutathione metabolism pathways were two key common pathways in both network pharmacology and metabonomics analysis. In ELISA experiments with the CCl₄-induced rat liver injury model, LCS was found to significantly reduce the levels of inflammatory parameters, decrease liver malondialdehyde (MDA) levels, and enhance the activities of hepatic antioxidant enzymes, which validated that LCS could inhibit liver injuries through anti-inflammatory property and by suppressing lipid peroxidation and improving the antioxidant defense system. Our work could provide new insights into the underlying pharmacological mechanisms of LCS against liver injuries, which is beneficial for its further investigation and modernization.

Network pharmacology approach to evaluate the therapeutic effects of mulberry leaf components for obesity

Obesity is a chronic condition that has become a serious public health challenge globally due to the association with a high incidence of complications. Mulberry leaf is one of the most commonly used medicinal and herbal medicines that has been reported to ameliorate obesity and hyperlipidemia. However, the mechanism remains unclear. In the present study, a network pharmacology approach was used to explore the potential mechanism underlying the effects of mulberry leaf extract on obesity. First, the potential targets of mulberry leaf and obesity were predicted using SwissTargetPrediction, Online Mendelian Inheritance in Man, GeneCards and Comparative Toxicogenomics Database databases, which were then used to construct the protein-protein interaction networks. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyzes were performed using R version 3.6.3. Finally, results of this network analysis were verified by using the mulberry leaf extract to treat high-fat diet-induced obese mice. In total, 24 target genes associated with obesity that could potentially be affected by mulberry leaf treatment were predicted by network pharmacology, using which top seven related pathways were determined by KEGG enrichment analysis. Triglyceride (TG) and total cholesterol (TC) levels in mice serum were detected using TG and TC assay kits. Hepatic fat accumulation was detected by H&E staining whereas liver lipid droplets were detected by Oil red O staining in mice tissues. The expression of IL-1β, NF-κB inhibitor α, inducible nitric oxide synthase, AMP-activated protein kinase (AMPK), sterol regulatory element-binding proteins and fatty acid synthase in the visceral white adipose tissues of mice was analyzed by western blotting. The expression of TNF-α, peroxisome proliferator activated receptor (PPAR)D, PPARG, fatty acid amide hydrolase (FAAH) and hydroxysteroid 11-β dehydrogenase 1 (HSD11B1) in the visceral white adipose tissues of mice was detected by reverse transcription-quantitative PCR. Mulberry leaf extract was found to reduce fat accumulation and hepatic lipid droplet formation. Mulberry leaf also alleviated inflammation and lipogenesis whilst promoting lipid catabolism and fatty acid oxidation by promoting the AMPK signaling pathway. The possible anti-obesity effects of mulberry leaf on the mice may be due to the downregulation of TNF-α, PPARD and PPARG and the upregulation of FAAH and HSD11B1. These results were consistent with the GO enrichment analysis and suggested that mulberry leaf may regulate lipid metabolism and catabolism, fatty acid metabolism and biosynthesis and the inflammatory response to reduce obesity.

Anti-asthmatic effects of Phlomis umbrosa Turczaninow using ovalbumin induced asthma murine model and network pharmacology analysis

BACKGROUND

Phlomis umbrosa Turczaninow has been used as a tradition herbal medicine for treating various inflammatory diseases.

PURPOSE

In present study, we explored the effects of P. umbrosa on asthma induced by ovalbumin (OVA) and elucidated the mechanism via in vivo verification and network pharmacology prediction.

METHODS

The animals were intraperitoneally injected OVA on day 1 and 14, followed by OVA inhalation on days 21, 22, and 23. The animals were daily treated P. umbrosa extract (PUE, 20 and 40 mg/kg) by oral gavage from day 18 to day 23.

RESULTS

PUE significantly decreased airway hyperresponsiveness, eosinophilia, and the production of inflammatory cytokines and OVA specific immunoglobulin E in animals with asthma, along with a reduction in airway inflammation and mucus secretion in lung tissue. In network analysis, antiasthmatic effects of PUE were closely related with suppression of mitogen-activated protein kinases and matrix metalloproteinases (MMPs). Consistent with the results from network analysis, PUE suppressed the phosphorylation of ERK and p65, which was accompanied by a decline in MMP-9 expression.

CONCLUSION

Administration of PUE effectively reduced allergic responses in asthmatic mice, which was associated with the suppressed phosphorylation of ERK and p65, and expression of MMP-9. These results indicate that PUE has therapeutic potential to treat allergic asthma.

A Network Pharmacology and Molecular Docking Strategy to Explore Potential Targets and Mechanisms Underlying the Effect of Curcumin on Osteonecrosis of the Femoral Head in Systemic Lupus Erythematosus

Background

Systemic lupus erythematosus (SLE) is a refractory immune disease, which is often complicated with osteonecrosis of the femoral head (ONFH). Curcumin, the most active ingredient of Curcuma longa with a variety of biological activities, has wide effects on the body system. The study is aimed at exploring the potential therapeutic targets underlying the effect of curcumin on SLE-ONFH by utilizing a network pharmacology approach and molecular docking strategy.

