Network Pharmacology-based Analysis Research Articles

Investigation of the Mechanism of Periploca forrestii against Rheumatoid Arthritis with Network Pharmacology-Based Analysis.

Periploca forrestii Schltr (P. forrestii) is an edible medicinal herb with various health benefits such as treating antirheumatoid arthritis (RA), reducing inflammation, and preventing tumor growth. The active ingredients in P. forrestii responsible for its protective effect against RA, however, remain unknown. In this study, the active ingredient of P. forrestii and its potential mechanism of action against RA were investigated by network pharmacology and enrichment analysis. The methods included predicting target genes of P. forrestii, constructing a protein interaction network, and performing gene-ontology (GO) and Kyoto-encyclopedia of genes and genomes (KEGG) enrichment analysis. We discovered targets of RA through retrieval of OMIM and GeneCards public databases. Cardiac glycosides (CGs) are considered the primarily active ingredients of P. forrestii, and the target genes of GCs were discovered to be overlapped with relevant targets of RA using the Venn diagram. After that, prediction of relevant targets of P. forrestii was accomplished with a network pharmacology-based approach. Through the Venn diagram, we discovered 99 genes shared in the target genes of P. forrestii and RA. Gene enrichment analysis showed that the mechanisms of CGs against RA are associated with 55 signaling pathways, including endocrine resistance, Epstein-Barr virus infection, bladder cancer, prostate cancer, and coronavirus disease (COVID-19) signaling pathways. Coexpression analysis indicated ADSL, ATIC, AR, CCND1, MDM2, and HSP90AA1 as the hub genes between putative targets of P. forrestii-derived CGs and known therapeutic targets of RA. In conclusion, we clarified the mechanism of action of P. forrestii against RA, which would provide a basis for further understanding the clinical application of P. forrestii.

Network pharmacology-based analysis of the mechanism of Saposhnikovia divaricata for the treatment of type I allergy

Context Saposhnikovia divaricata (Turcz.) Schischk (Apiaceae) (SD) has various pharmacological activities, but its effects on type I allergy (TIA) have not been comprehensively studied. Objective This study evaluates the treatment and molecular mechanisms of SD against TIA. Materials and methods The effective components and action targets of SD were screened using TCMSP database, and allergy-related targets of SD were predicted using GeneCards and OMIM database. The obtained target intersections were imported into David database for GO analysis, and used R software to perform KEGG analysis. The RBL-2H3 cells sensitised by DNP-IgE/DNP-BSA were treated with different concentrations of SD (root decoction, 0.5, 1, and 2 mg/mL), prim-O-glucosylcimifugin (POG, 10, 40, and 80 μg/mL) and the positive control drug–ketotifen fumarate (KF, 30 μM) for 12 h, then subjected to cell degranulation and qPCR analysis. Results Eighteen active compounds of SD and 38 intersection targets were obtained: TIA-related signal pathways mainly include calcium signal pathway, PI3K–Akt signal pathway and MAPK signal pathway. Taking the β-Hex release rate of the model group as the base, the release rate of SD and POG in high dose groups were 43.79% and 57.01%, respectively, which were significantly lower than model group (p < 0.01), and significantly lower than KF group (63.83%, p < 0.01, p < 0.05). SD and POG could down-regulate the expression of related proteins in the Lyn/Syk, PI3K/AKT and MAPK signalling pathways. Discussion and conclusion Saposhnikovia divaricata could inhibit IgE-induced degranulation of mast cells, providing a scientific basis for further research and clinical applications of SD in TIA treatment.

Therapeutic mechanism of emodin for treatment of rheumatoid arthritis: a network pharmacology-based analysis

