Results Of Network Pharmacology Research Articles

Network pharmacology combined with molecular docking and experimental validation to reveal the pharmacological mechanism of naringin against renal fibrosis.

To explore the pharmacological mechanism of naringin (NRG) in renal fibrosis (RF) based on network pharmacology combined with molecular docking and experimental validation. We used databases to screen for the targets of NRG and RF. The "drug-disease network" was established using Cytoscape. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of targets were performed using Metascape, and molecular docking was performed using Schrödinger. We established an RF model in both mice and cells to validate the results of network pharmacology. After screening the database, we identified 222 common targets of NRG and RF and established a target network. Molecular docking showed that the target AKT had a good interaction with NRG. We found that the phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathway was enriched by multiple targets and served as a target for experimental validation through GO and KEGG. The results revealed that NRG ameliorated renal dysfunction, reduced the release of inflammatory cytokines, decreased the expression of α-SMA, collagen I, and Fn, and recovered the expression of E-cad by inhibiting the PI3K/AKT signaling pathway. Our study used pharmacological analysis to predict the targets and mechanisms of NRG against RF. Furthermore, experiments proved that NRG inhibited RF effectively by targeting the PI3K/AKT signaling pathway.

Clinopodium chinense Kuntze ameliorates dextran sulfate sodium-induced ulcerative colitis in mice by reducing systematic inflammation and regulating metabolism.

Clinopodium chinense Kuntze (CC), traditional Chinese medicine with anti-inflammatory, anti-diarrheal, and hemostatic activities, has been used to treat dysentery and bleeding diseases for thousands of years, which are similar to the symptoms of ulcerative colitis (UC). To obtain a novel treatment for UC, an integrated strategy was developed in this study to investigate the effect and mechanism of CC against UC. The chemical characterization of CC was scanned by UPLC-MS/MS. Network pharmacology analysis was performed to predict the active ingredients and pharmacological mechanisms of CC against UC. Further, the results of network pharmacology were validated using LPS-induced RAW 264.7cells and DSS-induced UC mice. The production of pro-inflammatory mediators and biochemical parameters was tested using the ELISA kits. The expression of NF-κB, COX-2, and iNOS proteins was evaluated using Western blot analysis. Body weight, disease activity index, colon length, histopathological examination, and metabolomics analysis in colon tissues were carried out to confirm the effect and mechanism of CC. Based on the chemical characterization and literature collection, a rich database of ingredients in CC was constructed. Network pharmacology analysis provided five core components as well as revealed that the mechanism of CC against UC was highly related to inflammation, especially the NF-κB signaling pathway. In vitro experiments showed CC could inhibit inflammation by LPS-TLR4-NF-κB-iNOS/COX-2 signaling pathway in RAW264.7cells. Meanwhile, in vivo experimental results proved that CC significantly alleviated pathological features with increased body weight and colonic length, decreased DAI and oxidative damage, as well as mediated inflammatory factors like NO, PGE2, IL-6, IL-10, and TNF-ɑ. In addition, colon metabolomics analysis revealed CC could restore the abnormal endogenous metabolite levels in UC. 18 screened biomarkers were further enriched in four pathways including Arachidonic acid metabolism, Histidine metabolism, Alanine, aspartate and glutamate metabolism as well as the Pentose phosphate pathway. This study demonstrates that CC could alleviate UC by reducing systematic inflammation and regulating metabolism, which is beneficial for providing scientific data for the development of UC treatment.

Network pharmacology and experimental verification to explore the anti-migraine mechanism of Yufeng Ningxin Tablet.

Yufeng Ningxin Tablet (YNT) is a traditional Chinese medicine formula, that has been used clinically to treat migraine for many years. It is composed of one herb Pueraria lobata var. lobata (Willd.) Ohwi (Relevant Chinese name: Gegen). Previously, it has been recorded by traditional Chinese doctor that Gegen could be used as medicine to treat migraine. However, the underlying mechanism of action remains to be investigated. It was to explore the effect and mechanism of YNT on migraine based on network pharmacology and experimental verification. First, with the network pharmacology, the effective chemical components and target genes of YNT were filtrated, the YNT-compound-migraine-targets network was constructed. The protein-protein interaction network (PPI) and literature reports were combined to identify potential targets of YNT in the treatment of migraine. Then, the representative compounds of YNT were characterized by LC-MS/MS and the major effect components were identified. Finally, the prediction results of network pharmacology were verified by animal and cell experiments. 7 bioactive components of YNT could act on 97 migraine potential targets. The 5 bioactive components could be characterized comprehensively of YNT. The key therapeutic targets and pathways were collected including 5-HT, CGRP, inflammation and nociceptive factors, and NF-κB signaling pathway. Animal experiments showed that YNT could reduce the expression level of 5-HT, CGRP, NF-κB, c-fos and IL-1β. YNT could inhibit LPS-induced neuroinflammation by NF-κB in BV2 cells in vitro. Western blotting analysis results showed YNT inhibited the NF-κB and phospho-NF-κB levels. It is the first time to verify the consistency between the metabolic components of YNT by LC-MS/MS and the active components predicted by network pharmacology. Meanwhile, the potential mechanism of YNT in the treatment of migraine was studied by combining network pharmacology and in vitro and in vivo experiments.

