Biomarkers and coptis chinensis activity for rituximab-resistant diffuse large B-cell lymphoma: Combination of bioinformatics analysis, network pharmacology and molecular docking.

BACKGROUND: Rituximab resistance is one of the great challenges in the treatment of diffuse large B-cell lymphoma (DLBCL), but relevant biomarkers and signalling pathways remain to be identified. Coptis chinensis and its active ingredients have antitumour effects; thus, the potential bioactive compounds and mechanisms through which Coptis chinensis acts against rituximab-resistant DLBCL are worth exploring. OBJECTIVE: To elucidate the core genes involved in rituximab-resistant DLBCL and the potential therapeutic targets of candidate monomers of Coptis chinensis. METHODS: Using the Traditional Chinese Medicine System Pharmacology Database and Analysis Platform (TCMSP), the Similarity Ensemble Approach and Swiss Target Prediction, the main ingredients and pharmacological targets of Coptis chinensis were identified through database searches. Through the overlap between the pharmacological targets of Coptis chinensis and the core targets of rituximab-resistant DLBCL, we identified the targets of Coptis chinensis against rituximab-resistant DLBCL and constructed an active compound-target interaction network. The targets and their corresponding active ingredients of Coptis chinensis against rituximab-resistant DLBCL were molecularly docked. RESULTS: Berberine, quercetin, epiberberine and palmatine, the active components of Coptis chinensis, have great potential for improving rituximab-resistant DLBCL via PIK3CG. CONCLUSION: This study revealed biomarkers and Coptis chinensis-associated molecular functions for rituximab-resistant DLBCL.

Quality assessment and Q-markers discovery in Citri Sarcodactylis Fructus by integrating serum pharmacochemistry and network pharmacology.

INTRODUCTION: Citri Sarcodactylis Fructus (CSF), a common fruit and traditional Chinese medicine (TCM), has been hindered in its further development and research owing to the lack of comprehensive and specific quality evaluation standards. OBJECTIVE: This study aimed to establish clear TCM quality standards related to the therapeutic mechanisms of CSF and to provide a basis for subsequent research and development. METHODS: Ultra-high performance liquid chromatography coupled with hybrid quadrupole-orbitrap high-resolution mass spectrometry (UPLC-Q-orbitrap HRMS) technology was used to comprehensively identify CSF components and explore their absorbance levels in rat serum. Network pharmacology research methods were employed to investigate the potential mechanisms of action of the identified components in the treatment of major clinical diseases. Subsequently, a combination of HPLC chromatographic fingerprinting for qualitative analysis and multi-index content determination was used to evaluate the detectability of the identified quality markers (Q-markers). RESULTS: Twenty-six prototype components were tentatively characterized in rat serum. Network pharmacology analysis showed six effective components, namely 7-hydroxycoumarin, isoscopoletin, diosmin, hesperidin, 5,7-dimethoxycoumarin, and bergapten, which played important roles in the treatment of chronic gastritis, functional dyspepsia, peptic ulcer, and depression and were preliminarily identified as Q-markers. The results of content determination in 15 batches of CSF indicated significant differences in the content of medicinal materials from different origins. However, compared with the preliminarily determined Q-markers, all six components could be measured and were determined as Q-markers of CSF. CONCLUSION: The chemical Q-markers obtained in this study could be used for effective quality control of CSF.

Network Pharmacology-Based Approach for Investigating the Role of Xanthii Fructus in Treatment of Allergic Rhinitis.

Xanthii Fructus (XF) has been used for treatment of allergic rhinitis (AR), but its pharmacological mechanism of action remains unclear. We aimed to explore the potential mechanism of XF in treatment of AR by using a network pharmacology approach combined with in vivo verification experiments in this study. We identified 945 AR-related pathogenic genes, 11 active components in XF and 178 targets of those active components by corresponding databases. Finally, 54 targets of active components from XF in treatment of AR were identified by the Protein-protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, among which Tumor Necrosis Factor (TNF), Mitogen-activated Protein Kinase 3 (MAPK3), Prostaglandin G/H Synthase 2 (PTGS2), Epidermal Growth Factor Receptor (EGFR) showed strongest interactions. The molecular docking analysis showed that moupinamide could bind to EGFR at LEU704 and LEU703, and PTGS2 at TRP387; 24-Ethylcholest-4-en-3-one was identified to bind to MAPK3 at THR347. The validation of quantitative real-time reverse transcription PCR (RT-PCR) showed that XF decreased the levels of MAPK3, PTGS2, and EGFR expression in the nasal mucosa from AR mice gavaged with an XF water decoction. Meanwhile, the levels of interleukin (IL)-4, IL-5 and IL-13were also decreased after the treatment of XF by Enzyme-linked immunosorbent assay (ELISA). Our results provide the pharmacological mechanism and possible intervention targets of XF in treatment of AR.

