Systems pharmacology exploration of botanic drug pairs reveals the mechanism for treating different diseases

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

Background

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

Methods

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

Results

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

Conclusion

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

Network pharmacology-based strategy to investigate the effect and mechanism of α-solanine against glioma

BACKGROUND

An anti-tumour activity has been demonstrated for α-solanine, a bioactive compound extracted from the traditional Chinese herb Solanum nigrum L. However, its efficacy in the treatment of gliomas and the underlying mechanisms remain unclear. The aim of this study was to investigate the inhibitory effects of α-solanine on glioma and elucidate its mechanisms and targets using network pharmacology, molecular docking, and molecular biology experiments.

METHODS

Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was utilized to predict the potential targets of α-solanine. GeneCards was used to gather glioma-related targets, and the STRING online database was used to analyze protein-protein interaction (PPI) networks for the shared targets. Hub genes were identified from the resulting PPI network and further investigated using Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Additionally, prognostic and gene set enrichment analyses (GSEA) were carried out to identify potential therapeutic targets and their underlying mechanisms of action in relation to the prognosis of gliomas. In vitro experiments were conducted to verify the findings from the network pharmacology analysis.

RESULTS

A total of 289 α-solanine targets and 1149 glioma-related targets were screened, of which 78 were common targets. 11 hub genes were obtained, including SRC, HRAS, HSP90AA1, IGF1, MAPK1, MAPK14, KDR, STAT1, JAK2, MAP2K1, and IGF1R. The GO and KEGG pathway analyses unveiled that α-solanine was strongly associated with several signaling pathways, including positive regulation of MAP kinase activity and PI3K-Akt. Moreover, α-solanine (10 µM and 15 µM) inhibited the proliferation and migration but promoted the apoptosis of glioma cells. Finally, STAT1 was identified as a potential mediator of the effect of α-solanine on glioma prognosis.

CONCLUSION

α-Solanine can inhibit the proliferation and migration of gliomas by regulating multiple targets and signalling pathways. These findings lay the foundation for the creation of innovative clinical anti-glioma agents.

Molecular mechanism of Hedyotis Diffusae Herba in the treatment of lupus nephritis based on network pharmacology

Aims: To determine the bioactive components of Hedyotis Diffusae Herba (HDH) and the targets in treating lupus nephritis (LN), and so as to elucidate the protective mechanism of HDH against LN. Methods and results: An aggregate of 147 drug targets and 162 LN targets were obtained from online databases, with 23 overlapped targets being determined as potential therapeutic targets of HDH against LN. Through centrality analysis, TNF, VEGFA and JUN were screened as core targets. And the bindings of TNF with stigmasterol, TNF with quercetin, and VEGFA with quercetin were further validated by molecular docking. By conducting Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses for drug targets, disease targets and the shared targets, TNF signaling pathway, Toll-like receptor signaling pathway, NF-kappa B signaling pathway and HIF-1 signaling pathway, etc., were found in all these three lists, indicating the potential mechanism of HDH in the treatment of LN. Conclusion: HDH may ameliorate the renal injury in LN by targeting multi-targets and multi-pathways, including TNF signaling pathway, NF-kappa B signaling pathway, HIF-1 signaling pathway and so on, which provided novel insights into further researches of the drug discovery in LN.

Comparative Efficacy of East Asian Herbal Formulae Containing Astragali Radix-Cinnamomi Ramulus Herb-Pair against Diabetic Peripheral Neuropathy and Mechanism Prediction: A Bayesian Network Meta-Analysis Integrated with Network Pharmacology

The Astragali Radix-Cinnamomi Ramulus herb-pair (ACP) has been widely used in the treatment of diabetic peripheral neuropathy (DPN) as part of East Asian herbal medicine (EAHM). Eligible randomized controlled trials (RCTs) were identified by searching 10 databases. The outcomes investigated were response rate, sensory nerve conduction velocity (SNCV), and motor nerve conduction velocity (MNCV) in four regions of the body. The compounds in the ACP and their targets of action, disease targets, common targets, and other relevant information were filtered using network pharmacology. Forty-eight RCTs, with 4308 participants, and 16 different interventions were identified. Significant differences were observed in the response rate, MNCV, and SNCV, as all EAHM interventions were superior to conventional medicine or lifestyle modification. The EAHM formula containing the ACP ranked highest in more than half of the assessed outcomes. Furthermore, major compounds, such as quercetin, kaempferol, isorhamnetin, formononetin, and beta-sitosterol, were found to suppress the symptoms of DPN. The results of this study suggest that EAHM may increase therapeutic efficacy in DPN management, and EAHM formulations containing the ACP may be more suitable for improving treatment response rates to NCV and DPN therapy.