Methods

Curcumin and its drug targets were identified using network analysis. First, the Swiss target prediction, GeneCards, and OMIM databases were mined for information relevant to the prediction of curcumin targets and SLE-ONFH-related targets. Second, the curcumin target gene, SLE-ONFH shared gene, and curcumin-SLE-ONFH target gene networks were created in Cytoscape software followed by collecting the candidate targets of each component by R software. Third, the targets and enriched pathways were examined by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Eventually, a gene-pathway network was constructed and visualized by Cytoscape software; key potential central targets were verified and checked by molecular docking and literature review.

Results

201 potential targets of curcumin and 170 related targets involved in SLE-ONFH were subjected to network analysis, and the 36 intersection targets indicated the potential targets of curcumin for the treatment of SLE-ONFH. Additionally, for getting more comprehensive and accurate candidate genes, the 36 potential targets were determined to be analyzed by network topology and 285 candidate genes were obtained finally. The top 20 biological processes, cellular components, and molecular functions were identified, when corrected by a P value ≤ 0.05. 20 related signaling pathways were identified by KEGG analysis, when corrected according to a Bonferroni P value ≤ 0.05. Molecular docking showed that the top three genes (TP53, IL6, VEGFA) have good binding force with curcumin; combined with literature review, some other genes such as TNF, CCND1, CASP3, and MMP9 were also identified.

Conclusion

The present study explored the potential targets and signaling pathways of curcumin against SLE-ONFH, which could provide a better understanding of its effects in terms of regulating cell cycle, angiogenesis, immunosuppression, inflammation, and bone destruction.

Exploring the Pharmacological Mechanism of Liuwei Dihuang Decoction for Diabetic Retinopathy: A Systematic Biological Strategy-Based Research

OBJECTIVE

To explore the pharmacological mechanism of Liuwei Dihuang decoction (LDD) for diabetic retinopathy (DR).

METHODS

The potential targets of LDD were predicted by PharmMapper. GeneCards and other databases were used to collect DR genes. Cytoscape was used to construct and analyze network DR and LDD's network, and DAVID was used for Gene Ontology (GO) and pathway enrichment analysis. Finally, animal experiments were carried out to verify the results of systematic pharmacology.

RESULTS

Five networks were constructed and analyzed: (1) diabetic retinopathy genes' PPI network; (2) compound-compound target network of LDD; (3) LDD-DR PPI network; (4) compound-known target network of LDD; (5) LDD known target-DR PPI network. Several DR and treatment-related targets, clusters, signaling pathways, and biological processes were found. Animal experiments found that LDD can improve the histopathological changes of the retina. LDD can also increase erythrocyte filtration rate and decrease the platelet adhesion rate (P < 0.05) and decrease MDA and TXB2 (P < 0.05). Compared with the model group, the retinal VEGF and HIF-1α expression in the LDD group decreased significantly (P < 0.05).

CONCLUSION

The therapeutic effect of LDD on DR may be achieved by interfering with the biological processes (such as response to insulin, glucose homeostasis, and regulation of angiogenesis) and signaling pathways (such as insulin, VEGF, HIF-1, and ErbB signaling pathway) related to the development of DR that was found in this research.

Exploring the Mechanism of Gyejibokryeong-hwan against Atherosclerosis Using Network Pharmacology and Molecular Docking

Gyejibokryeong-hwan (GBH) is a traditional formula comprised of five herbal medicines that is frequently used to treat blood stasis and related complex multifactorial disorders such as atherosclerosis. The present study used network pharmacology and molecular docking simulations to clarify the effect and mechanism of the components of GBH. Active compounds were selected using Oriental Medicine Advanced Searching Integrated System (OASIS) and the Traditional Chinese Medicine System Pharmacology Database and Analysis Platform (TCMSP), and target genes linked to the selected components were retrieved using Search Tool for Interacting Chemicals (STITCH) and GeneCards. Functional analysis of potential target genes was performed through the Annotation, Visualization and Integrated Discovery (DAVID) database and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and molecular docking confirmed the correlation between five core compounds (quercetin, kaempferol, baicalein, ellagic acid, and baicalin) and six potential target genes (AKT1, CASP3, MAPK1, MAPK3, NOS2, and PTGS2). Molecular docking studies indicated that quercetin strongly interacted with six potential target proteins. Thus, these potential target proteins were closely related to TNF, HIF-1, FoxO, and PI3K-Akt signal pathways, suggesting that these factors and pathways may mediate the beneficial effects of GBH on atherosclerosis. Our results identify target genes and pathways that may mediate the clinical effects of the compounds contained within GBH on atherosclerosis.