Active compounds and potential targets of Shuganning injection in the treatment of hepatocellular carcinoma by network pharmacology and in vitro validation.

Shuganning injection (SGNI), a TCM (traditional Chinese medicine) injection with good hepatoprotective effects, exerted therapeutic effects on hepatocellular carcinoma (HCC). However, the active compounds and effects of SGNI on HCC remain unclear. The objective of this study was to investigate the active compounds and potential targets of SGNI in the treatment of HCC, and explore the molecular mechanisms of main compounds. Network pharmacology was applied to predict the active compounds and targets of SGNI on cancer. The interactions between active compounds and target proteins were validated by drug affinity responsive target stability (DARTS), cellular thermal shift assay (CETSA), and pull-down assay. The in vitro test of the effects and mechanism of vanillin and baicalein was elucidated by MTT, western blot, immunofluorescence, and apoptosis analysis. According to compound characteristics, targets, etc., two typical active ingredients (vanillin and baicalein) were selected as representatives to explore the effects on HCC. Vanillin (an important food additive) bound to NF-κB1 and baicalein (a bioactive flavonoid) bound to FLT3 (FMS-like tyrosine kinase 3) were confirmed in this study. Vanillin and baicalein both inhibited cell viability and promoted apoptosis of Hep3B and Huh7 cells. In addition, both vanillin and baicalein could enhance the activation of the p38/MAPK (mitogen-activated protein kinase) signaling pathway, which may partially explain the anti-apoptosis effects of the two compounds. In conclusion, two active compounds of SGNI, vanillin and baicalein, promoted apoptosis of HCC cells via binding with NF-κB1 or FLT3, and regulating the p38/MAPK pathway. Baicalein and vanillin may be good candidates for HCC treatment on drug development.

Integrated network pharmacology and experimental validation to explore the mechanisms underlying naringenin treatment of chronic wounds.

Naringenin is a citrus flavonoid with various biological functions and a potential therapeutic agent for skin diseases, such as UV radiation and atopic dermatitis. The present study investigates the therapeutic effect and pharmacological mechanism of naringenin on chronic wounds. Using network pharmacology, we identified 163 potential targets and 12 key targets of naringenin. Oxidative stress was confirmed to be the main biological process modulated by naringenin. The transcription factor p65 (RELA), alpha serine/threonine-protein kinase (AKT1), mitogen-activated protein kinase 1 (MAPK1) and mitogen-activated protein kinase 3 (MAPK3) were identified as common targets of multiple pathways involved in treating chronic wounds. Molecular docking verified that these four targets stably bound naringenin. Naringenin promoted wound healing in mice in vivo by inhibiting wound inflammation. Furthermore, in vitro experiments showed that a low naringenin concentration did not significantly affect normal skin cell viability and cell apoptosis; a high naringenin concentration was cytotoxic and reduced cell survival by promoting apoptosis. Meanwhile, comprehensive network pharmacology, molecular docking and in vivo and in vitro experiments revealed that naringenin could treat chronic wounds by alleviating oxidative stress and reducing the inflammatory response. The underlying mechanism of naringenin in chronic wound therapy involved modulating the RELA, AKT1 and MAPK1/3 signalling pathways to inhibit ROS production and inflammatory cytokine expression.

Integrated Lipidomics and Network Pharmacology Reveal Mechanism of Memory Impairment Improvement by Yuanzhi San.

Memory impairment (MI) is caused by a variety of causes, endangering human health. Yuanzhi San (YZS) is a common prescription used for the treatment of MI, but its mechanism of action needs further exploration. The purpose of this study was to investigate this mechanism through lipidomics and network pharmacology. Sprague Dawley (SD) rats were divided randomly into the normal, model, and YZS groups. The rats were gavaged with aluminum chloride (200 mg/kg) and intraperitoneally injected with D-galactose (400 mg/kg) every day for 60 days, except for the normal group. From the 30th day, YZS (13.34 g/kg) was gavaged once a day to the rats in the YZS group. Post-YZS treatment, ultra-high-performance liquid chromatography-mass spectrometry (UHPLC/MS) analysis was implemented to conduct a lipidomics study in the hippocampus of rats with memory impairment induced by aluminum chloride and D-galactose. Eight differential metabolites were identified between the normal group and the model group, whereas between the model group and the YZS group, 20 differential metabolites were established. Metabolic pathway analysis was performed on the aforementioned lipid metabolites, all of which were involved in sphingolipid and glycerophospholipid metabolism. Furthermore, serum pharmacochemistry analysis of YZS was carried out at the early stage of our research, which discovered 62 YZS prototype components. The results of the network pharmacology analysis showed that they were related to 1030 genes, and 451 disease genes were related to MI. There were 73 intersections between the YZS and MI targets. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these targets were closely related to the sphingolipid metabolic, calcium signaling, and other pathways. The integrated approach of lipidomics and network pharmacology was then focused on four major targets, including PHK2, GBA, SPTLC1, and AChE, as well as their essential metabolites (glucosylceramide, N-acylsphingosine, phosphatidylserine, phosphatidylcholine, and phosphatidylcholine) and pathways (sphingolipid, glycerophospholipid, and arachidonic acid metabolism). The significant affinity of the primary target for YZS was confirmed by molecular docking. The obtained results revealed that the combination of lipidomics and network pharmacology could be used to determine the effect of YZS on the MI biological network and metabolic state, and evaluate the drug efficacy of YZS and its related mechanisms of action.