To investigate the therapeutic mechanism of emodin in the treatment of rheumatoid arthritis (RA) using a network pharmacology-based method and validate this mechanism in a fibroblast-like synovial cell line. The PubChem, Targetnet, SwissTargetPrediction, Genecards, OMIM, and DisGeNET databases were searched to obtain emodin targets and RA-related genes. A protein-protein interaction (PPI) network was constructed, and GO and KEGG pathway enrichment analyses were carried out to analyze the intersection genes. AutoDock4.2.6 software was used to simulate molecular docking between emodin and its candidate targets. In a cultured fibroblast-like synovial cell line (MH7A), the effects of different concentrations of emodin on proliferation of tumor necrosis factor-α (TNF-α)-induced cells were investigated using CCK-8 assay, cell scratch experiment and flow cytometry; the changes in the expressions of nuclear factor-κB (NF-κB) pathway proteins were detected using Western blotting, and the mRNA expressions of the hub genes were examined with RT-qPCR. We identified 32 intersection genes of emodin and RA, and the key targets including CAPS3, ESR1, and MAPK14 involved mainly the NF-κB signaling pathway. Cell scratch experiment and flow cytometry demonstrated a strong inhibitory effect of emodin on MH7A cell proliferation. Treatment with TNF-α significantly increased the cellular expressions of the NF-κB pathway proteins, which were obviously lowered by treatment with 80 μmol/L emodin. The results of RT-qPCR showed that TNF-α treatment obviously up-regulated the expressions of the hub genes COX2 and P38MAPK, and emodin treatment significantly down-regulated the expressions of MAPK and PTGS2 and up-regulated the expression of CASP3. The therapeutic effect of emodin on RA is mediated mainly through regulation of cell proliferation, apoptosis, and the NF-κB pathway.

Network pharmacology-based analysis of the effects of puerarin on sarcopenia.

BackgroundWith the acceleration of population aging, sarcopenia will place a heavy burden on families and society. Thus, effective treatments urgently need to be developed to slow down the development of sarcopenia. This study adopted a network pharmacological approach to explore the possible mechanisms of puerarin in treating sarcopenia.MethodsThe potential therapeutic targets of puerarin were obtained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database, while the targets of sarcopenia were obtained from the GeneCards, DisGeNET, Online Mendelian Inheritance in Man (OMIM), and Therapeutic Target Database (TTD) databases. The protein-protein interaction (PPI) network was generated by BisoGenet, and core targets were identified by a topological analysis. To determine the potential targeting pathways, the core targets were further imported into the Metascape platform for the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The results were visualized using an online bioinformatics tool.ResultsWe identified 53 targets for puerarin and 129 targets for sarcopenia. A total of 206 core targets, which were considered potential therapeutic targets, were identified from the merged PPI network. Further, the GO and KEGG analyses revealed that the functions of the core targets and related pathways were mainly associated with the cell cycle, apoptosis, protein synthesis, and proteolysis.ConclusionsPuerarin has the potential to treat sarcopenia through the regulation of the cell cycle, apoptosis, and protein homeostasis. Our study has laid a foundation for further studies on drug development and pharmacological experiments in the treatment of sarcopenia.

New Insight into Drugs to Alleviate Atopic March via Network Pharmacology-Based Analysis.

In the present study, a subject of atopic dermatitis (AD) is exposed progressively to allergic rhinitis (AR) and asthma (AS), which is defined as atopic march (AM). However, both the targets and compounds against AM are still largely unknown. Hence, we investigated the overlapping targets related directly to the occurrence and development of AD, AR, and AS through public databases (DisGeNET, and OMIM). The final overlapping targets were considered as key targets of AM, which were visualized by a Venn diagram. The protein–protein interaction (PPI) network was constructed using R package software. We retrieved the association between targets and ligands via scientific journals, and the ligands were filtered by physicochemical properties. Lastly, we performed a molecular docking test (MDT) to identify the significant ligand on each target. A total of 229 overlapping targets were considered as AM causal elements, and 210 out of them were interconnected with each other. We adopted 65 targets representing the top 30% highest in degree centrality among 210 targets. Then, we obtained 20 targets representing the top 30% greatest in betweenness centrality among 65 targets. The network analysis unveiled key targets against AM, and the MDT confirmed the affinity between significant compounds and targets. In this study, we described the significance of the eight uppermost targets (CCL2, CTLA4, CXCL8, ICAM1, IL10, IL17A, IL1B, and IL2) and eight ligands (Bindarit, CTLA-4 inhibitor, Danirixin, A-205804, AX-24 HCl, Y-320, T-5224, and Apilimod) against AM, providing a scientific basis for further experiments.

Network Pharmacology Deciphers the Action of Bioactive Polypeptide in Attenuating Inflammatory Osteolysis via the Suppression of Oxidative Stress and Restoration of Bone Remodeling Balance.