Application of network pharmacology and molecular docking to elucidate the potential mechanism of Eucommia ulmoides-Radix Achyranthis Bidentatae against osteoarthritis

BACKGROUND

Osteoarthritis is a disabling disease, which seriously affects the quality of life of patients. Increasing evidence has indicated that Chinese herbal medicine including Eucommia ulmoides (EU) and Radix Achyranthis Bidentatae (RAB) have potential in the treatment of osteoarthritis, and this is associated with their multi-target and multi-link action characteristics. Although their potential anti-arthritic activity has been reported, the exact mechanism of EU-RAB action in osteoarthritis remains unexplored. Therefore, this study explores the mechanism of EU-RAB against osteoarthritis using network pharmacology and molecular docking technology.

METHODS

Public databases including TCMSP、BATMAN-TCM、OMIM and Genecards were used to predict the bioactive ingredients and putative targets of EU-RAB against osteoarthritis. Enrichment analysis was performed to expound the biological functions and associated pathways of the hub targets. Cytoscape software was used to construct a "compounds-targets-pathways" network for elucidating the comprehensive molecular mechanism of EU-RAB against osteoarthritis. Molecular docking was used to verify the correlation between the main active ingredients and hub targets.

RESULTS

Network pharmacological analysis of EU-RAB in the treatment of osteoarthritis, identified 50 active ingredients including quercetin, kaempferol, wogonin, and baicalein with important biological effect. A total of 68 key targets were screened, including IL-6, EGFR, MAPK8, etc., and they were found to be enriched in a series of signaling pathways, such as apoptosis, TNF, MAPK, PI3K/AKT, and IL-17 signaling pathways. Moreover, molecular docking analysis showed that the main ingredients were tightly bound to the core targets, further confirming the anti-arthritic effects.

CONCLUSION

Based on network pharmacology and molecular docking analysis, the present study provides insights into the potential mechanism of EU-RAB in osteoarthritis after successfully screening for associated key target genes and signaling pathways. These findings further provide a theoretical basis for further pharmacological research into the potential mechanism of EU-RAB in osteoarthritis.

Dissecting Chemical Composition and Cardioprotective Effects of Fuzhengkangfu Decoction against Doxorubicin-Induced Cardiotoxicity by LC-MS and Bioinformatics Approaches

Cardiotoxicity of doxorubicin (DOX) has gained increasing attention in clinical application. Fuzhengkangfu (FZK) decoction, a traditional Chinese herbal formula of replenishing Qi strengthening spleen, has been used to treat various cardiovascular diseases. However, the chemical composition, the protective effects of FZK, and the underlying mechanisms are yet unclear. In this study, an high-performance liquid chromatography-mass spectrometry (HPLC-MS) analytical method was established for the structural identification of constituents in FZK extracts. Target prediction and enrichment analysis of the identified ingredients were performed. The cell viability was measured via (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) (MTT) assay. The protective effects of FZK on cell survival, mitochondrial membrane potential, intracellular calcium homeostasis, and cell apoptosis were detected. The level of relevant proteins was measured by Western blot. The effect of FZK on the antitumor activity of DOX was evaluated in HeLa cells. A total of 42 major chemical constituents were identified in FZK extracts by HPLC-MS. A comprehensive target prediction of these constituents retrieved 46 pathways, of which several key pathways were related to mitochondrial dysfunction, including metabolic pathways and calcium signaling pathways. Furthermore, FZK ameliorated DOX-induced H9C2 cell apoptosis and increased the Bcl-2/Bax ratio. Also, it moderated the loss of mitochondrial membrane potential and reduced the intracellular calcium overload, which are the major targets of DOX-induced injury. These results confirmed that FZK ameliorates DOX-induced cardiotoxicity via antiapoptotic and mitochondrial protection but does not affect the antitumor activity of DOX.

A bioinformatics investigation into the pharmacological mechanisms of javanica oil emulsion injection in non-small cell lung cancer based on network pharmacology methodologies

Background

Javanica oil emulsion injection (JOEI) is an effective therapeutic option for patients with non-small cell lung cancer (NSCLC), but its mechanisms have not been fully elucidated.

Methods

In this study, we utilized network pharmacology to systematically investigate the bioactive components and targets of JOEI, identify common targets in NSCLC, and understand and evaluate the underlying mechanism of JOEI in the treatment of NSCLC through expression level, correlation, enrichment, Cox, survival and molecular docking analyses. The results indicated that five compounds of JOEI interact with five pivotal targets (LDLR, FABP4, ABCB1, PTGS2, and SDC4) that might be strongly correlated with the JOEI-mediated treatment of NSCLC.