Application of network composite module analysis and verification to explore the bidirectional immunomodulatory effect of Zukamu granules on Th1 / Th2 cytokines in lung injury.

ETHNOPHARMACOLOGICAL RELEVANCE: Zukamu granules (ZKMG), as the preferred drug for the treatment of colds in Uygur medical theory, has been used for 1500 years. It is also widely used in China and included in the National Essential Drugs List (2018 edition). It has unique anti-inflammatory, antitussive and analgesic effects. AIM OF THE STUDY: Aiming at the research of traditional Chinese medicine (TCM) with the characteristics of overall regulation of body diseases and the immune regulation mechanism with the concept of integrity, this paper put forward the integrated application of network composite module analysis and animal experiment verification to study the immune regulation mechanism of TCM. MATERIALS AND METHODS: The active components and targets of ZKMG were predicted, and network module analysis was performed to explore their potential immunomodulatory mechanisms. Then acute lung injury (ALI) mice and idiopathic pulmonary fibrosis (IPF) rats were used as pathological models to observe the effects of ZKMG on the pathological conditions of infected ALI and IPF rats, determine the contents of Th1, Th2 characteristic cytokines and immunoglobulins, and study the intervention of GATA3/STAT6 signal pathway. RESULTS: The results of network composite module analysis showed that ZKMG contained 173 pharmacodynamic components and 249 potential targets, and four key modules were obtained. The immunomodulatory effects of ZKMG were related to T cell receptor signaling pathway. The validation results of bioeffects that ZKMG could carry out bidirectional immune regulation on Th1/Th2 cytokines in the stage of ALI and IPF, so as to play the role of regulating immune homeostasis and organ protection. CONCLUSIONS: The network composite module analysis and verification method is an exploration to study the immune regulation mechanism of TCM by combining the network module prediction analysis with animal experiments, which provides a reference for subsequent research.

Integrating network pharmacology approach and experimental validation to reveal the alleviation of Shenkangning capsule on chronic nephritis.

ETHNOPHARMACOLOGICAL RELEVANCE: Shenkangning (SKN), a Chinese patent medicine composed by eight Chinese medicinal herbs, is commonly applied to treat chronic glomerulonephritis (CGN) in clinic. However, its mechanism is still not clear now. AIM OF THE STUDY: This study is designed to evaluate the SKN-provided alleviation on adriamycin (ADR)-induced nephropathy, to reveal its mechanism by integrating network pharmacology analysis and experimental evidences, and to further find the main drug that makes a major contribution to its efficacy. MATERIALS AND METHODS: ADR was intravenously injected to mice to induce focal segmental glomerulosclerosis (FSGS). Renal histological evaluation was conducted. The level of urinary protein, and serum amounts of creatinine, urea nitrogen (BUN) and albumin were detected. The potential mechanisms were predicted by network pharmacology analysis and further validated by Real-time polymerase chain reaction (RT-PCR), Western-blot and enzyme-linked immunosorbent assay (ELISA). RESULTS: SKN (1, 10 g/kg) improved ADR-induced nephropathy in mice. Network pharmacology results predicted that inflammation and oxidative stress were crucially involved in the SKN-provided amelioration on nephropathy. SKN reduced the activation of nuclear factor-κB (NF-κB) and the expression of some pro-inflammatory cytokines, and increased the activation of nuclear factor erythroid 2-related factor 2 (Nrf2) and the expression of its downstream genes in ADR-induced nephropathy in mice. Furthermore, SKN also restored the reduced expression of both podocin and synaptopodin, which are podocyte-associated proteins. Further results showed that the toxic drug Danfupian (DFP) had no contribution to the SKN-provided alleviation on ADR-induced nephropathy in mice. After integrating the results from evaluating anti-inflammation, anti-oxidant and anti-injury of podocytes in vitro and from comparing the activity of the whole SKN and SKN without Astragali Radix (Huangqi, HQ) in vivo, we found that HQ played a crucial contribution to the SKN-provided amelioration on ADR-induced nephropathy in mice. CONCLUSION: SKN improved ADR-induced nephropathy through suppressing renal inflammation and oxidative stress injury via abrogating NF-κB activation and activating Nrf2 signaling pathway. HQ played a main contribution to the SKN-provided amelioration on ADR-induced nephropathy.