Oxidative stress involves enormously in the development of chronic inflammatory bone disease, wherein the overproduction of reactive oxygen species (ROS) negatively impacts the bone remodeling via promoting osteoclastogenesis and inhibiting osteogenesis. Lacking effective therapies highlights the importance of finding novel treatments. Our previous study screened a novel bioactive peptide D7 and demonstrated it could enhance the cell behaviors and protect bone marrow mesenchymal stem cells (BMSCs). Since BMSCs are progenitor cells of osteoblast (OB), we therefore ask whether D7 could also protect against the progress of inflammatory osteolysis. To validate our hypothesis and elucidate the underlying mechanisms, we first performed network pharmacology-based analysis according to the molecule structure of D7, and then followed by pharmacological evaluation on D7 by in vitro lipopolysaccharide(LPS)-induced models. The result from network pharmacology identified 20 candidate targets of D7 for inflammatory osteolysis intervention. The further analysis of Gene Ontology (GO)/KEGG pathway enrichment suggested the therapeutic effect of D7 may primarily affect osteoclast (OC) differentiation and function during the inflammatory osteolysis. Through validating the real effects of D7 on OC and OB as postulated, results demonstrated suppressive effects of D7 on LPS-stimulated OC differentiation and resorption, via the inhibition on OC marker genes. Contrarily, by improving the expression of OB marker genes, D7 displayed promotive effects on OB differentiation and alleviated LPS-induced osteogenic damage. Further mechanism study revealed that D7 could reduce LPS-induced ROS formation and strengthen antioxidants expressions in both OC and OB precursors, ameliorating LPS-triggered redox imbalance in bone remodeling. Taken together, our findings unveiled therapeutic effects of D7 against LPS-induced inflammatory osteolysis through the suppression of oxidative stress and the restoration of the bone remodeling process, providing a new therapeutic candidate for chronic inflammatory bone diseases.

Gancao Nurish-Yin Decoction medicated serum inhibits growth and migration of ovarian cancer cells: Network pharmacology-based analysis and biological validation

Ovarian cancer is one of the leading causes of death in women. It is also an important factor for an increased worldwide gynecological death observed recently. Here, we have elucidated the effect and mechanisms of Gancao Nurish-Yin Decoction (GNYD) on the viability of ovarian cancer cells. Network pharmacology analysis was performed to explore the putative therapeutic targets of GNYD on the ovarian cancer cells. Experiments at the cellular and molecular levels using ovarian cancer cells were performed to further verify the effect of GNYD. According to the network pharmacology analysis, 282 genes related to the targets of GNYD were identified. Among them, 123 genes were found to be overlapping as the potential targets for treating ovarian cancer. Subsequent experiments proved that GNYD medicated serum has significantly inhibited the survival, growth and migration of the ovarian cancer cells. The number of apoptotic cells has increased after the treatment with GNYD medicated serum, and a higher proportion of cells were arrested at G2/M phase. Importantly, genes present in the AMPK-p53/p21 pathway were found to be significantly promoted. Thus, this study has not only demonstrated the potential therapeutic value of GNYD in inhibiting the survival, growth and migration of ovarian cancer cells in vitro, but also provide clues for further exploring the pharmacological and molecular mechanisms of Chinese medicine preparations acting on various types of cancer.

Anemone chinensis Bunge aqueous enema alleviates dextran sulfate sodium-induced colitis via inhibition of inflammation and regulation of the colonic mucosal microbiota

Ethnopharmacological relevanceAlthough the incidence of ulcerative colitis (UC) increases every year, there is still a lack of satisfactory treatment options. Anemone chinensis Bunge (AB), a traditional Chinese herb, is a potent compound that can be prepared as a decoction, and then administered as an enema to relieve UC symptoms. However, the therapeutic effect and mechanisms of aqueous AB on UC are still unknown.Aim of the study: This study investigates the potential therapeutic value and mechanism of AB aqueous enema for UC. Materials and methodsFirst, the practical components in aqueous AB were extracted and identified by UPLC-MS/MS. Second, the potential active targets and target genes related to UC were predicted, mapped, and analyzed by network pharmacology. Then, the effects of AB aqueous enema on UC were assessed using the dextran sulfate sodium (DSS)-induced colitis model with mice. Finally, the level of inflammation, the expression level of proteins associated with the colonic mucosal barrier, and the microbiota associated with the intestinal mucosal were investigated. ResultsFourteen active ingredients in AB were identified. The network pharmacology-based analysis demonstrated that the active ingredients possibly affected ten key targets, such as IL-6, TNF, and PTGS2. They are also related to the tight junction proteins ZO-1, occludin, and claudin-1.Furthermore, mice treated with DSS developed severe mucosal colitis. AB aqueous enema decreased the disease activity index (DAI), significantly inhibited colonic damage, and greatly decreased colon length shortening (p < 0.05).AB also significantly restored tight junction proteins and the associated mucin proteins mucin-2 (MUC2) and mucin-3A (MUC3A). In addition, the diversity of the gut microbiota after administration of DSS was significantly decreased. However, the diversity was entirely restored after AB treatment. Recovery of the abundance of colonic mucosal bacteria, especially Lactobacillus reuteri and Lactobacillus gasseri, occurred at the species level after AB treatment. In vitro, AB can be utilized by the two bacteria, especially under glucose deficiency. ConclusionsOur study demonstrated that the AB aqueous enema alleviated colitis by restoring intestinal barrier proteins and regulating the gut microbiota.