Centipeda minima active components and mechanisms in lung cancer

BACKGROUND

Traditional 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.

METHODS

We 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.

RESULTS

We 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.

CONCLUSIONS

This 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.

Screening of Active Ingredients from Wendan Decoction in Alleviating Palmitic Acid-Induced Endothelial Cell Injury

(1) Objective: Traditional Chinese medicine (TCM) plays an important role in the treatment of numerous illnesses. As a classic Chinese medicine, Wendan Decoction (WDD) encompasses a marvelous impact on the remedy of hyperlipidemia. It is known that hyperlipidemia leads to cardiovascular injury, therefore anti-vascular endothelial cell injury (AVECI) may be an underlying molecular mechanism of WDD in the cure of hyperlipidemia. However, there is no relevant research on the effect of WDD on vascular endothelial cells and its pharmacodynamic substances. Therefore, the purpose of this study was to investigate the protective effect of WDD on vascular endothelial cells. (2) Methods: The chemical constituents of WDD were determined by LC-MS/MS technology. The protective effects of 16 batches of WDD on samples from human umbilical vein endothelial cells (HUVECs) were evaluated. Finally, gray relation analysis (GRA) and partial least squares regression (PLSR) were used to analyze the potential correlation between chemical ingredients and AVECI. (3) Results: The results indicated that WDD had apparent protective effect on endothelial cells, and pharmacological properties in 16 batches of WDD tests were apparently discrepant. The GRA and PLSR showed that trigonelline, liquiritin, hesperidin, hesperetin, scopoletin, morin, quercetin, isoliquiritigenin, liquiritigenin and formononetin may be the active ingredients of AVECI in WDD. (4) Conclusions: WDD has a protective effect on endothelial cell injury induced by palmitic acid, which may be related to its component content. This method was suitable for the search of active components in classical TCM.

Extracellular vesicles mediate biological information delivery: A double-edged sword in cardiac remodeling after myocardial infarction

Acute myocardial infarction (AMI) is a severe ischemic disease with high morbidity and mortality worldwide. Maladaptive cardiac remodeling is a series of abnormalities in cardiac structure and function that occurs following myocardial infarction (MI). The pathophysiology of this process can be separated into two distinct phases: the initial inflammatory response, and the subsequent longer-term scar revision that includes the regression of inflammation, neovascularization, and fibrotic scar formation. Extracellular vesicles are nano-sized lipid bilayer vesicles released into the extracellular environment by eukaryotic cells, containing bioinformatic transmitters which are essential mediators of intercellular communication. EVs of different cellular origins play an essential role in cardiac remodeling after myocardial infarction. In this review, we first introduce the pathophysiology of post-infarction cardiac remodeling, as well as the biogenesis, classification, delivery, and functions of EVs. Then, we explore the dual role of these small molecule transmitters delivered by EVs in post-infarction cardiac remodeling, including the double-edged sword of pro-and anti-inflammation, and pro-and anti-fibrosis, which is significant for post-infarction cardiac repair. Finally, we discuss the pharmacological and engineered targeting of EVs for promoting heart repair after MI, thus revealing the potential value of targeted modulation of EVs and its use as a drug delivery vehicle in the therapeutic process of post-infarction cardiac remodeling.

Defining the Potential Targets for Biological Activity of Isoegomaketone Based on Network Pharmacology and Molecular Docking Methods