Effect and mechanism of chlorogenic acid on cognitive dysfunction in mice by lipopolysaccharide-induced neuroinflammation.

Neuroinflammation is an important factor causing numerous neurodegenerative pathologies. Inflammation can lead to abnormal neuronal structure and function and even death, followed by cognitive dysfunction. There is growing evidence that chlorogenic acid has anti-inflammatory effects and immunomodulatory activity. The aim of this study was to elucidate the potential targets and molecular mechanisms of chlorogenic acid in the treatment of neuroinflammation. We used the lipopolysaccharide-induced neuroinflammation mouse model and the lipopolysaccharide-stimulated BV-2 cells in vitro model. Behavioral scores and experiments were used to assess cognitive dysfunction in mice. HE staining and immunohistochemistry were used to assess neuronal damage in the mouse brain. Immunofluorescence detected microglia polarization in mouse brain. Western blot and flow cytometry detected the polarization of BV-2 cells. The migration of BV-2 cells was detected by wound healing assay and transwell assay. Potential targets for chlorogenic acid to exert protective effects were predicted by network pharmacology. These targets were then validated using molecular docking and experiments. The results of in vivo experiments showed that chlorogenic acid had an obvious ameliorating effect on neuroinflammation-induced cognitive dysfunction. We found that chlorogenic acid was able to inhibit BV-2 cells M1 polarization and promote BV-2 cells M2 polarization in vitro while also inhibiting the abnormal migration of BV-2 cells. Based on the network pharmacology results, we identified the TNF signaling pathway as a key signaling pathway in which chlorogenic acid exerts anti-neuroinflammatory effects. Among them, Akt1, TNF, MMP9, PTGS2, MAPK1, MAPK14, and RELA are the core targets for chlorogenic acid to function. Chlorogenic acid can inhibit microglial polarization toward the M1 phenotype and improve neuroinflammation-induced cognitive dysfunction in mice by modulating these key targets in the TNF signaling pathway.

Phillygenin Ameliorates Carbon Tetrachloride-Induced Liver Fibrosis: Suppression of Inflammation and Wnt/β-Catenin Signaling Pathway.

Liver fibrosis (LF) is caused by the chronic wound healing response to liver injury from various origins. Among the causes, inflammatory response is the central trigger of LF. Phillygenin (PHI) is a lignan derived from Forsythia suspensa, which has significant anti-inflammatory properties. However, the effect of PHI on improving LF and the underlying mechanism have rarely been studied. In this study, we used carbon tetrachloride (CCl4) to establish a mouse model of LF. Through histological analysis of liver tissue, and measurement of the levels of hepatocyte damage markers (ALT, AST, TBIL, TBA) and four indicators of LF (Col IV, HA, LN, PC-III) in serum, it was shown that PHI improved liver function and reduced the progress of LF. Subsequently, the detection of fibrogenic biomarkers in liver tissue showed that PHI inhibited the activation of hepatic stellate cells (HSCs). Next, the expression of inflammatory markers in liver tissue/serum was detected by immunohistochemistry, RT-qPCR, and ELISA, suggesting that PHI inhibited inflammation during LF. Similarly, in vitro experiments also confirmed that PHI could inhibit lipopolysaccharide-induced inflammatory responses in RAW264.7 cells, which showed strong anti-inflammatory effects. In addition, the results of network pharmacology, molecular docking, RT-qPCR and western blot confirmed that PHI could alleviate CCl4-induced LF by inhibiting the Wnt/β-catenin pathway. In conclusion, our research showed that PHI curbed LF through inhibition of HSC activation and collagen accumulation via inhibiting multiple profibrogenic factors, modulating a variety of inflammatory factors, and suppressing the Wnt/β-catenin pathway.

Network pharmacology and molecular docking study for biological pathway detection of cytotoxicity of the yellow jasmine flowers

BackgroundThe yellow jasmine flower (Jasminum humile L.) is a fragrant plant belonging to the Oleaceae family with promising phytoconstituents and interesting medicinal uses. The purpose of this study was to characterize the plant metabolome to identify the potential bioactive agents with cytotoxic effects and the underlying mechanism of cytotoxic activity.MethodsFirst, HPLC–PDA-MS/MS was used to identify the potential bioactive compounds in the flowers. Furthermore, we assessed the cytotoxic activity of the flower extract against breast cancer (MCF-7) cell line using MTT assay followed by the cell cycle, DNA-flow cytometry, and Annexin V-FITC analyses alongside the effect on reactive oxygen species (ROS). Finally, Network pharmacology followed by a molecular docking study was performed to predict the pathways involved in anti-breast cancer activity.ResultsHPLC–PDA-MS/MS tentatively identified 33 compounds, mainly secoiridoids. J. humile extract showed a cytotoxic effect on MCF-7 breast cancer cell line with IC50 value of 9.3 ± 1.2 µg/mL. Studying the apoptotic effect of J. humile extract revealed that it disrupts G2/M phase in the cell cycle, increases the percentage of early and late apoptosis in Annexin V-FTIC, and affects the oxidative stress markers (CAT, SOD, and GSH-R). Network analysis revealed that out of 33 compounds, 24 displayed interaction with 52 human target genes. Relationship between compounds, target genes, and pathways revealed that J. humile exerts its effect on breast cancer by altering, Estrogen signaling pathway, HER2, and EGFR overexpression. To further verify the results of network pharmacology, molecular docking was performed with the five key compounds and the topmost target, EGFR. The results of molecular docking were consistent with those of network pharmacology.ConclusionOur findings suggest that J. humile suppresses breast cancer proliferation and induces cell cycle arrest and apoptosis partly by EGFR signaling pathway, highlighting J. humile as a potential therapeutic candidate against breast cancer.