Network pharmacology-based analysis of the mechanism of Radix Paeoniae Alba against Toosendan Fructus-induced hepatotoxicity

Network pharmacology-based analysis of the mechanism of Radix Paeoniae Alba against Toosendan Fructus-induced hepatotoxicity

The Hypolipidemic Effect of Dalbergia odorifera T. C. Chen Leaf Extract on Hyperlipidemic Rats and Its Mechanism Investigation Based on Network Pharmacology.

Objective The aim of this study was to explore the hypolipidemic effect and mechanism of Dalbergia odorifera T. C. Chen leaf extract. Methods The hypolipidemic effect of D. odorifera leaf extract was investigated using a hyperlipidemic rat model. Then, its mechanism was predicted using network pharmacology methods and verified using western blotting. Results Compared with the levels in the model group, the serum levels of triglyceride (TG), total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-C) decreased significantly, whereas the serum level of high-density lipoprotein cholesterol (HDL-C) increased dramatically after treatment with the extract. The degrees of hepatocyte steatosis and inflammatory infiltration were markedly attenuated in vivo. Then, its hyperlipidemic mechanism was predicted using network pharmacology-based analysis. Thirty-five key targets, including sterol regulatory element-binding protein cleavage-activating protein (SCAP), sterol regulatory element-binding protein-2 (SREBP-2), 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR), low-density lipoprotein receptor (LDLR), and ten signaling pathways, were associated with hyperlipidemia. Finally, it was verified that the extract downregulated the protein levels of SCAP, SREBP-2, and HMGCR, and upregulated protein levels of LDLR. Conclusion These findings provided additional evidence of the hypolipidemic effect of D. odorifera leaf extract.

Network Pharmacology-Based Analysis of Pogostemon cablin (Blanco) Benth Beneficial Effects to Alleviate Nonalcoholic Fatty Liver Disease in Mice.

Nonalcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease and is associated with high morbidity and mortality. Pogostemon cablin (Blanco) Benth/Huo Xiang (HX) is a perennial herb with unique anti-oxidant and anti-inflammatory properties, and thus, can positively affect liver function. In this study, we used network pharmacology to predict the potential mechanism of HX on NAFLD. Pharmacological experiments were used to verify the effect of HX on the functions of NAFLD. Network pharmacology identified nine components that interacted with 82 NAFLD-related targets, revealing four target genes: TNF, IL6, TP53, and AKT1. HX prevents the development and progression of NAFLD through different pathways and targets with quercetin-regulated lipid metabolism, anti-inflammatory, and anti-oxidant pathways playing an essential role in the treatment of NAFLD. Compared with feeding HFD, HX significantly attenuated lipid accumulation in vivo with mice and also in vitro with mouse liver cells. A high dose of HX decreased hepatocyte lipid accumulation and the abundance of SREBF1 and FASN. Validation experiments revealed that HX inhibited the activation of NF-κB/IκB signaling and decreased the release and levels of pro-inflammatory factors (TNF-α and IL-6). These data suggest that HX can attenuate abnormal lipid metabolic responses and enhance antioxidant mechanisms. Thus, the pharmacological effects from plants used in traditional Chinese medicine are achievde through a multi-level response.

Uncovering Bupi Yishen Formula Pharmacological Mechanisms Against Chronic Kidney Disease by Network Pharmacology and Experimental Validation.