Results

The expression level analysis demonstrated that NSCLC tissues exhibit low expression of FABP4, ABCB1, LDLR and PTGS2 and high SDC4 expression. According to the correlation analysis, a decrease in FABP4 expression was strongly correlated with decreases in LDLR and ABCB1, and a decrease in LDLR was strongly correlated with decreased PTGS2 and increased in SDC4 expression. Cox and survival analyses showed that the survival rate of the high-risk group was significantly lower than that of the low-risk group (p = 0.00388). In the survival analysis, the area under the curve (AUC) showed that the pivotal gene model exhibited the best predictive capacity over 4 years (AUC = 0.613). Moreover, the molecular docking analysis indicated that LDLR, FABP4, ABCB1, PTGS2 and SDC4 exhibit good binding activity with the corresponding compounds.

Conclusion

In conclusion, this study predicted and verified that the mechanism of JOEI against NSCLC involves multiple targets and signaling pathways. Furthermore, this study provides candidate targets for the treatment of NSCLC, lays a good foundation for further experimental research and promotes the reasonable application of JOEI in clinical treatment.

A Computational Toxicology Approach to Screen the Hepatotoxic Ingredients in Traditional Chinese Medicines: Polygonum multiflorum Thunb as a Case Study

In recent years, liver injury induced by Traditional Chinese Medicines (TCMs) has gained increasing attention worldwide. Assessing the hepatotoxicity of compounds in TCMs is essential and inevitable for both doctors and regulatory agencies. However, there has been no effective method to screen the hepatotoxic ingredients in TCMs available until now. In the present study, we initially built a large scale dataset of drug-induced liver injuries (DILIs). Then, 13 types of molecular fingerprints/descriptors and eight machine learning algorithms were utilized to develop single classifiers for DILI, which resulted in 5416 single classifiers. Next, the NaiveBayes algorithm was adopted to integrate the best single classifier of each machine learning algorithm, by which we attempted to build a combined classifier. The accuracy, sensitivity, specificity, and area under the curve of the combined classifier were 72.798, 0.732, 0.724, and 0.793, respectively. Compared to several prior studies, the combined classifier provided better performance both in cross validation and external validation. In our prior study, we developed a herb-hepatotoxic ingredient network and a herb-induced liver injury (HILI) dataset based on pre-clinical evidence published in the scientific literature. Herein, by combining that and the combined classifier developed in this work, we proposed the first instance of a computational toxicology to screen the hepatotoxic ingredients in TCMs. Then Polygonum multiflorum Thunb (PmT) was used as a case to investigate the reliability of the approach proposed. Consequently, a total of 25 ingredients in PmT were identified as hepatotoxicants. The results were highly consistent with records in the literature, indicating that our computational toxicology approach is reliable and effective for the screening of hepatotoxic ingredients in Pmt. The combined classifier developed in this work can be used to assess the hepatotoxic risk of both natural compounds and synthetic drugs. The computational toxicology approach presented in this work will assist with screening the hepatotoxic ingredients in TCMs, which will further lay the foundation for exploring the hepatotoxic mechanisms of TCMs. In addition, the method proposed in this work can be applied to research focused on other adverse effects of TCMs/synthetic drugs.

Mechanisms of Compound Kushen Injection for the Treatment of Lung Cancer Based on Network Pharmacology

Background

Compound Kushen Injection (CKI) is a Chinese patent drug that shows good efficacy in treating lung cancer (LC). However, its underlying mechanisms need to be further clarified.

Methods

In this study, we adopted a network pharmacology method to gather compounds, predict targets, construct networks, and analyze biological functions and pathways. Moreover, molecular docking simulation was employed to assess the binding potential of selected target-compound pairs.

Results

Four networks were established, including the compound-putative target network, protein-protein interaction (PPI) network of LC targets, compound-LC target network, and herb-compound-target-pathway network. Network analysis showed that 8 targets (CHRNA3, DRD2, PRKCA, CDK1, CDK2, CHRNA5, MMP1, and MMP9) may be the therapeutic targets of CKI in LC. In addition, molecular docking simulation indicated that CHRNA3, DRD2, PRKCA, CDK1, CDK2, MMP1, and MMP9 had good binding activity with the corresponding compounds. Furthermore, enrichment analysis indicated that CKI might exert a therapeutic role in LC by regulating some important pathways, namely, pathways in cancer, proteoglycans in cancer, PI3K-Akt signaling pathway, non-small-cell lung cancer, and small cell lung cancer.

Conclusions

This study validated and predicted the mechanism of CKI in treating LC. Additionally, this study provides a good foundation for further experimental studies and promotes the reasonable application of CKI in the clinical treatment of LC.