Arctium lappa leaves based on network pharmacology and experimental validation attenuate atherosclerosis by targeting the AMPK-mediated PPARG/LXRα pathway.

Arctium lappa (A. lappa) leaves are widely used in various traditional Chinese herbal formulae to ameliorate atherosclerosis (AS) and its complications such as stroke; however, there is no literature reporting the anti-atherosclerotic effect and mechanism of A. lappa leaves thus far. In the present study, we used network pharmacology and molecular docking approaches to examine the protective effect and potential mechanism of A. lappa leaves against AS in vivo and in vitro. From the network pharmacology, PPARG, HMGCR and SREBF2 were identified as the core targets of A. lappa leaves against AS. Further enrichment analyses of GO and KEGG pathways suggested that A. lappa leaves might play an anti-AS role by regulating metabolic processes and PPAR signalling pathways. The results of molecular docking experiment revealed that the major components of A. lappa leaves interacted with cholesterol efflux-regulating core proteins (PPARG, LXRα, ABCA1, and ABCG1), AMPK and SIRT1. Both in vivo and in vitro experimental results demonstrated that treatment with A. lappa leaves significantly lowered TC and LDL-C, increased HDL-C, and reduced cholesterol accumulation in the liver and aorta of the AS rat model and the foam cell model. Importantly, both in vivo and in vitro experimental results demonstrated that A. lappa leaves regulate the activity of the PPARG/LXRα signalling and AMPK/SIRT1 signalling pathways. Moreover, after treatment with the AMPK inhibitor Compound C in vitro, the improvement induced by A. lappa leaves was significantly reversed. In conclusion, A. lappa leaves attenuated AS-induced cholesterol accumulation by targeting the AMPK-mediated PPARG/LXRα pathway and promoting cholesterol efflux.

Study on the Mechanism of Improving HIV/AIDS Immune Function with Jian Aikang Concentrated Pill Based on Network Pharmacology Combined with Experimental Validation.

Purpose: This study was the first to screen the active compounds of Jian Aikang Concentrated Pill (JAKCP) with network pharmacology, predict its potential targets, screen the signaling pathways, and combine with cellular experimental validation to explore the potential mechanism of JAKCP for the treatment of acquired immunodeficiency syndrome (AIDS). Methods: The main compounds and targets of Chinese herbs in JAKCP were identified by TCMSP; the targets of AIDS were collected from Genecards, Online Mendelian Inheritance in Man (OMIM), Disgenet, Therapeutic Target Database (TTD) and Drugbank; the network of "Chinese herbs-active compounds-targets" for JAKCP was constructed by Cytoscape, and protein-protein interaction (PPI) network was constructed using STRING to generate the intersection targets, Metascape was conducted to analyze the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and the network of "main active compounds-core targets-pathways" was constructed by Cytoscape. Finally, the effect of JAKCP on the survival rate of HIV pseudovirus-infected MT-4 cells was investigated by CCK-8 assay, and the predicted targets were verified by ELISA, qPCR and Western blot. Results: A total of 147 active compounds of JAKCP were screened covering 351 targets and 416 AIDS disease targets were obtained, besides 140 intersection targets and 321 KEGG pathways were collected. Ultimately, quercetin, kaempferol, stigmasterol, beta-sitosterol, epigallocatechin gallate were identified as the important compounds, the core targets are HSP90AA1, IL-10, IL-6, TNF, IL-1ß, TP53, and IL-1ɑ, and the biological pathways and processes mainly include T cell activation, regulation of DNA-binding transcription factor activity and apoptotic signaling pathway. Experiments on the targets of "T cell activation" demonstrated that JAKCP promotes the survival of HIV pseudovirus-infected MT-4 cells. Also, JAKCP down-regulated mRNA and protein levels of IL-1ɑ, IL-1ß, and IL-6 while up-regulated mRNA and protein levels of IL-2, IL-6ST, and IL-10 in vitro. Conclusion: JAKCP exerted regulatory immune functions through multi-component, multi-target and multi-pathway, thereby providing novel ideas and clues for the treatment of AIDS.

To study the mechanism of Scutellariae Radix and Astragaloside in the treatment of lung cancer based on network pharmacology.