Chronic kidney disease (CKD) is a leading public health problem with high morbidity and mortality, but the therapies remain limited. Bupi Yishen Formula (BYF) - a patent traditional Chinese medicine (TCM) formula - has been proved to be effective for CKD treatment in a high-quality clinical trial. However, BYF’s underlying mechanism is unclear. Thus, we aimed to reveal BYF pharmacological mechanism against CKD by network pharmacology and experimental studies. Network pharmacology-based analysis of the drug-compound-target interaction was used to predict the potential pharmacological mechanism and biological basis of BYF. We performed a comprehensive study by detecting the expression levels of fibrotic and inflammatory markers and main molecules of candidate signal pathway in adenine-induced CKD rats and TGF-β1-induced HK-2 cells with the treatment of BYF by western blotting and RT-qPCR analyses. Using small interfering RNA, we assessed the effect of BYF on the TLR4-mediated NF-κB mechanism for CKD renal fibrosis and inflammation. Network pharmacology analysis results identified 369 common targets from BYF and CKD. Based on these common targets, the BYF intervention pathway was analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. We found that Toll-like receptor (TLR) and NF-κB signaling pathways were enriched. Then, we demonstrated that BYF significantly improved the adenine-induced CKD rat model condition by kidney dysfunction improvement and reversing renal fibrosis and inflammation. Subsequently, we investigated BYF’s effect on the TLR4/NF-κB signaling pathway. We found that TLR4 and phospho-NF-κB (p-p65 and p-IKβα) expression was significantly upregulated in adenine-induced CKD rats, then partially downregulated by BYF. Furthermore, BYF inhibited fibrotic and inflammatory responses, as well as TLR4, p-p65, and p-IKβα in TGF-β1-induced HK-2 cells. Additionally, the BYF inhibitory effect on fibrosis and inflammation, and NF-κB pathway activation were significantly reduced in TGF-β1-induced HK-2 cells transfected with TLR4 siRNA. Altogether, these findings demonstrated that the suppression of TLR4-mediated NF-κB signaling was an important anti-fibrotic and anti-inflammatory mechanism for BYF against CKD. It also provided a molecular basis for new CKD treatment drug candidates.

Multimodal Identification by Transcriptomics and Multiscale Bioassays of Active Components in Xuanfeibaidu Formula to Suppress Macrophage-Mediated Immune Response.

Xuanfeibaidu Formula (XFBD) is a Chinese medicine used in the clinical treatment of coronavirus disease 2019 (COVID-19) patients. Although XFBD has exhibited significant therapeutic efficacy in clinical practice, its underlying pharmacological mechanism remains unclear. Here, we combine a comprehensive research approach that includes network pharmacology, transcriptomics, and bioassays in multiple model systems to investigate the pharmacological mechanism of XFBD and its bioactive substances. High-resolution mass spectrometry was combined with molecular networking to profile the major active substances in XFBD. A total of 104 compounds were identified or tentatively characterized, including flavonoids, terpenes, carboxylic acids, and other types of constituents. Based on the chemical composition of XFBD, a network pharmacology-based analysis identified inflammation-related pathways as primary targets. Thus, we examined the anti-inflammation activity of XFBD in a lipopolysaccharide-induced acute inflammation mice model. XFBD significantly alleviated pulmonary inflammation and decreased the level of serum proinflammatory cytokines. Transcriptomic profiling suggested that genes related to macrophage function were differently expressed after XFBD treatment. Consequently, the effects of XFBD on macrophage activation and mobilization were investigated in a macrophage cell line and a zebrafish wounding model. XFBD exerts strong inhibitory effects on both macrophage activation and migration. Moreover, through multimodal screening, we further identified the major components and compounds from the different herbs of XFBD that mediate its anti-inflammation function. Active components from XFBD, including Polygoni cuspidati Rhizoma, Phragmitis Rhizoma, and Citri grandis Exocarpium rubrum, were then found to strongly downregulate macrophage activation, and polydatin, isoliquiritin, and acteoside were identified as active compounds. Components of Artemisiae annuae Herba and Ephedrae Herba were found to substantially inhibit endogenous macrophage migration, while the presence of ephedrine, atractylenolide I, and kaempferol was attributed to these effects. In summary, our study explores the pharmacological mechanism and effective components of XFBD in inflammation regulation via multimodal approaches, and thereby provides a biological illustration of the clinical efficacy of XFBD.

UPLC-MS/MS and Network Pharmacology-Based Analysis of Bioactive Anti-Depression Compounds in Betel Nut.