Isoegomaketone is a water-soluble natural ketone compound that is commonly present in Rabdosia angustifolia and Perilla frutescens. At present, it is known that isoegomaketone has a wide range of pharmacological activity, but there has been no thorough investigation of its potential targets. As a result, we examined the potential targets of isoegomaketone using the network pharmacology approach. In our study, the TCM Database@Taiwan was utilized to search for the chemical formula. The pharmacological characteristics of isoegomaketone were then evaluated in silico using the Swiss Absorption, Distribution, Metabolism, and Excretion (Swiss ADME) and Deep Learning-Acute Oral Toxicity (DL-AOT) methods, and the potential isoegomaketone target genes were identified using a literature study. Additionally, using the clusterProfiler R package 3.8.1, the Gene Ontology (GO) enrichment analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of target genes were performed. In order to obtain the protein interaction network, we simultaneously submitted the targets to the STRING database. After this, we performed molecular docking with respect to targets and isoegomaketone. Finally, we created visual networks of protein-protein interactions (PPI) and examined these networks. Our results showed that isoegomaketone had good drug-likeness, bioavailability, medicinal chemistry friendliness, and acceptable toxicity. Subsequently, through the literature analysis, 48 target genes were selected. The bioinformatics analysis and network analysis found that these target genes were closely related to the biological processes of isoegomaketone, such as atherosclerotic formation, inflammation, tumor formation, cytotoxicity, bacterial infection, virus infection, and parasite infection. These findings show that isoegomaketone may interact with a wide range of proteins and biochemical processes to form a systematic pharmacological network, which has good value for the creation and use of drugs.

Network Pharmacology and Molecular Docking Analysis Reveal Insights into the Molecular Mechanism of Shengma-Gegen Decoction on Monkeypox

Background: A new viral outbreak caused by monkeypox has appeared after COVID-19. As of yet, no specific drug has been found for its treatment. Shengma-Gegen decoction (SMGGD), a pathogen-eliminating and detoxifying agent composed of four kinds of Chinese herbs, has been demonstrated to be effective against several viruses in China, suggesting that it may be effective in treating monkeypox, however, the precise role and mechanisms are still unknown. Methods: Network pharmacology was used to investigate the monkeypox-specific SMGGD targets. These targets were analyzed via String for protein-to-protein interaction (PPI), followed by identification of hub genes with Cytoscape software. Function enrichment analysis of the hub targets was performed. The interactions between hub targets and corresponding ligands were validated via molecular docking. Results: Through screening and analysis, a total of 94 active components and 8 hub targets were identified in the TCM-bioactive compound-hub gene network. Molecular docking results showed that the active components of SMGGD have strong binding affinity for their corresponding targets. According to functional analysis, these hub genes are mainly involved in the TNF, AGE-RAGE, IL-17, and MAPK pathways, which are linked to the host inflammatory response to infection and viral replication. Therefore, SMGGD might suppress the replication of monkeypox virus through the MAPK signaling pathway while also reducing inflammatory damage caused by viral infection. Conclusion: SMGGD may have positive therapeutic effects on monkeypox by reducing inflammatory damage and limiting virus replication.

Quercetin and Luteolin may be the New Effective Drugs for Radiation Pneumonitis: Based on a Systems Pharmacology

Background: The occurrence of radiation pneumonia not only affects the efficacy of radiotherapy, but also seriously threatens the health of patients undergoing radiotherapy for lung cancer. Studies have suggested that a feining granule is a potentially effective drug for the treatment of radiation pneumonitis, but its mechanism and main components are still unclear. Our study used bioinformatics methods to analyze the main drug Aster tataricus L. f. in feining granules and aims to gain the main mechanism in the treatment of radiation pneumonitis. Methods: Analyzed the effective drug components and targets of A tataricus through the Traditional Chinese Medicine Systems Pharmacology website. And obtained gene targets related to radiation pneumonia through the website of OMIM, Genecard, and Disgenet. Protein–protein interaction (PPI), gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the obtained drugs and gene-related targets were conducted. Verify the effects of small molecule drugs on corresponding targets by conducting molecular docking experiments. Results: In total, 193 targets were identified for 13 molecules of A tataricus, and 897 genes were identified to be related to radiation pneumonia. Finally, we obtained 111 genes by crossing drug and disease-related target genes. Using PPI, GO, and KEGG analysis, we found TP53, HSP90AA1, RELA, JUN, AKT1, mitogen-activated protein kinase 1 ( MAPK1), tumor necrosis factor ( TNF), and interleukin-6 ( IL-6) are the most critical genes, which were mainly focused on the GOs of DNA-binding transcription factor, RNA polymerase II-specific DNA-binding transcription factor and protein serine/threonine kinase activity, and the pathways of lipids and atherosclerosis, advanced glycation end products and their receptors, and IL-17. Conclusion: Through molecular docking experiments, it was found that the small molecules of quercetin and luteolin bind tightly to RELA and JUN proteins. We reveal the mechanism of action of A tataricus in the treatment of radiation pneumonia. Quercetin and luteolin may be effective small molecules for radiation pneumonitis.