Analysis of Effect of Schisandra in the Treatment of Myocardial Infarction Based on Three-Mode Gene Ontology Network

Schisandra chinensis is a commonly used traditional Chinese medicine, which has been widely used in the treatment of acute myocardial infarction in China. However, it has been difficult to systematically clarify the major pharmacological effect of Schisandra, due to its multi-component complex mechanism. In order to solve this problem, a comprehensive network analysis method was established based-on “component–gene ontology–effect” interactions. Through the network analysis, reduction of cardiac preload and myocardial contractility was shown to be the major effect of Schisandra components, which was further experimentally validated. In addition, the expression of NCOR2 and NFAT in myocyte were experimentally confirmed to be associated with Schisandra in the treatment of AMI, which may be responsible for the preservation effect of myocardial contractility. In conclusion, the three-mode gene ontology network can be an effective network analysis workflow to evaluate the pharmacological effects of a multi-drug complex system.

A Network Pharmacology Approach to Explore Mechanism of Action of Longzuan Tongbi Formula on Rheumatoid Arthritis

Longzuan Tongbi Formula (LZTB) is an effective proved prescription in Zhuang medicine for treating active rheumatoid arthritis (RA). However, its active ingredients, underlying targets, and pharmacological mechanism are still not clear in treating RA. We have applied network pharmacology to study LZTB and found that 8 herbs in LZTB and 67 compounds in the 8 herbs are involved in the regulation of RA-related genes; we have conducted pathway analysis of overlapping genes and found that 7 herbs participate in the regulations of 24 pathways associated with RA and that 5 herbs in the 7 herbs and 25 compounds in the 5 herbs participate in the regulation of hsa05323 (rheumatoid arthritis). The results indicated that all herbs in LZTB and some compounds in those herbs participate in the treatment of RA; 25 compounds are main active ingredients and hsa05323 (rheumatoid arthritis) is the major pathway in the treatment of RA. We have also found that three pathways (inflammatory mediator regulation of TRP channels, PPAR signaling pathway, and mTOR signaling pathway) might have some effect on the treatment of RA.

Chrysin protects human osteoarthritis chondrocytes by inhibiting inflammatory mediator expression via HMGB1 suppression

High‑mobility group box chromosomal protein (HMGB‑1) contributes to osteoarthritis (OA) by modulating various oxidative, inflammatory and apoptotic signaling pathways. The effect of chrysin (CH), a natural plant flavonoid, and its functional interaction with HMGB‑1, was investigated in a chondrocyte model of OA. Human chondrocytes were pre‑treated with CH, and then subsequently treated with IL‑1β to induce the formation of chondrocytes similar to those found in OA joints. Next, the expression level of HMGB‑1 was determined by immunofluorescence and western blot analysis. Additionally, inflammatory factor expression was measured by ELISA, and cell apoptosis was analyzed with flow cytometry. To further explore the effects of CH, HMGB‑1 expression was silenced following CH treatment with small interfering (si)RNA. The results demonstrated that CH inhibited cell apoptosis, dose‑dependently reduced matrix metalloproteinase (MMP) 13, collagenase and IL‑6 expression, and increased collagen α‑1 (II) chain (COL2A1) expression in human osteoarthritis chondrocytes. These effects of CH were accompanied by decreased HMGB‑1 expression. Additionally, the expression of MMP13, collagenase, IL‑6 and COL2A1, as well as apoptosis, was significantly reduced by HMGB‑1 siRNA. These results demonstrated that HMGB‑1 is critical for the protective effect of CH on human osteoarthritis chondrocytes, including cell apoptosis and inflammatory factor inhibition, which suggests that CH may have potential therapeutic effect in treating OA by protecting human osteoarthritis chondrocytes via HMGB1 suppression.

Systematic Investigation of Scutellariae Barbatae Herba for Treating Hepatocellular Carcinoma Based on Network Pharmacology

As the fifth most common type of malignant cancers globally, hepatocellular carcinoma (HCC) is the second leading cause of cancer-related mortality worldwide. As a long-time medicinal herb in Traditional Chinese Medicine (TCM), Scutellariae Barbatae Herba (SBH) has also been used for treating various cancers including HCC, but its underlying mechanisms have not been completely clarified. Presently, an innovative network-pharmacology platform was introduced to systematically elucidate the pharmacological mechanisms of SBH against HCC, adopting active ingredients prescreening, target fishing, and network analysis. The results revealed that SBH appeared to work on HCC probably through regulating 4 molecular functions, 20 biological processes, and hitting on 21 candidate targets involved in 40 pathways. By in-depth analysis of the first-ranked signaling pathway and hit genes, only TTR was highly and specially expressed in the liver tissue. TTR might play a crucial role in neutrophil degranulation pathway during SBH against HCC. Hence, TTR might become a therapeutic target of HCC. The study investigated the anti-hepatoma mechanisms of SBH from a holistic perspective, which provided a theoretical foundation for further experimental research and rational clinical application of SBH.