BackgroundBetel nuts have long been used in traditional Chinese medicine. In our study, the bioactive components of betel nut were systematically investigated, and the main components and their target genes in the treatment of depression were predicted.MethodsThe metabolites of the kernels and peels were analyzed with a UPLC–MS/MS system. Mass spectrometry outcomes were annotated by MULTIAQUANT. “Compound‐disease targets” were utilized to construct a pharmacology network.ResultsA total of 873 metabolites were identified, with a high abundance of flavonoids, alkaloids, and phenols. Moreover, the abundance of flavonoids, alkaloids, and phenols in the kernel was significantly higher than that in the peel. A high abundance of catechin, arginine, and phenylalanine was detected in the kernel, while a high abundance of arginine, arecoline, and aminobutyric acid was detected in the peel. Catechins and cyanoside were the most abundant flavonoids in the kernel and peel, respectively. Arecoline was the most abundant alkaloid. A total of 111 metabolites showed a significant difference between the kernels and peels. The relative abundance of 40 differential metabolites was higher than 100,000, including 14 primary metabolites, 12 flavonoids, 4 phenols, and 4 alkaloids. Among the 40 high abundance metabolites, 20 were higher in the kernel and 20 in the peel. In addition, the enrichment of metabolic pathways found that the kernel and peel of the fruit adopted different metabolic pathways for the synthesis of flavonoids and alkaloids. Network pharmacology prediction showed that 93 metabolites could target 141 depression-related genes. The main components of betel nut intervention in depression were predicted to include L-phenylalanine, protocatechuic acid, okanin, nicotinic acid, L-tyrosine, benzocaine, syringic acid, benzocaine, phloretic acid, cynaroside, and 3,4-dihydroxybenzaldehyde.ConclusionBetel nuts are rich in natural metabolites, and some of these metabolites can participate in the intervention of depression. In addition, the metabolites showed distinct characteristics between the kernel and peel. Therefore, it is necessary to comprehensively and rationally use betel nuts.

Network Pharmacology-Based Analysis on the Action Mechanism of Oleanolic Acid to Alleviate Osteoporosis.

Oleanolic acid (OA) is a triterpenoid commonly found in plants and has shown extensive pharmaceutical activities. This study aimed to investigate the underlying mechanism of antiosteoporosis (OP) action of OA by utilizing the network pharmacology approach and molecular docking methods. First, the targets of OA were identified using the GeneCards, Stitch, and Swisstarget databases, and the targets related to OP were mined using the NCBI, Genecards, and DisGeNet databases. The overlapped targets of OA and OP were regarded as candidate targets, and the String database was used to obtain the protein–protein interactions among the targets. Then, Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway enrichment pathways of the candidate targets were performed using the DAVID database. In addition, the top 16 targets in the protein interaction network were used for molecular docking. Finally, an animal model constructed using d-galactose-induced oxidative stress and a low-calcium diet with accelerated bone loss was used to verify the in vivo effects of OA on osteoporotic mice. A total of 42 candidate targets for OA to treat OP were obtained. According to the protein–protein interaction network, MAPK1 showed the highest connectivity with other proteins. Additionally, GO analysis identified the top 20 biological processes, 9 cellular components, and top 20 molecular functions. Moreover, the candidate targets were mainly involved in 13 signaling pathways such as TNF signaling pathway, insulin resistance, MAPK signaling pathway, apoptosis, and PI3K-Akt signaling pathways. Furthermore, molecular docking revealed that OA has a high degree of connections with 16 key proteins. In addition, the anti-OP effects of OA are further validated through the in vivo model. Altogether, our study elucidated the candidate targets for OA to alleviate OP, explored the protein–protein interactions and related signaling pathways of the targets, and validated the anti-OP effects of OA. It could provide a better understanding of the action mechanism in OA to treat OP.

A network pharmacology approach to investigate the anticancer mechanism of cinobufagin against hepatocellular carcinoma via downregulation of EGFR-CDK2 signaling

Hepatocellular carcinoma (HCC) is one of the deadliest cancers with high mortality and poor prognosis, and the investigation on new approaches and effective drugs for HCC therapy is of great significance. In our study, we demonstrate that treatment with cinobufagin, a natural compound isolated from traditional chinese medicine Chansu, reduces proliferation and the colony formation capacity of the human hepatoma cells in vitro, in addition, cinobufagin induces mitotic arrest in human hepatoma cells. The results of a network pharmacology-based analysis show that EGFR, MAPK1, PTK2, CDK2, MAPK3, ESR1, CDK1, PRKCA, AR, and CSNK2A1 are the key targets involved in the anti-tumor activities of cinobufagin, additionally, several signaling pathways such as proteoglycans in cancer, pathways in cancer, HIF-1 signaling pathway, VEGF signaling pathway, ErbB signaling pathway, and PI3K-AKT signaling pathway are identified as the potential pathways involved in the inhibitory effects of cinobufagin against HCC. Furthermore, at the molecular level, we find that cinobufagin decreases EGFR expression and CDK2 activity in human hepatoma cells. Inhibition of EGFR or CDK2 expression could not only suppress the growth of tumor cells but also enhance the inhibitory effects of cinobufagin on the proliferative potential of human hepatoma cells. We also demonstrate that EGFR positively regulates CDK2 expression. Furthermore, EGFR inhibitor gefitinib or CDK2 inhibitor CVT-313 synergistically enhances anticancer effects of cinobufagin in human hepatoma cells. Taken together, these findings indicate that cinobufagin may exert antitumor effects by suppressing EGFR-CDK2 signaling, and our study suggests that cinobufagin may be a novel, promising anticancer agent for the treatment of HCC.