Protective effects and mechanisms of Yi Qi Huo Xue Fang in cerebral ischemic stroke based on network pharmacology and experimental verification

Ethnopharmacological relevanceYi Qi Huo Xue Fang (YQHXF) is an effective formula for treating cerebral ischemic stroke (CIS). However, its active ingredients and mechanism of action remain unclear. Aim of the studyThis study aimed to reveal the mechanism of action of YQHXF in the treatment of ischemic stroke based on network pharmacology and experimental validation. Materials and methodsThis study identified the chemical components in YQHXF and the components absorbed by rat serum based on UPLC-Q-TOF/MS technology and used network pharmacology to predict key candidate targets. A protein-protein-interaction (P-P-I) network was constructed using String 11.0 database and Cytoscape, and R software for gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis. Finally, molecular docking combined with animal experiments was used to verify network pharmacology results. ResultsThis study identified and confirmed 36 chemical components of YQHXF and five chemical ingredients that were absorbed into the blood of rats and screened 66 key candidate targets. All targets in the P-P-I network were mainly related to inflammation and vascular processes. KEGG enrichment results revealed that these 66 key candidate targets were primarily involved in the “AGE-RAGE signaling pathway,” “TNF-α signaling pathway, and “T cell receptor signaling pathway.” Molecular docking results revealed that Prostaglandin-endoperoxidase synthase 2(PTGS-2), Nitric oxide synthase, endothelial (NOS3), and peroxisome proliferator-activated receptor gamma (PPARG) were more stably bound to their active ingredients. Animal experiments demonstrated that YQHXF promoted M2 polarization, inhibited M1 polarization in microglia, and promoted angiogenesis, which may be related to the PPARG pathway. ConclusionThis study revealed the key active components and effective targets of YQHXF, identified the mechanism of action of YQHXF, laid the foundation for further research on YQHXF, and provided ideas for developing new drugs for CIS.

Reduction in gefitinib resistance mediated by Yi-Fei San-Jie pill in non-small cell lung cancer through regulation of tyrosine metabolism, cell cycle, and the MET/EGFR signaling pathway

Ethnopharmacological relevanceThe Chinese herbal prescription Yi-Fei San-Jie pill (YFSJ) has been used for adjuvant treatment in patients with lung cancer for a long time. Aim of the studyReports have indicated that the combination of gefitinib (Gef) with YFSJ inhibits the proliferation of EGFR-TKI-resistant cell lines by enhancing cellular apoptosis and autophagy in non-small cell lung cancer (NSCLC). However, the molecular mechanisms underlying the effect of YFSJ on EGFR-TKI resistance and related metabolic pathways remain to be explored. Materials and methodsIn our report, ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), metabolomics, network pharmacology, bioinformatics, and biological analysis methods were used to investigate the mechanism. ResultsThe UPLC-MS/MS data identified 42 active compounds of YFSJ extracts. YFSJ extracts can enhance the antitumor efficacy of Gef without hepatic and renal toxicity in vivo. The analysis of the metabolomics pathway enrichment revealed that YFSJ mainly affected the tyrosine metabolism pathway in rat models. Moreover, YFSJ has been shown to reverse Gef resistance and improve the effects of Gef on the cellular viability, migration capacity, and cell cycle arrest of NSCLC cell lines with EGFR mutations. The results of network pharmacology and molecular docking analyses revealed that tyrosine metabolism-related active compounds of YFSJ affect EGFR-TKIs resistance in NSCLC by targeting cell cycle and the MET/EGFR signaling pathway; these findings were validated by western blotting and immunohistochemistry. ConclusionsYFSJ inhibits NSCLC by inducing cell cycle arrest in the G1/S phase to suppress tumor growth, cell viability, and cell migration through synergistic effects with Gef via the tyrosine metabolic pathway and the EGFR/MET signaling pathway. To summarize, the findings of the current study indicate that YFSJ is a prospective complementary treatment for Gef-resistant NSCLC.

Network pharmacology and molecular docking combined with widely targeted metabolomics to elucidate the potential compounds and targets of Euphorbia helioscopia seeds for the treatment of pulmonary fibrosis