The protective effects of Mai-Luo-Ning injection against LPS-induced acute lung injury via the TLR4/NF-κB signalling pathway

BACKGROUND

Acute lung injury (ALI) is a severe inflammatory disorder associated with high morbidity and mortality rates. Various therapeutic strategies for ALI have been proposed over the last few decades; however, the treatment options remain limited. Mai-Luo-Ning injection (MLN), a traditional Chinese medical formulation, has been extensively used for the treatment of respiratory diseases. Nevertheless, the effects of MLN on ALI remain unclear.

PURPOSE

This study aimed to investigate the protective and therapeutic effects of MLN on lipopolysaccharide-induced ALI mouse models and RAW 264.7 cells, and further explore the underlying mechanism of these effects.

METHODS

The therapeutic activity of MLN was evaluated using an in vivo ALI model and an in vitro model of RAW 264.7 macrophages. UHPLC-ESI-Q-TOF-MS/MS was used to investigate the chemical constituents of the MLN. The material basis and potential protective mechanism of MLN were analyzed using network pharmacology. The roles of MLN in inhibiting the Toll-like receptor 4 (TLR4)/ nuclear factor kappa B (NF-κB) signalling pathway were investigated via western blotting, real-time polymerase chain reaction, enzyme-linked immunosorbent assay, and immunofluorescence staining.

RESULTS

In vivo experiments demonstrated that MLN ameliorated LPS-induced histological changes in lung tissues and reduced lung wet/dry weight ratio, total protein concentration in the bronchoalveolar lavage fluid and myeloperoxidase activity. Furthermore, MLN downregulated the in vivo and in vitro expression of pro-inflammatory cytokines such as tumour necrosis factor-alpha, interleukin-6, and interleukin-1β. Network pharmacology analysis revealed that MLN could act synergistically through multiple targets and pathways and exert a protective effect, possibly through inhibiting TLR4/ NF-κB signalling pathways. Western blotting and immunofluorescence experiments further confirmed that MLN could regulate the expression of TLR4, MyD88, phospho-IκB-α, and phospho-NF-κB p65 in the TLR4/NF-κB signalling pathway and decrease the translocation of phospho-NF-κB p65 into the nucleus.

CONCLUSION

This study suggests that MLN has a potential protective effect against LPS-induced ALI, which might be associated with the inhibition of the TLR4/NF-κB signalling pathway. Therefore, MLN is worthy of further investigation as a potential candidate for the treatment of ALI in the future.

Efficacy and Pharmacological Mechanism of Poria cocos-Based Formulas Combined With Chemotherapy for Ovarian Cancer: A Integrated Systems Pharmacology Study

Previous studies have shown that Poria cocos-based formulas combined with chemotherapy can improve the quality of life of ovarian cancer patients. However, the results are still controversial. We systematically searched the literature from eight databases to evaluate the efficacy and safety of Poria cocos-based formulas in combination with paclitaxel-carboplatin in treating ovarian cancer (OC). Subsequently, network pharmacology, molecular docking and cell experiments were performed to further verify the underlying molecular mechanism. Thirteen randomized controlled trials, including 922 patients with OC, were enrolled in the study. The results indicated that Poria cocos-based compounds combined with paclitaxel-carboplatin significantly improved patients' tumor response rate, traditional Chinese medicine syndrome score, Karnofsky Performance Scale, physical and social function, and reduced side effects of chemotherapy compared to the paclitaxel-carboplatin alone. According to the network pharmacological analysis, tumulosic acid were the most bioactive compounds of Poria cocos. BCL2L1 is highly expressed in OC and is associated with a worse prognosis which could become potential drug target. Functional enrichment analysis suggested that the anti-OC effect of Poria cocos may be related to PI3K-Akt signaling pathway. The molecular docking results indicated that tumulosic acid might inhibit OC by regulating BCL2L1. Vitro experiment confirmed tumulosic acid that induced cell apoptosis by modulating PI3K/AKT signaling and BCL2L1. Our study may provide a clinical basis and theoretical rationale for combining Poria cocos-based formulas with chemotherapy for OC. In addition, the integrated pharmacological strategy proposed in our study provides an excellent example for exploring the mechanism of complex formulas.