The anti-tumor effect of OP-B on ovarian cancer in vitro and in vivo, and its mechanism: An investigation using network pharmacology-based analysis

Ethnopharmacological relevanceMaidong (Liliaceae) is used as a yin-nourishing medication for the treatment of cardiovascular disease, inflammation, and assistant cancer chemotherapy in the clinic. Ophiopogonin B (OP-B), a major saponin extracted from Maidong, is reported to have potential antitumor activities against various human cancers. However, the effects of OP-B on human ovarian cancer (OC) and the potential mechanisms of action are yet elusive.Aim of the study: In this study, we aimed to explore the potential molecular mechanisms of OP-B in the treatment of OC using network pharmacology. In vivo and in vitro experiments were conducted to further verify the therapeutic effects of OP-B on OC. Materials and methodsTo investigate the functions of OP-B against OC holistically, the related targets of OP-B and OC were each predicted based on four public databases. Subsequently, the identified PPI network was constructed to detect the hub potential targets. In addition, GO and KEGG enrichment analysis were applied by Metascape database. Furthermore, we simultaneously investigated the anticancer effects of OP-B on SKOV3 and A2780 human ovarian cancer cells using a cell viability assay, transwell assay, and an image-based cytometric assay. The quantitative real-time PCR and western-blot assay were used to validate the RNA and protein levels of target genes in OP-B treated OC cells. At last, SKOV3-bearing BALB/c nude mice were applied to observe the effectiveness and toxicity of OP-B. ResultsThrough network pharmacological analysis, OP-B was found to play a critical role in OC via multiple targets and pathways, especially the STAT3 signaling pathways. In addition, in vitro experiments found OP-B suppressed SKOV3 and A2780 cells proliferation in a time and concentration dependent manner, and markedly impaired cancer cell migration. Flow cytometry analysis revealed that OP-B significantly increased early and late apoptosis, induced G2/M phase cell cycle arrest in SKOV3 cells and G0/G1 phase cell cycle arrest in A2780 cells. Moreover, OP-B administration down-regulated the expression of p-STAT3 protein, whereas the RNA expression and total protein levels of STAT3 were not altered. Finally, in vivo experiments confirmed the therapeutic effects of OP-B on OC in nude mice with low toxicity in heart, liver, lung, and kidney. ConclusionOP-B could efficiently suppress OC cellular proliferation, migration and induce apoptosis, cell cycle arrest mainly via the regulation of STAT3 signaling pathway. This study provides a promising potential application for an alternative to chemotherapy in ovarian cancer.

Network Pharmacology-Based Analysis on the Curative Effect of Kunxian Capsules against Rheumatoid Arthritis.

Kunxian capsules (KCs), a Chinese patent medicine, have been clinically proven to be effective in the treatment of rheumatoid arthritis (RA). However, the chemical profile of KC remains to be characterized, and the mechanism underlying the protective effect against RA is yet to be elucidated. Here, a network pharmacology-based approach was adopted, integrated with the chemical profiling of KC by UHPLC-Q-TOF/MS. As a result, a total of 67 compounds have been identified from KC extract, among which 43 were authenticated by comparison to the mass spectrum of standard chemicals. ADME behaviors of the chemical constituents of KC were predicted, resulting in 35 putative active ingredients. Through target prediction of both active ingredients of KC and RA and PPI analysis, core targets were screened out, followed by biological process and related pathway enrichment. Then, a TCM-herb-ingredient-target-pathway network was constructed and a multicomponent, multitarget, and multipathway synergistic mechanism was proposed, providing an information basis for further investigation. The active pharmaceutical ingredients included mainly terpenoids (such as triptolide and celastrol), sesquiterpene pyridines (such as wilforgine and wilforine), and flavonoids (such as icariin, epimedin A, B, and C, and 2″-O-rhamnosylicariside II).