BackgroundThe whole herb of Euphorbia helioscopia has been traditionally used for treating pulmonary tuberculosis, malaria, warts, lung cancer and bacillary dysentery for a long time in China. However, E. helioscopia seeds are often discarded and its medicinal value is often ignored, resulting in a waste of resources. MethodIn this work, widely targeted metabolomics based on UPLC-ESI-QTRAP-MS/MS methods and metware database (MWDB) were firstly used to identify the chemical compositions of EHS. Besides, network pharmacology, molecular docking and molecular dynamics simulation were performed for elucidating the potential compounds and targets of E. helioscopia seeds for the treatment of pulmonary fibrosis via common database (like TCMSP, Genecards, DAVID, STRING) and common software (like Sybyl, Cytoscape, Pymol and Schrödinger). ResultThe results of widely targeted metabolomics showed 231 compounds including 12 categories were identified. The highest content compositions are lipids (33.89%) followed by amino acids and derivatives (21.78%), nucleotides and derivatives (15.73%), as well as the content of functional ingredients like phenolic acids (7.33%), alkaloids (7.03%) and flavonoids (4.51%) are relatively high. Besides, the results of network pharmacology and molecular docking showed that EHS presented anti-pulmonary fibrosis medicinal value through multi-ingredients, multi-targets and multi-pathways approach. Key ingredients including 9-Hydroxy-12-oxo-15(Z)-octadecenoic acid, Nordihydrocapsiate, 1-O-Salicyl-d-glucose, 9-(Arabinosyl)hypoxanthine, Xanthosine and Galangin-7-O-glucoside. Key targets including SRC, HSP90AA1, AKT1, EGFR, JUN, EP300 and VEGFA, and key signaling pathways mainly related to AGE-RAGE, EGFR tyrosine kinase inhibitor resistance, VEGF and HIF-1 signaling pathway. Molecular dynamics simulation showed that HSP90AA1 and 9-Hydroxy-12-oxo-15(Z)-octadecenoic complex (with the highest docking score) have a stable combination effect. ConclusionIn conclusion, this study revealed the chemical compositions of EHS and its anti-pulmonary fibrosis medicinal effect for the first time, it will provide scientific insight for the development of EHS as medicinal resource.

Network Pharmacology Study of Bioactive Components and Molecular Mechanisms of the Glycoside Fraction from Picrorhiza scrophulariiflora Against Experimental Colitis.

To explore the potential mechanism of glycosidic fraction of Picrorhiza scrophulariiflora Pennell (GPS) extract for the treatment of colitis using UPLC-QTOF-MS analysis, network pharmacology and experimental research. The active components of GPS extract were identified by UPLC-QTOF-MS analysis and extracted their targets from the databases, which was used for network pharmacology analysis. Kyoto Encyclopedia of genes and genomes (KEGG) pathway analysis was performed to discover potential therapeutic mechanisms, and the network pharmacology results were then validated by in vivo and in vitro experiments. The results showed that GPS extract significantly alleviated the clinical signs of colitis, including body weight, disease activity index, colon shortening, and colon tissue damage, and inhibited the transcription and production of colonic IL-1β and IL-6 in DSS-induced colitis mice. In vitro, GPS extract also significantly suppressed nitric oxide (NO) production, iNOS expression, IL-1β and IL-6 transcription of LPS-activated RAW 264.7 cells. Network pharmacology integrated with experimental validation identified that GPS extract significantly suppressed Akt, p38, ERK, and JNK phosphorylation in vivo and in vitro, and luteolin, apocynin, caffeic acid, caffeic acid methyl ester, luteoloside, picroside II, aucubin, cinnamic acid, vanillic acid, and sweroside were the main components responsible for the anti-inflammatory effect of GPS. These findings demonstrate that the potential anti-inflammatory effect of GPS extract against colitis is achieved through suppressing PI3K/Akt and MAPK pathways, and that the abovementioned active components mainly exerted its anti-inflammatory effect. The therapeutic effect of GPS extract on colitis is related to PI3K/Akt and MAPK pathways, which is a promising remedy for colitis therapy.

Clean-DM1, a Korean Polyherbal Formula, Improves High Fat Diet-Induced Diabetic Symptoms in Mice by Regulating IRS/PI3K/AKT and AMPK Expressions in Pancreas and Liver Tissues.

To investigate the effects of Clean-DM1 (C-DM1), a polyherbal formulation of Radix Scrophulariae, Radix Astragali, Rhizoma Atractylodis, and Radix Salviae Miltiorrhizae, on high-fat diet (HFD)-induced diabetes mice. The information about active components of C-DM1 extract and molecular mechanism was obtained from network pharmacology analysis. Main compounds of C-DM1 extract by high performance liquid chromatography-mass spectrometry (HPLC-MS) analysis were conducted for quality control. For in vivo study, mice were induced diabetes by HFD for 12 weeks. The mice in the normal group (Nor) were maintained with a regular diet and treated with saline by gavage. The HFD model mice were randomly divided into 3 groups, including a HFD diabetic model group, a C-DM1 extract-administered group (C-DM1, 500 mg/kg), and metformin-administered groups (Met, 500 mg/kg), 8 mice in each group. Food intake, body weight (BW), and fasting blood glucose (FBG) levels were recorded weekly for 4 weeks. After 4 weeks of treatment, alanine aminotransferase (ALT), aspartate aminotransferase (AST), blood glucose, low-density lipoprotein cholesterol (LDL-C) were determined using an automated clinical chemistry analyzer, and homeostatic model for assessing insulin resistance (HOMA-IR) levels and oral glucose tolerance test (OGTT) were detected. The histopathological changes of liver and pancreatic tissues were observed by hematoxylin-eosin staining. Insulin receptor substrate (IRS)/phosphatidylinositol 3 kinase (PI3K)/ protein kinase B (AKT) and adenosine 5'-monophosphate-activated protein kinase (AMPK) expressions in liver and pancreas tissues were detected by Western blot analysis. HPLC-MS identified dihydroisotanshinone, dihydroisotanshinone I, cryptotanshinone, harpagoside, and atractyloside A in C-DM1 extract. The administration of C-DM1 extract significantly decreased body weight, calorie intake, and the levels of blood glucose and insulin in the diabetic mice (P<0.05 or P<0.01). The C-DM1 extract administration improved the impaired glucose tolerance and insulin resistance in the diabetic mice and significantly decreased the levels of LDL-C, ALT and AST (P<0.01). The C-DM1 extract inhibited the histopathological changes of fatty liver and hyperplasia of pancreatic islets in the diabetic mice. The C-DM1 extract significantly increased the phosphorylation of IRS, AKT, and AMPK and the expression of PI3K in pancreas and liver tissues (P<0.05 or P<0.01), which was consistent with the analysis results of network pharmacology. C-DM1 extract improved diabetes symptoms in long-term HFD-induced mice by regulation of IRS/PI3K/AKT and AMPK expressions in pancreas and liver tissues, suggesting that C-DM1 formulation may help prevent the progression of T2DM.