Hesperidin protects against IL-1β-induced inflammation in human osteoarthritis chondrocytes

Hesperidin is a vitamin P flavonoid compound primarily present in citrus fruits, which possesses an anti-inflammatory effect. The functional role of hesperidin in interleukin (IL)-1β-stimulated human osteoarthritis (OA) chondrocytes is still unknown. In the present study, anti-inflammatory effects of hesperidin in IL-1β-stimulated chondrocytes were investigated. The results demonstrated that hesperidin treatment markedly decreased nitric oxide and prostaglandin E2 production and markedly downregulated inducible nitric oxide synthase and cyclooxygenase-2 expression in IL-1β-stimulated OA chondrocytes. In addition, hesperidin markedly reduced IL-1β-induced matrix metalloproteinase (MMP)-3 and MMP-13 expression in human OA chondrocytes. Furthermore, hesperidin markedly decreased the activation of nuclear factor (NF)-κB in human OA chondrocytes. In conclusion, it was revealed for the first time that hesperidin inhibited inflammatory responses in IL-1β-stimulated human chondrocytes, potentially through inhibiting the activation of the NF-κB signaling pathway. These data suggest that hesperidin may be a potential agent for the treatment of OA.

Anti-endometriosis Mechanism of Jiawei Foshou San Based on Network Pharmacology

Jiawei Foshou San (JFS) is the new formula originated from classic Foshou San formula, composed with ligustrazine, ferulic acid, and tetrahydropalmatine. Previously JFS inhibited the growth of endometriosis (EMS) with unclear mechanism, especially in metastasis, invasion, and epithelial-mesenchymal transition. In this study, network pharmacology was performed to explore potential mechanism of JFS on EMS. Through compound-compound target and compound target-EMS target networks, key targets were analyzed for pathway enrichment. MMP-TIMP were uncovered as one cluster of the core targets. Furthermore, autologous transplantation of EMS rat's model were used to evaluate in vivo effect of JFS on invasion, metastasis and epithelial-mesenchymal transition. JFS significantly suppressed the growth, and reduced the volume of ectopic endometrium, with modification of pathologic structure. In-depth study, invasion and metastasis were restrained after treating with JFS through decreasing MMP-2 and MMP-9, increasing TIMP-1. Meanwhile, JFS promoted E-cadherin, and attenuated N-cadherin, Vimentin, Snail, Slug, ZEB1, ZEB2, Twist. In brief, anti-EMS effect of JFS might be related to the regulation of epithelial-mesenchymal transformation, thereby inhibition of invasion and metastasis. These findings reveal the potential mechanism of JFS on EMS and the benefit for further evaluation.

Network pharmacology-based prediction of active compounds and molecular targets in Yijin-Tang acting on hyperlipidaemia and atherosclerosis

ETHNOPHARMACOLOGICAL RELEVANCE

Yijin-Tang (YJT) is a traditional prescription for the treatment of hyperlipidaemia, atherosclerosis and other ailments related to dampness phlegm, a typical pathological symptom of abnormal body fluid metabolism in Traditional Korean Medicine. However, a holistic network pharmacology approach to understanding the therapeutic mechanisms underlying hyperlipidaemia and atherosclerosis has not been pursued.

AIM OF THE STUDY

To examine the network pharmacological potential effects of YJT on hyperlipidaemia and atherosclerosis, we analysed components, performed target prediction and network analysis, and investigated interacting pathways using a network pharmacology approach.

MATERIALS AND METHODS

Information on compounds in herbal medicines was obtained from public databases, and oral bioavailability and drug-likeness was screened using absorption, distribution, metabolism, and excretion (ADME) criteria. Correlations between compounds and genes were linked using the STITCH database, and genes related to hyperlipidaemia and atherosclerosis were gathered using the GeneCards database. Human genes were identified and subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis.

RESULTS

Network analysis identified 447 compounds in five herbal medicines that were subjected to ADME screening, and 21 compounds and 57 genes formed the main pathways linked to hyperlipidaemia and atherosclerosis. Among them, 10 compounds (naringenin, nobiletin, hesperidin, galangin, glycyrrhizin, homogentisic acid, stigmasterol, 6-gingerol, quercetin and glabridin) were linked to more than four genes, and are bioactive compounds and key chemicals. Core genes in this network were CASP3, CYP1A1, CYP1A2, MMP2 and MMP9. The compound-target gene network revealed close interactions between multiple components and multiple targets, and facilitates a better understanding of the potential therapeutic effects of YJT.

CONCLUSIONS

Pharmacological network analysis can help to explain the potential effects of YJT for treating dampness phlegm-related diseases such as hyperlipidaemia and atherosclerosis.