The aim of the study wasto explore the target and potential mechanism of Scutellariae Radix and Astragaloside in the treatment of lung cancer infection by network pharmacology. The target information of baicalein and flavonin was mined from CTD database and Swiss database. Genecards database, DRUGBANK database, and OMIM database were used to search for lung cancer related genes. The target protein network map (PPI) was drawn by using the STRING database analysis and Cytoscape3.7.1 software. With the help of Perl language, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and gene function analysis (GO) enrichment analysis were carried out by using the biological program package of R language. In total, 347 biological targets of Astragaloside and Scutellariae Radix were identified through the collection and analysis of multiple databases. In total, 1526 lung cancer targets were obtained from a multi-disease database. The "component-target" network of Astragaloside and Scutellariae Radix was constructed, and the protein interaction network (PPI) of the overlapping targets was analyzed to identify the key targets of drug-influenced diseases. In addition, KEGG pathway analysis and GO enrichment analysis were performed on the overlapping targets to explore the mechanism of Scutellariae Radix and Astragaloside in the treatment of lung cancer. Scutellariae Radix and Astragaloside have the characteristics of multi-component, multi-target and multi-pathway in the treatment of lung cancer, which provides a new idea and scientific basis for further research on the molecular mechanism of the antilung cancer effect of Scutellariae Radix and Astragaloside.

Molecular Mechanism of Gleditsiae Spina for the Treatment of High-Grade Serous Ovarian Cancer Based on Network Pharmacology and Pharmacological Experiments.

Background: Gleditsiae Spina, widely used in traditional Chinese medicine, has a good curative effect on malignant tumors such as ovarian cancer, but the mechanism is not clear. So, we aimed to analyze the pharmacological mechanism of Gleditsiae Spina in the treatment of high-grade serous ovarian cancer (HGSC) based on network pharmacology and biological experiments. Methods: The main active ingredients of Gleditsiae Spina were identified by high performance liquid chromatography (HPLC) and mass spectrometry (MS), and the active ingredients were performed by ADME screening. The component targets of Gleditsiae Spina were screened using the PharmMapper platform, and differentially expressed genes in normal and HGSC tissues were identified through the GEO database. Thereafter, the network of "active ingredient-targets" was constructed by cytoscape 3.7.2 software. The protein-protein interaction network was established by the BioGenet database to mine the potential protein function. Biological processes and pathways were analyzed through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. The binding ability of the core components of the Gleditsiae Spina and the core target of HGSC was verified by molecular docking and molecular dynamics simulation, and the therapeutic effect of Gleditsiae Spina was proved in vitro through cytotoxicity experiments. The effect of Gleditsiae Spina on the core pathway is obtained by western blotting. Results: Gleditsiae Spina had cytotoxicity on HGSC based on network pharmacology and biological experiments. Luteolin, genistein, D-(+)-tryptophan, ursolic acid, and berberine are the identified core active ingredients of Gleditsiae Spina for regulating HGSC, with HPSE, PI3KCA, AKT1, and CTNNB1as the ideal targets. The prediction results were verified by molecular docking, molecular dynamic simulation, cell viability, and western blot analysis. Conclusion: Gleditsiae Spina mainly downregulates the expression of heparanase and ß-catenin to affect the composition of tumor cytoplasmic matrix and can regulate the PI3K-AKT pathway, integrating multiple targets and multiple pathways to play a therapeutic role. It also provides a theoretical basis for the prevention of ovarian cancer and its treatment using traditional Chinese medicine in the future.

Mechanism of action of Tripterygium wilfordii for treatment of idiopathic membranous nephropathy based on network pharmacology.

BACKGROUND: Although thunder god vine (Tripterygium wilfordii) has been widely used for treatment of idiopathic membranous nephropathy (IMN), the pharmacological mechanisms underlying its effects are still unclear. This study investigated potential therapeutic targets and the pharmacological mechanism of T. wilfordii for the treatment of IMN based on network pharmacology. METHODS: Active components of T. wilfordii were obtained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. IMN-associated target genes were collected from the GeneCards, DisGeNET, and OMIM databases. VENNY 2.1 was used to identify the overlapping genes between active compounds of T. wilfordii and IMN target genes. The STRING database and Cytoscape 3.7.2 software were used to analyze interactions among overlapping genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of the targets were performed using Rx64 4.0.2 software, colorspace, stringi, DOSE, clusterProfiler, and enrichplot packages. RESULTS: A total of 153 compound-related genes and 1485 IMN-related genes were obtained, and 45 core genes that overlapped between both categories were identified. The protein-protein interaction network and MCODE results indicated that the targets TP53, MAPK8, MAPK14, STAT3, IFNG, ICAM1, IL4, TGFB1, PPARG, and MMP1 play important roles in the treatment of T. wilfordii on IMN. Enrichment analysis showed that the main pathways of targets were the AGE signaling pathway, IL-17 signaling pathway, TNF signaling pathway, and Toll-like receptor signaling pathway. CONCLUSION: This study revealed potential multi-component and multi-target mechanisms of T. wilfordii for the treatment of IMN based on network pharmacological, and provided a scientific basis for further experimental studies.