Mechanisms of Xuefu Zhuyu Decoction in the treatment of coronary heart disease based on integrated metabolomics and network pharmacology approach

Coronary heart disease (CHD) has become the leading cause of mortality, morbidity, and disability worldwide. Though the therapeutic effect of Xuefu Zhuyu Decoction (XFZY) on CHD has been demonstrated in China, the active ingredients and molecular mechanisms of XFZY have not been elucidated. The purpose of the current study is to explore the molecular mechanisms of XFZY in the treatment of CHD via network pharmacology, metabolomics, and experimental validation. First, we established a CHD rat model by permanently ligating the left anterior descending coronary artery (LAD), and evaluated the therapeutic effect of XFZY by hemorheology and histopathology. Second, network pharmacology was employed to screen the active ingredients and potential targets of XFZY for the treatment of CHD. Metabolomic was applied to identify the molecules present in the serum after XFZY treatment. Third, the results of network pharmacology and metabolomics were further analyzed by Cytoscape to elucidate the core ingredients and pathways. Finally, the obtained key pathways were verified by transmission electron microscopy and immunofluorescence assay. The results showed that XFZY was effective in the treatment of CHD in the rat model, and the highest dose exerted the best effect. Network pharmacology analysis revealed 215 active ingredients and 129 key targets associated with XFZY treatment of CHD. These targets were enriched in pathways of cancer, lipid and atherosclerosis, fluid shear stress and atherosclerosis, proteoglycans in cancer, chemical carcinogenesis - receptor activation, HIF-1 signaling, et al. Serum metabolomic identified 1081 metabolites involved in the therapeutic effect of XFZY on CHD. These metabolites were enriched in taurine and hypotaurine metabolism, histidine metabolism, retrograde endocannabinoid signaling pathways, et al. Cytoscape analysis combining the data from serum metabolomic and network pharmacology revealed that energy metabolism as the core pathway for XFZY treatment of CHD. Electron microscope observation identified changes in the level of autophagy in the mitochondrial structure of cardiomyocytes. Immunofluorescence assay showed that the expression levels of autophagy-related proteins LC3-B and P62/SQSTM1 were consistent with the levels of autophagy observed in mitochondria. In conclusion, our findings suggest that the possible mechanisms of XFZY in the treatment of CHD are reducing the level of autophagy, improving energy metabolism, and maintaining mitochondrial homeostasis in cardiomyocytes. Our study also shows that the combined strategies of network pharmacology, metabolomics, and experimental validation may provide a powerful approach for TCM pharmacology study.

An herbal formulation "Shenshuaifu Granule" alleviates cisplatin-induced nephrotoxicity by suppressing inflammation and apoptosis through inhibition of the TLR4/MyD88/NF-κB pathway.