Clinical therapy of hyaluronic acid combined with platelet-rich plasma for the treatment of knee osteoarthritis

Knee osteoarthritis is the most common degenerative disease of the joints caused by articular cartilage injury, degradation of the joint edge and subchondral bone hyperplasia. Various treatments are used to alleviate the symptoms of patients with knee osteoarthritis, including analgesics and intra-articular injections. Platelet-rich plasma (PRP) is an autologous and multifunctional platelet concentrate of the blood, which stimulates the cartilage healing process and improves the damage caused by articular disease. Hyaluronic acid (HA) is an effective treatment for patients with knee osteoarthritis. In the current study, the effectiveness of PRP and HA combination therapy administered via intra-articular injections for patients with knee osteoarthritis was analyzed. A total of 360 patients with knee osteoarthritis were randomized into four different treatment groups as follows: Double-blind treatment with PRP (2-14 ml); double-blind treatment with HA (0.1-0.3 mg); combination therapy of PRP and HA; and placebo groups. Following treatment, all patients were evaluated using the Western Ontario and McMaster Universities Arthritis Index (WOMAC) and Common Toxicity Criteria. The most common treatment-emergent adverse events were hypertension and proteinuria. The current study demonstrated that PRP and HA treatment significantly improved arthralgia, and PRP treatment was determined to be significantly more effective than HA treatment using the WOMAC pain score (P<0.05). PRP and HA combination treatment significantly improved arthralgia, reduced humoral and cellular immune responses and promoted angiogenesis, which improved the patients' histological parameters compared with PRP or HA treatment alone. These results suggested that PRP and HA combination treatment may be a potential treatment option for patients with knee osteoarthritis in the future.

Protective Effects of Peucedanum japonicum Extract against Osteoarthritis in an Animal Model Using a Combined Systems Approach for Compound-Target Prediction

Peucedanum japonicum Thunberg is an herbal medicine used to treat neuralgia, rheumatoid arthritis, and inflammatory-related diseases. However, its effects on osteoarthritis (OA) and its regulatory mechanisms have not been investigated by network analysis. Here, we investigated the pharmacological effects of Peucedanum japonicum extract (PJE) on OA, by combining in vivo effective verification and network pharmacology prediction. Rats in which OA was induced by monosodium iodoacetate (MIA) were treated with PJE (200 mg/kg), and histopathological parameters, weight bearing distribution and inflammatory factors in serum and joint tissue were measured after 28 days of treatment. Additionally, in silico network analysis was used to predict holistic OA regulatory mechanisms of PJE. The results showed that PJE exerted potential protective effects by recovering hind paw weight bearing distribution, alleviating histopathological features of cartilage and inhibiting inflammatory mediator levels in the OA rat model. Furthermore, network analysis identified caspase-3 (CASP3), caspase-7 (CASP7), and cytochrome P450 2D6 (CYP2D6) as potential target genes; in addition, the TNF (Tumor necrosis factor) signaling pathway was linked to OA therapeutic action. Our combined animal OA model and network analysis confirmed the therapeutic effects of PJE against OA and identified intracellular signaling pathways, active compounds and target genes linked to its therapeutic action.

Exploring the Pharmacological Mechanism of Danzhi Xiaoyao Powder on ER-Positive Breast Cancer by a Network Pharmacology Approach

Background

Breast cancer is the most common malignancy among women worldwide, but the long-term endocrine therapy is frequently associated with adverse side effects. Danzhi Xiaoyao powder (DXP) is a herbal formula that has an effect on breast cancer, especially ER-positive breast cancer. However, the active compounds, potential targets, and pharmacological and molecular mechanism of its action against cancer remain unclear.

Methods

A network pharmacology approach comprising drug-likeness evaluation, oral bioavailability prediction, Caco-2 permeability prediction, multiple compound target prediction, multiple known target collection, breast cancer genes collection, and network analysis has been used in this study.

Results

Four networks are set up—namely, ER-positive breast cancer network, compound-compound target network of DXP, DXP-ER-positive breast cancer network, and compound-known target-ER-positive breast cancer network. Some ER-positive breast cancer and DXP related targets, clusters, biological processes, and pathways, and several potential anticancer compounds are found.

Conclusion

This network analysis successfully predicted, illuminated, and confirmed the molecular synergy of DXP for ER-positive breast cancer, got potential anticancer active compounds, and found the potential ER-positive breast cancer associated targets, cluster, biological processes, and pathways. This work also provides clues to the researcher who explores ethnopharmacological or/and herbal medicine's or even multidrugs' various synergies.

A Network Pharmacology Approach to Uncover the Multiple Mechanisms of Hedyotis diffusa Willd. on Colorectal Cancer

Background

As one of the most frequently diagnosed cancer diseases globally, colorectal cancer (CRC) remains an important cause of cancer-related death. Although the traditional Chinese herb Hedyotis diffusa Willd. (HDW) has been proven to be effective for treating CRC in clinical practice, its definite mechanisms have not been completely deciphered.

Objective

The aim of our research is to systematically explore the multiple mechanisms of HDW on CRC.

Methods

This study adopted the network pharmacology approach, which was mainly composed of active component gathering, target prediction, CRC gene collection, network analysis, and gene enrichment analysis.