Network Pharmacology Integrated Molecular Docking Revealed the Mechanism of Jianpi Yiqi Taohua Decoction Against Ulcerative Colitis.

BACKGROUND Jianpi Yiqi Taohua decoction (JYTD) has shown therapeutic effects in ulcerative colitis (UC). However, the pharmacological mechanism of JYTD against UC remains unclear. MATERIAL AND METHODS Compounds and targets of JYTD and UC-related genes were screened from public databases. Integrated analysis was performed to identify therapeutic targets of UC, followed by functional enrichment analysis. Protein-protein interaction interaction (PPI) and pharmacological networks were then established. Molecular docking was used to validate the affinity of compounds and their targets. Further, the efficacy of JYTD was evaluated by meta-analysis. Relevant studies were searched from 5 databases. Outcomes were complete response rate (CRR) and overall response rate (ORR), and pooled results were estimated by risk ratio (RR) with  corresponding 95% confidence intervals (CIs). RESULTS The pharmacological network identified 13 herbal medicines, 28 compounds, 54 targets, and 20 pathways. Stigmasterol, liquiritigenin, and naringenin were potential active compounds, and PRKCA, NFKB1, ESR1, NTRK1, AKT1, PPARG, RXRA, and VDR were hub targets. Pathway analysis revealed that genes were mainly involved in the cellular response to lipids. Molecular docking indicated that AKT1, NFKB1, ESR1, NTRK1, PRKCA, and PPARG exhibited good affinity to 6 key compounds of JYTD. Then, meta-analysis revealed that Tao Hua decoction treatment significantly improved CRR (RR, 1.21; 95% CI, 1.06-1.37; P=0.004) and ORR (RR, 1.16; 95% CI, 1.08-1.24; P<0.001). CONCLUSIONS JYTD was found to have preventive and therapeutic effects on UC through multiple compounds, targets, and pathways. These findings enhanced our understanding of the potential pharmacological mechanisms of JYTD against UC.

Serum Pharmacochemistry Combining Network Pharmacology to Discover the Active Constituents and Effect of Xijiao Dihuang Tang Prescription for Treatment of Blood-Heat and Blood-Stasis Syndrome-Related Disease.

Xijiao Dihuang Tang (XDT), a classic TCM prescription, has been used to clinically treat blood-heat and blood-stasis syndrome- (BHSS-) related diseases, including hemorrhagic stroke and sepsis. However, the active constituents and mechanism of XDT in the treatment of BHSS-related diseases have not been elucidated due to the lack of appropriate methodologies. In this study, serum pharmacochemistry and network pharmacology were used to explore the active constituents and the mechanism of XDT in the treatment of BHSS-related diseases. The effects of XDT were evaluated using dry yeast-induced rats as rat models with BHSS, which demonstrated the antipyretic and anticoagulant properties of XDT. The HPLC-QTOF/MS/MS assay was used to identify 60 serum constituents of XDT (SCXDT). Then, 338 targets of 60 SCXDT were predicted by integrating multiple databases and the MACCS fingerprint similarity prediction method. The degree of topological properties with targets of 19 key active constituents in SCXDT was identified and evaluated in glutamate-induced PC12 cells. Subsequently, 338 targets of 60 SCXDT were mainly involved in biological processes such as inflammation, coagulation, cell proliferation, and apoptosis, as well as oxidative contingencies via compound-target-disease network analysis. The core targets including IL-1ß, IL-6, TNF, NOS3, and MAPK1 were identified using protein-protein interaction network analysis, whereas dozens of signaling pathways such as the p38MAPK signaling pathway were identified using functional pathway enrichment analysis. The results indicated that XDT has broad therapeutic and neuroprotective effects on inflammation, coagulation, oxidative stress, cell proliferation, and apoptosis in dry yeast-induced rats with BHSS and glutamate-induced PC12 cells by regulating the p38MAPK signaling pathway. This study not only discovered the active constituents of XDT but also elaborated its mechanisms in the treatment of BHSS-related diseases by intervening in a series of targets, signaling pathways, and biological processes such as inflammation, coagulation, oxidative stress, neuroprotection. The findings in this study provide a novel strategy for exploring the therapeutic efficacy of TCM prescriptions.

Methodology improvement for network pharmacology to correct the deviation of deduced medicinal constituents and mechanism: Xian-Ling-Gu-Bao as an example.