Shenshuaifu Granule (SSF) is an in-hospital preparation approved by the Guangdong Food and Drug Administration of China. It has been clinically used against kidney diseases for more than 20 years with a definite curative effect. Cisplatin (CDDP) is a first-line chemotherapeutic drug in clinical practice, primarily excreted by the kidney with nephrotoxicity as a common side effect. Approximately 5-20% of cancer patients develop acute kidney injury (AKI) after chemotherapy; however, prevention and control strategies are currently unavailable. Therefore, it is important to identify safe and effective drugs that can prevent the nephrotoxicity of CDDP. SSF is an herbal formulation with 8 herbs, and has been used to protect the kidney in China. Nonetheless, its mechanism in relieving CDDP nephrotoxicity remains unclear. Therefore, this work attempt to prove that SSF can alleviate CDDP nephrotoxicity. We also explore its mechanism. First, Thin Layer Chromatography (TLC) of a few herbs in SSF were performed for quality control. Several open-access databases were used to identify the active ingredients of SSF, their corresponding targets, and CDDP-induced nephrotoxicity targets. We performed Protein-Protein Interaction (PPI), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Next, the results of network pharmacology were validated using CDDP-induced nephrotoxicity mouse models. Renal function in the mice was assessed by analyzing the levels of serum creatinine (Scr) and blood urea nitrogen (BUN). On the other hand, renal damage was assessed by determining the level of tubular injury and apoptotic cells using Periodic acid-Schiff (PAS) staining and Terminal Dutp Nick End-Labeling (TUNEL) staining, respectively. The expression of inflammatory and apoptotic-related targets including IL-1β, IL-6, TNF-α, Cox-2, Bax, Bcl-2, Cleaved-caspase 3, and Cleaved-caspase 9 was determined using Western Blot (WB) and Immunohistochemistry (IHC). Furthermore, WB was used to analyze the expression of proteins associated with the TLR4/MyD88/NF-κB pathway in the kidneys of mice with CDDP-induced nephrotoxicity. Finally, molecular docking simulations were performed to evaluate the binding abilities between major active ingredients of SSF and core targets. Through network pharmacology, we identified 127 active ingredients of SSF and their corresponding 134 targets. Additional screening identified 14 active ingredients and 17 targets for further analysis. In biological process (BP), the targets were enriched in inflammation and apoptosis, among others. In KEGG terms, they were enriched in apoptosis and NF-κB pathways. Animal experiments revealed that SSF significantly reduced the levels of Scr and BUN and prevented renal tubular damage in mice treated with CDDP. In addition, SSF inhibited inflammation and apoptosis by targeting the TLR4/MyD88/NF-κB pathway. Molecular docking revealed good binding capacities of active ingredients and core targets. In summary, the experimental findings were consistent with the network pharmacological predictions. SSF can inhibit inflammation and apoptosis by targeting the TLR4/MyD88/NF-κB pathway. Taken together, our data suggest that SSF is an alternative agent for the treatment of CDDP-induced nephrotoxicity.

Effect of Siegesbeckiae Herba on immune-inflammation of rheumatoid arthritis: Data mining and network pharmacology

Rheumatoid arthritis (RA) is an autoimmune disease, resulting in an overall poor prognosis. Siegesbeckiae Herba is a natural botanical herb that possesses a variety of biological activities, particularly its anti-rheumatism property. This study collected the clinical data of 7657 RA patients who received treatment with traditional Chinese medicine prescriptions before December 2021 in the Department of Rheumatology, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine. The levels of immune-inflammatory indicators including Hs-CRP, ESR, RF, C3, C4, IgA, IgG, and IgM were observed before and after the treatment. Association rules between Siegesbeckiae Herba and immune-inflammatory indicators were analyzed by Apriori algorithm. Protein-protein interaction network diagram, core gene and drug-active ingredient-target diagram were drawn by Cytoscape3.7.2 software. GO and KEGG analysis was performed by DAVID database. Autodock software was used to conduct molecular docking and in vitro experiments were performed to verify the action mechanism of Siegesbeckiae Herba on RA. Data mining results showed that the use of Siegesbeckiae Herba was strongly associated with the improvement of immune-inflammatory markers of RA. The results of network pharmacology and molecular docking showed that the main target proteins including Bax, CASP3, CASP8, CASP9, COX2, TNF, and IL-17 of Siegesbeckiae Herba were closely related to apoptosis and inflammatory signaling pathways in the treatment of RA. In vitro cell experiments results showed that Kirenol, the main active ingredient of Siegesbeckiae Herba, up-regulated the expressions of pro-apoptotic proteins Bax, caspase3, caspase8, and caspase9 in RA-fibroblast-like synoviocytes (RA-FLSs) and down-regulated the expressions of COX2, TNF, and IL-17. Siegesbeckiae Herba promoted the apoptosis of RA-FLSs and alleviated immune-inflammatory responses in RA.

Sanhuang xiexin decoction synergizes insulin/PI3K-Akt/FoxO signaling pathway to inhibit hepatic glucose production and alleviate T2DM.

Sanhuang Xiexin Decoction (SHXXD) is a classic prescription for the treatment of diabetes. Excessive hepatic glucose production (HGP) is a major determinant of the occurrence and development of diabetes. Inhibition of HGP can significantly improve type 2 diabetes mellitus (T2DM). To investigate the mechanism by which SHXXD inhibits HGP. First, a mouse model of T2DM was established through high-fat diet (HFD) feeding combined with streptozotocin (STZ) injection to determine the pharmacodynamic effect of SHXXD in T2DM mice. Then, the possible pathways induced by SHXXD in the treatment of T2DM were predicted by network pharmacology combined with transcriptomics (including target prediction, network analysis and enrichment analysis). Finally, the specific mechanism of SHXXD was elucidated by in vitro experiments. In vivo experiments showed that SHXXD reduced fasting blood glucose and alleviated weight loss in T2DM mice. Improved glucose clearance rates and insulin sensitivity improve dyslipidemia, liver tissue structural abnormalities and inflammatory cell infiltration as well as increase glycogen storage in T2DM mice. The results of network pharmacology and transcriptome analysis showed that SHXXD contained 378 compounds and 2625 targets. In total, 292 intersection targets were identified between the differentially expressed genes (DEGs) of the liver tissue insulin resistance (IR) related dataset GSE23343. KEGG enrichment analysis showed that the insulin/PI3K-Akt/FoxO signaling pathway may be related to SHXXD-mediated improvements in T2DM. In vitro experimental results showed that SHXXD increased glucose consumption by HepG2-IR cells and improved their insulin sensitivity. RT‒qPCR and Western blotting results showed that SHXXD inhibited hepatic gluconeogenesis through the insulin/PI3K-Akt/FoxO signaling pathway by promoting IGFIR, PIK3R1 and AKT2 expression and subsequently inhibiting PEPCK and FBP1 expression via phosphorylation of Foxo1. In addition, PI3K/Akt deactivated p-GSK3β through phosphorylation, thereby promoting GS expression and increasing glycogen synthesis. SHXXD can target the liver to cooperate with the insulin/PI3K-Akt/FoxO signaling pathway to inhibit HGP to alleviate T2DM.