Mechanism exploration of Gouqi-wentang formula against type 2 diabetes mellitus by phytochemistry and network pharmacology-based analysis and biological validation

BackgroundThe Gouqi-wentang formula (GQWTF) is a herbal formula used by Academician Xiao-lin Tong for the clinical treatment of T2DM. GQWTF is beneficial to qi, nourishes Yin, clears heat, and promotes fluid production, but the effective components and their mechanism of action remain unclear.MethodsThe main components of GQWTF were detected by LC–MS, and the multi-target mechanisms of GQWTF in T2DM were elucidated using network pharmacology analysis, including target prediction, protein–protein interaction network construction and analysis, Gene Ontology (GO) terms, Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway annotation, and other network construction. Finally, the efficacy of the GQWTF was verified using biological experiments.ResultsFirst, the “herb-channel tropism” network suggested that GQWTF focuses more on treating diseases by recuperating the liver, which is considered as an important insulin-sensitive organ. Subsequently, a total of 16 active ingredients in GQWTF were detected and screened, and their biological targets were predicted. Then, “compound-target” network was constructed, where enrichment analysis of GQWTF targets reflected its potential pharmacological activities. After T2DM-related target identification, 39 cross targets of GQWTF and T2DM were obtained, and 30 key targets highly responsible for the beneficial effect of GQWTF on T2DM were identified by PPI analysis. GO analysis of these key targets showed that many biological processes of GQWTF in treating T2DM are key in the occurrence and development of T2DM, including components related to inflammatory/immune response, insulin, and metabolism. KEGG analysis revealed the regulation of multiple signalling pathways, such as insulin resistance, PPAR signalling pathway, FoxO signalling pathway, Fc epsilon RI signalling pathway, and pathways that influence diabetes primarily by regulating metabolism as well as other T2DM directly related pathways. Furthermore, a “formula-compound-pathway-symptom” network was constructed to represent a global view of GQWTF in the treatment of T2DM.ConclusionsThis study explored the mechanism of action of GQWTF in T2DM by multi-component and multi-target multi pathways, which could provide a theoretical basis for the development and clinical application of GQWTF.

Uncovering the active components, prospective targets, and molecular mechanism of Baihe Zhimu decoction for treating depression using network pharmacology-based analysis

Ethnopharmacological relevanceBaihe Zhimu decoction (BZD) is a classical traditional Chinese medicinal herbal formula. It consists of two herbal medicines, Rhizoma Anemarrhenae (Zhimu), the rhizomes of Anemarrhena asphodeloides Bge. (Liliaceae), and Bulbus Lilii (Baihe), the bulbs of Lilium brownii var. Viridulum Baker (Liliaceae). BZD has been widely used in China to treat depression and verified to be effective without evident side effects. Aim of the studyThe aim of this study was to elucidate the active components, potential targets, and molecular mechanism of Baihe Zhimu decoction for treating depression. Materials and methodsIn this research, a chronic unpredictable mild stress (CUMS) mice was first established to evaluate the pharmacological effects of BZD for treating depression. A component database was then constructed for BZD. High-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (HPLC-QTOF-MS) technique was used to identify the components in BZD and blood-absorbed components. Further screening and validation of protein targets were performed by molecule docking. The component-target binding affinity was validated by surface plasmon resonance analysis (SPR) assay. The related pathways were predicted by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Relative proteins in the predicted pathways were finally assessed by Western blot. ResultsThe pharmacology evaluation experiment demonstrated that BZD could improve depressive-like behavior, inhibit the hippocampal secretion of pro-inflammatory cytokines and reduce neuronal apoptosis in CUMS mice model. A component database containing 163 components and a target database covering 1286 proteins were constructed. HPLC-QTOF-MS assay identified twenty-six components from BZD and ten components absorbed into rat plasma after an intragastric treatment with BZD. Next, 56 underlying targets were screened out by a virtual high-throughput screening approach. Twenty-seven of them were further screened out and confirmed by molecular docking. Afterward, a component-target network was established, and the component-protein binding affinities were validated by SPR assays. By KEGG pathway enrichment analysis, two signaling pathways PI3K/Akt and MAPK were predicted as the potential signaling cascades. Finally, Western blot showed that BZD dramatically reversed the suppression of PI3K/Akt/GSK-3β pathway and the activation of MAPK pathway in CUMS mice model. ConclusionsBZD demonstrated a substantial pharmacological effect on CUMS mice model. Network pharmacology-based analysis predicted that ten blood-absorbed components can act on 27 target proteins. KEGG and Western blotting analysis suggested that BZD could exert antidepressant effects by regulating the PI3K/Akt and MAPK signaling pathways.