ETHNOPHARMACOLOGICAL RELEVANCE: Network pharmacology is extremely adaptive for investigating traditional ethnic drugs, especially the herbal medicines. However, challenges still hang over many related studies due to the limitations in the methodology of conventional network pharmacology. AIM OF THE STUDY: Our work was aimed to investigate the methodology limitations of conventional network pharmacology with Xian-Ling-Gu-Bao (XLGB) as a representative, meanwhile, propose the strategies for coping with these issues. MATERIALS AND METHODS: Predicted phytochemical constituents formed virtual XLGB. The constituents in realistic XLGB samples was detected by liquid chromatography-mass spectrometry (LC-MS) to correct the constituent deviation resulted from virtual prediction. Multivariate statistical analysis of quantitative target data were used to reveal the relation of target profile between drug and disease. The key constituents and targets were screened and compared between virtual and realistic XLGB through network analysis. After enrichment analysis, reversing network pharmacology was performed to exclude weak targets and re-construct the interaction from key pathways to key targets. Finally, the core constituents and action mechanism of XLGB were deduced. RESULTS: Significant deviation of phytochemical constituents was found between virtual and realistic XLGB. As expected, this deviation led to a cascade of deviation ranging from deduced key constituents to key targets and key pathways. Moreover, many key KEGG pathways were enriched and screened out, however, they were almost irrelevant to the studied disease. These results systemically illustrated the limitations in the methodology of conventional network pharmacology. Importantly, the strategies for coping with these limitations were proposed, such as high-throughput detection of the realistic samples, multivariate analysis of target profile and combined enrichment analysis. Finally, based on the improved network pharmacology, the medicinal constituents and mechanism of XLGB against osteoarthritis were effectively deduced. CONCLUSIONS: Our work highlighted the necessity and proposed the strategies for improving the methodology of conventional network pharmacology. The corrected results from improved network pharmacology provided promising directions for future research on XLGB.

Discovery of Therapeutic Candidates for Diabetic Retinopathy Based on Molecular Switch Analysis: Application of a Systematic Process.

The pathogenesis of diabetic retinopathy (DR) is complicated, and there is no effective drug. Oxidative stress-induced human retinal microvascular endothelial cells (HRMECs) injury is one of the pathogenic factors for DR. Molecular switches are considered high-risk targets in disease progression. Identification of molecular switch is crucial to interpret the pathogenesis of disease and screen effective ingredients. In this study, a systematic process was executed to discover therapeutic candidates for DR based on HRMECs injury. First of all, the molecular mechanism of HRMECs oxidative stress injury was revealed by transcriptomics and network pharmacology. We found that oxidative stress was one of the pivotal pathogenic factors, which interfered with vascular system development, inflammation, cell adhesion, and cytoskeleton damaged HRMECs through crosstalk. Then, network topology analysis was used to recognize molecular switches. The results indicated that the Keap1-Nrf2-ARE signaling pathway was the molecular switch in HRMECs oxidative stress injury. On this basis, the HEK293-ARE overexpression cell line was applied to obtain 18 active traditional Chinese medicine (TCM) ingredients. Furthermore, andrographolide, one of the 18 candidates, was applied in the HRMECs oxidative stress model to evaluate the accuracy of the systematic process. The efficacy evaluation results showed that andrographolide could regulate oxidative stress, vascular system development, inflammation, adhesion, and skeleton tissue to inhibit HRMECs injury cooperatively. And its mechanism was related to the Nrf2 signaling pathway. Overall, our data suggest that the Nrf2 signaling pathway is the molecular switch in the HRMECs oxidative stress injury. 18 potential Nrf2 agonists are likely to be promising DR candidates.

Systematic characterization of the metabolites of defatted walnut powder extract in vivo and screening of the mechanisms against NAFLD by UPLC-Q-Exactive Orbitrap MS combined with network pharmacology.