Results

The network analysis showed that 10 targets might be the therapeutic targets of HDW on CRC, namely, HRAS, PIK3CA, KRAS, TP53, APC, BRAF, GSK3B, CDK2, AKT1, and RAF1. The gene enrichment analysis implied that HDW probably benefits patients with CRC by modulating pathways related to cancers, infectious diseases, endocrine system, immune system, nervous system, signal transduction, cellular community, and cell motility.

Conclusions

This study partially verified and predicted the pharmacological and molecular mechanism of HDW against CRC from a holistic perspective, which will also lay a foundation for the further experimental research and clinical rational application of HDW.

Platelet-rich plasma shows beneficial effects for patients with knee osteoarthritis by suppressing inflammatory factors

Knee osteoarthritis is a degenerative disease that may develop due ageing, obesity, strain, congenital abnormal joints, joint deformity or trauma. It is caused by many factors, such as degradation of articular cartilage injury, joint edge and subchondral bone hyperplasia of reactivity. Platelet-rich plasma (PRP) is an autologous blood sample that contains highly concentrated platelets and multiple cell growth factors. PRP promotes synovial cell proliferation and differentiation and may recover cartilage morphology. In the present study, the clinical efficacy of PRP was investigated in patients with knee osteoarthritis aged between 18 and 30 years in a phase-III clinical study. Following an 8-week baseline, patients with knee osteoarthritis were randomized into once-weekly, double-blind treatment with PRP (2-14 ml) or placebo groups. The results indicated that patients with osteoarthritis treated with PRP had modulated plasma concentrations of inflammatory factors and pro-angiogenic factors compared with the placebo group. Treatment responses were assessed by median percent reduction in inflammatory and pro-angiogenic factors and these improved with PRP treatment compared with the placebo. Clinical data indicated that PRP alleviated knee osteoarthritis and reduced humoral and cellular immune responses that led to beneficial effects on histological parameters. Inflammation was significantly alleviated in patients receiving PRP compared with the placebo group. The most common treatment-emergent adverse events in the presence of PRP were hypertension and proteinuria. In conclusion, treatment with PRP for patients with knee osteoarthritis presented beneficial effects in alleviating joint inflammation, cartilage destruction and bone damage, and repairing joint tissue. These results suggested that PRP may be a potential therapeutic agent for knee osteoarthritis.

Exploring the pharmacological mechanism of Yanghe Decoction on HER2-positive breast cancer by a network pharmacology approach

ETHNOPHARMACOLOGICAL RELEVANCE

Certain Chinese medicine formulae from traditional Chinese Medicine (TCM) are effective for treating and preventing diseases in clinical practice. Yanghe Decoction (YHD) is a Chinese medicine formula that is used to treat breast cancer, especially HER-positive breast cancer; however, the active compounds, potential targets, and pharmacological and molecular mechanism of its action against cancer remain unclear. Therefore, further investigation is required.

METHODS

A network pharmacology approach comprising drug-likeness evaluation, oral bioavailability prediction, Caco-2 permeability prediction, multiple compound target prediction, multiple know target collection, breast cancer genes collection, and network analysis has been used in this study.

RESULTS

Four networks are set up, including HER2-positive breast cancer network, compound-compound target network of YHD, YHD-HER2-positive breast cancer network and compound-known target-HER2-positive breast cancer network, and some HER2-positive breast cancer and YHD related targets, clusters, biological processes and pathways are found. We also found some potential anti-cancer compounds.

CONCLUSION

Our works successfully predict, illuminate and confirm the molecular synergy of YHD for HER2-positive breast cancer and found the potential HER2-positive breast cancer associated targets, cluster, biological processes and pathways. This study not only provide clues to the researcher who explores pharmacological and molecular mechanism of YHD acting on HER2-positive breast cancer, but also demonstrates a feasible method for discovering potential drugs from Chinese medicine formulae.

A Network Pharmacology Approach to Explore the Pharmacological Mechanism of Xiaoyao Powder on Anovulatory Infertility

Aim. To explore the pharmacological mechanism of Xiaoyao powder (XYP) on anovulatory infertility by a network pharmacology approach. Method. Collect XYP's active compounds by traditional Chinese medicine (TCM) databases, and input them into PharmMapper to get their targets. Then note these targets by Kyoto Encyclopedia of Genes and Genomes (KEGG) and filter out targets that can be noted by human signal pathway. Get the information of modern pharmacology of active compounds and recipe's traditional effects through databases. Acquire infertility targets by Therapeutic Target Database (TTD). Collect the interactions of all the targets and other human proteins via String and INACT. Put all the targets into the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to do GO enrichment analysis. Finally, draw the network by Cytoscape by the information above. Result. Six network pictures and two GO enrichment analysis pictures are visualized. Conclusion. According to this network pharmacology approach some signal pathways of XYP acting on infertility are found for the first time. Some biological processes can also be identified as XYP's effects on anovulatory infertility. We believe that evaluating the efficacy of TCM recipes and uncovering the pharmacological mechanism on a systematic level will be a significant method for future studies.