Design, synthesis and anticancer activity studies of 3-(coumarin-3-yl)-acrolein derivatives: Evidenced by integrating network pharmacology and vitro assay.

Coumarin derivatives have diverse structures and show various significant biological activities. Aiming to develop more potent coumarin derivatives for cancer treatment, a series of coumarin acrolein hybrids were designed and synthesized by using molecular hybridization approach, and investigated for their antiproliferative activity against A549, KB, Hela and MCF-7 cancer cells as well as HUVEC and LO2 human normal cells. The results indicated that most of the synthesized compounds displayed remarkable inhibitory activity towards cancer cells but low cytotoxicity on normal cells. Among all the compounds, 5d and 6e were the most promising compounds against different cancer cell lines, especially for A549 and KB cells. The preliminary action mechanism studies suggested that compound 6e, the representative compound, was capable of dose-dependently suppressing migration, invasion and inducing significant apoptosis. Furthermore, the combined results of network pharmacology and validation experiments revealed that compound 6e induced mitochondria dependent apoptosis via the PI3K/AKT-mediated Bcl-2 signaling pathway. In summary, our study indicated compound 6e could inhibit cell proliferation, migration, invasion and promote cell apoptosis through inhibition of PI3K/AKT signaling pathway in human oral epidermoid carcinoma cells. These findings demonstrated the potential of 3-(coumarin-3-yl)-acrolein derivatives as novel anticancer chemotherapeutic candidates, providing ideas for further development of drugs for clinical use.

Centipeda minima active components and mechanisms in lung cancer

BackgroundTraditional Chinese medicine (TCM) has been extensively used for neoplasm treatment and has provided many promising therapeutic candidates. We previously found that Centipeda minima (C. minima), a Chinese medicinal herb, showed anti-cancer effects in lung cancer. However, the active components and underlying mechanisms remain unclear. In this study, we used network pharmacology to evaluate C. minima active compounds and molecular mechanisms in lung cancer.MethodsWe screened the TCMSP database for bioactive compounds and their corresponding potential targets. Lung cancer-associated targets were collected from Genecards, OMIM, and Drugbank databases. We then established a drug-ingredients-gene symbols-disease (D-I-G-D) network and a protein–protein interaction (PPI) network using Cytoscape software, and we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses using R software. To verify the network pharmacology results, we then performed survival analysis, molecular docking analysis, as well as in vitro and in vivo experiments.ResultsWe identified a total of 21 C. minima bioactive compounds and 179 corresponding targets. We screened 804 targets related to lung cancer, 60 of which overlapped with C. minima. The top three candidate ingredients identified by D-I-G-D network analysis were quercetin, nobiletin, and beta-sitosterol. PPI network and core target analyses suggested that TP53, AKT1, and MYC are potential therapeutic targets. Moreover, molecular docking analysis confirmed that quercetin, nobiletin, and beta-sitosterol, combined well with TP53, AKT1, and MYC respectively. In vitro experiments verified that quercetin induced non-small cell lung cancer (NSCLC) cell death in a dose-dependent manner. GO and KEGG analyses found 1771 enriched GO terms and 144 enriched KEGG pathways, including a variety of cancer related pathways, the IL-17 signaling pathway, the platinum drug resistance pathway, and apoptosis pathways. Our in vivo experimental results confirmed that a C. minima ethanol extract (ECM) enhanced cisplatin (CDDP) induced cell apoptosis in NSCLC xenografts.ConclusionsThis study revealed the key C. minima active ingredients and molecular mechanisms in the treatment of lung cancer, providing a molecular basis for further C. minima therapeutic investigation.

Network pharmacology and experimental validation to reveal the target of matrine against PRRSV

Porcine reproductive and respiratory syndrome (PRRS) is an epidemic animal infectious disease worldwide. In our previous research it was suggested that matrine could inhibit PRRSV infection both invitro and invivo, but the antiviral mechanisms are still undecided. Network pharmacology can well solve the difficult problem of "multiple targets, multiple pathways" in the research of TCM action targets. The results of network pharmacology indicated that matrine exerts its anti-PRRSV effect by targeting HSPA8 and HSP90AB1. The results of real-time fluorescent quantitative PCR and western blot showed that infection with PRRSV induced a significant increase in the expression of HSPA8 and HSP90AB1 whereas matrine treatment could significantly reverse it, and the number of viruses of PRRSV also decreased. In this study, the method of network pharmacology was used to explore HSPA8 and HSP90AB1 which were the potential targets of matrine against PRRSV on Marc-145 cells.

PI3K-Akt signaling pathway based on network pharmacology for the anti-Alzheimer's disease effect of licorice stem flavonoids.