ETHNOPHARMACOLOGICAL RELEVANCE: Walnut kernel, a well-known TCM, is often used after being defatted in tradition. And defatted walnut powder extract (DWPE) has the actions of tonifying the liver and kidney, dissipating stagnation and removing blood stasis, which has the effect on non-alcoholic fatty liver disease (NAFLD). However, the effective components of DWPE in vivo were unclear and the multiple mechanisms of DWPE against NAFLD have not been explored. AIM OF THE STUDY: The studies were performed to screen the effective substances in vivo by identification of the metabolites of DWPE in rats and to seek the potential mechanisms of DWPE on NAFLD by construction of the network pharmacology based on metabolites and verification of the highly correlated pathway. MATERIALS AND METHODS: To explore the effective substances in vivo, the metabolites of DWPE were identified in SD rats' bio-samples through UPLC-Q-Exactive Orbitrap MS. To analyze the mechanisms of DWPE on NAFLD, a Metabolite-Target-Disease network was established and the potential mechanisms were predicted. Then, highly correlated pathway was verified in animal and cells studies. RESULTS: A total of 52 metabolites of DWPE were identified in vivo, which were derived from gallic acid, ellagic acid (EA) and glansreginin A (Gla A). The possible metabolic pathways were phase Ⅰ (hydroxylation, hydrolyzation, etc) and phase Ⅱ metabolic reactions (methylation, sulfation and glucuronidation). Furthermore, in the network pharmacology, 54 core targets were enriched into pathways in cancer, nitrogen metabolism and other 9 pathways, which were essential pathways of DWPE against NAFLD. And the mechanism of nitrogen metabolism was verified in both of animal and cells studies. The results showed that DWPE could decline the concentration of ammonia and increase the expressions of carbonic anhydrase 2 (CA2) and carbamoylphosphate synthetase (CPS1) in nitrogen metabolism. CONCLUSION: Taken together, the study revealed the absorption components and their metabolic pathways and demonstrated the mechanism of nitrogen metabolism of DWPE on anti-NAFLD.

Screening tumor specificity targeted by arnicolide D, the active compound of Centipeda minima and molecular mechanism underlying by integrative pharmacology.

ETHNOPHARMACOLOGICAL RELEVANCE: Herb-derived anti-tumor agents, such as paclitaxel and vincristine, exert significant but varied effectivenesses towards different cancer types. Similarly, Centipeda minima (CM) is a well-known traditional Chinese medicine that has been used to treat rhinitis, relieve pain and reduce swelling, and recently found to exert overwhelming anti-tumor effects against breast cancer, colon cancer, and nasopharyngeal carcinoma with different response rates. However, what is the optimizing cancer model that benefits most from CM, and what is the specific target underlying still require more exclusive and profound investigations. AIMS OF THE STUDY: This study aimed to explore the dominant tumor model and specific target of CM by integrative pharmacology and biological experiments. MATERIALS AND METHODS: The most predominant and specific cancer types that are sensitive to CM were screened and identified based on a combination network pharmacology and bioinformatics analysis. Compound-target network and protein-protein interaction of CM-related cancer targets were carried out to determine the most abundant active compound. Simultaneously, the priority target responsible for CM-related anti-tumor efficacy was further validated by molecular docking and in vitro experiments. RESULTS: In total, approximately 42% (8/19) of the targets were enriched in prostate cancer (p = 1.25E-09), suggesting prostate cancer would be the most sensitive tumor response to CM-related efficacy. Furthermore, we found that arnicolide D (ARD), the most abundant and representative active compound of CM, could directly bind to Src with binding energy of -7.3 kcal/mol, implying Src would be the priority target responsible for CM-related anti-tumor efficacy. Meanwhile, the results were further validated by solvent-induced protein precipitation (SIP) assay. In addition, PCR and WB results also revealed that either CM or ARD could not influence the gene expression of Src, while significantly decreased its protein expression instead, which further suggested that ARD might markedly shortene the Src protein half-life to promote Src protein degradation, thereby achieving significant anti-prostate cancer efficacy. CONCLUSION: Our findings not only suggest CM as a promising Src-targeting candidate for prostate cancer treatment, but also bring up a strategy for understanding the personalization of herbal medicines by using integrative pharmacology.

Mechanism by which Eucommia ulmoides leaves Regulate Nonalcoholic fatty liver disease based on system pharmacology.

ETHNOPHARMACOLOGICAL RELEVANCE: Eucommia ulmoides (E. ulmoides) leaves are included in the Chinese Pharmacopoeia, and are traditionally used to treat hypertension, obesity, diabetes, and other diseases. Numerous pharmacological studies have shown that E. ulmoides has a good effect on lowering blood lipids and can improve obesity and nonalcoholic fatty liver. AIM: To study the mechanism of E. ulmoides leaves in regulating nonalcoholic fatty liver disease by combining prediction and validation. METHODS: Using network pharmacology, and molecular docking to predict E. ulmoides in regulating the action mechanism and potential active ingredients of nonalcoholic fatty liver, large hole adsorption resin enrichment active sites, in vitro experiments were performed to verify its fat-lowering effect and mechanism. RESULTS: The major components of E. ulmoides leaves exhibited good combination with lipid metabolism-regulating core proteins, particularly flavonoids. EUL 50 significantly reduced lipid accumulation, and increased PPARγ. Compared with the control group, the autophagy level increased after the administration of EUL 50. PPARγ decreased significantly after the addition of chloroquine (CQ, autophagy inhibitor). CONCLUSION: The active ingredients in E. ulmoides leaves regulating nonalcoholic fatty liver disease are mainly flavonoids and phenolics. EUL 50 may play a role in lowering lipids by regulating PPARγ expression through inducing autophagy.