Active ingredients were screened by TCMSP and swissADME, meanwhile, PharmMapper combined with UniProt database was used to predict the active ingredient target information, GeneCard database was employed to obtain Alzheimer's disease (AD)-related genes, Cytoscapes 3.7.2 software was utilized to map the active ingredient-target effect. Besides, Cytoscapes 3.7.2 software Bisogenet and Cyto NCA plug-in combined with STRING platform were utilized to map the protein-protein interaction (PPI) network, DAVID was employed for GO annotation, while KEGG plug-in was used for KEGG pathway enrichment. Mice were tested for inflammatory damage induced by intracerebral injection of lipopolysaccharide (LPS), as well as learning memory and anxiety by water maze and open field tests. In addition, the expression of Caspase-3 and Caspase-9, together with inflammatory factors TNF-α, IL-6, and IL-1β was analyzed in serum. The expression levels of proteins related to PI3K-Akt signaling pathway in the brain were detected by Western blot (WB) assay. According to the results of network pharmacology, there were 35 active ingredients of licorice stem and leaf flavonoids screened, which exerted the anti-Alzheimer's disease (AD) effects via 67 targets and activated 41 signaling pathways including the PI3K-Akt pathway. Furthermore, Behavioural results revealed that Licorice stem and leaf flavonoids improved the learning and memory abilities of model mice and significantly improved the anxiety caused by inflammatory brain damage. Moreover, as suggested by HE staining and TUNEL staining of brain sections, Glycyrrhiza glabra stem and leaf flavonoids alleviated morphological lesions and cell nuclear damage in brain tissue. Results: of brain homogenate supernatant assay demonstrated that Glycyrrhiza glabra stem and leaf flavonoids had a significant effect on the levels of oxidative indicators superoxide dismutase (SOD), catalase (CAT), malonaldehyde (MDA), acetylcholine (Ach), acetylcholinesterase (AchE), Caspase-3, Caspase-9 and serum inflammatory factors TNF-α, IL-6 and IL-1β. Additionally, WB assay results indicated that the PI3K-Akt signaling pathway was activated.

Integrative network pharmacology and in silico analyses identify the anti-omicron SARS-CoV-2 potential of eugenol

Eugenol as a natural product is the source of isoniazid, and purified eugenol is extensively used in the cosmetics industry and the productive processes of edible spices. Accumulating evidence suggested that eugenol exerted potent anti-microorganism and anti-inflammation effects. Application of eugenol effectively reduced the risk of atherosclerosis, arterial embolism, and Type 2 diabetes. A previous study confirmed that treatment with eugenol attenuated lung inflammation and improved heart functions in SARS-CoV-2 spike S1-intoxicated mice. In addition to the study, based on a series of public datasets, computational analyses were conducted to characterize the acting targets of eugenol and the functional roles of these targets in COVID-19. The binding capacities of eugenol to conservative sites of SARS-CoV-2 like RNA-dependent RNA polymerase (RdRp) and mutable site as spike (S) protein, were calculated by using molecular docking following the molecular dynamics simulation with RMSD, RMSF, and MM-GBSA methods. The results of network pharmacology indicated that six targets, including PLAT, HMOX1, NUP88, CTSL, ITGB1 andTMPRSS2 were eugenol-SARS-CoV-2 interacting proteins. The omics results of in-silico study further implicated that eugenol increased the expression of SCARB1, HMOX1 and GDF15, especially HMOX1, which were confirmed the potential interacting targets between eugenol and SARS-CoV-2 antigens. Enrichment analyses indicated that eugenol exerted extensive biological effects such as regulating immune infiltration of macrophage, lipid localization, monooxyenase activity, iron ion binding and PPAR signaling. The results of the integrated analysis of eugenol targets and immunotranscription profile of COVID-19 cases shows that eugenol also plays an important role in strengthen of immunologic functions and regulating cytokine signaling. As a complement to the integrated analysis, the results of molecular docking indicated the potential binding interactions between eugenol and four proteins relating to cytokine production/release and the function of T type lymphocytes, including human TLR-4, TCR, NF-κB, JNK and AP-1. Furthermore, results of molecular docking and molecular dynamics (100ns) simulations implicated that stimulated modification of eugenol to the SARS-CoV-2 Omicron Spike-ACE2 complex, especially for human ACE2, and the molecular interaction of eugenol to SARS-CoV-2 RdRp, were no less favorable than two positive controls, molnupiravir and nilotinib. Dynamics (200ns) simulations indicated that the binding capacities and stabilities of eugenol to finger subdomain of RdRp is no less than molnupiravir. However, the simulated binding capacity of eugenol to SARS-CoV-2 wild type RBD and Omicron mutant RBD were less than nilotinib. Eugenol was predicted to have more favor LD50 value and lower cytotoxicity than two positive controls, and eugenol can pass through the blood-brain barrier (BBB). In a brief, eugenol is helpful for attenuating systemic inflammation induced by SARS-CoV-2 infection, due to the direct interaction of eugenol to SARS-CoV-2 proteins and extensive bio-manipulation of pro-inflammatory factors. This study carefully suggests eugenol is a candidate compound of developing drugs and supplement agents against SARS-CoV-2 and its Omicron variants.