Network pharmacology-based approach to understand the effect and mechanism of Danshen against anemia

ETHNOPHARMACOLOGICAL RELEVANCE

Danshen, the dried rhizome of Salvia miltiorrhiza Bge., is widely used to treat cardio-cerebrovascular diseases in China. However, its role in nourishing blood, which has been detailed in historical literature for thousands of years, is perpetually disputed in the academic field. Moreover, there is no systematic research on Danshen in treating anemia. This research aimed to investigate the effects and mechanisms of Danshen on anemia in a zebrafish model based on the results of a network pharmacology study.

MATERIALS AND METHODS

The network pharmacology study was based on the screening of chemical components and related targets from TCMSP and SwissADME database. The genes associated with anemia were obtained from DisgeNet database, and the genes with the intersection of Danshen target genes were screened out. The Cytoscape 3.7.2 software package was used to construct the "ingredient-target-pathway" network. The exploration of target interaction by String system and the enrichment analysis by Metascape system, was used to discover the possible anti-anemia action mechanism of Danshen. Then, a zebrafish anemia model was induced by vinorelbine followed by the administration of aqueous/ethanol extract of Danshen in contrast to SiWu Decoction (SWD), which is generally acknowledged as a positive drug for tonifying blood. Afterward, the red blood cell signal, cardiac output, and blood flow velocity were detected to evaluate their blood-enriching effects. Quantitative real-time polymerase chain reaction (qPCR) was used to analyze the mRNA levels of hematopoietic-related factors, which were predicted in network pharmacology.

RESULTS

Compounds and target screening hinted that 115 chemical targets from Danshen were related to anemia, KEGG pathway enrichment results suggested that the mechanism of Danshen in treating anemia was significantly related to the Jak-STAT signaling pathway. Pharmacodynamic results showed that aqueous extract of Danshen (DSAE) and ethanol extract of Danshen (DSEE) markedly enhanced the number of red blood cells, cardiac output, and blood flow velocity. Compared with DSAE, DSEE exerted anti-anemia effects at a lower dose; however, along with higher toxicity. PCR data demonstrated that DSAE and DSEE treatment both upregulated the mRNA expression of erythroid hematopoiesis-related factors in the Epo-JAK-STAT signaling pathway, such as Gata-1, Epo, EpoR, Jak2, STAT3, and STAT5. In general, DSAE exhibited higher activation of this signaling than DSEE.

CONCLUSIONS

These results indicated that DSAE and DSEE both possess blood-enriching functions related with their ability to promote Jak-STAT signaling. DSAE exerted lower toxicity and attenuated anemia over a wider dose range than DSEE, which suggests that DSAE may be more suitable for the treatment for anemia. These results presented experimental evidence for the clinical use of Danshen as an intervention for anemia, especially in chemotherapy-induced anemia.

Exploring the Critical Components and Therapeutic Mechanisms of Perilla frutescens L. in the Treatment of Chronic Kidney Disease via Network Pharmacology

Chronic kidney disease (CKD) is a chronic progressive disease that seriously threatens human health. Some patients will continue to progress into the CKD stage 3–5 (also called chronic renal failure), which is mainly manifested by a decline in renal function and multi-system damage. Perilla frutescens (L.) Britton. (Lamiaceae) is one of the most widely used traditional Chinese medicine (TCM) herbs in CKD, especially in CKD stage 3–5. But its active components and mechanisms are still unclear. In this study, we used network pharmacology to analyze the active components of P. frutescens and the main therapeutic targets for intervention in CKD stage 3–5. Then, the key components were selected for enrichment analysis and identified by high performance liquid chromatograph (HPLC). Finally, we verified the critical components through molecular docking, and in vitro experiments. The results show that 19 main active components of P. frutescens were screened, and 108 targets were intersected with CKD stage 3–5. The PPI network was constructed and found that the core nodes AKT1, TP53, IL6, TNF, and MAPK1 may be key therapeutic targets. Enrichment analysis shows that related targets may be involved in regulating various biological functions, and play a therapeutic role in CKD stage 3–5 by regulating apoptosis, T cell receptor, and PI3K-AKT signaling pathways. Molecular docking indicates that the key active components were well docked with its corresponding targets. Five active components were identified and quantified by HPLC. According to the results, luteolin was selected as the critical component for further verification. In vitro experiments have shown that luteolin can effectively alleviate adriamycin (ADR)-induced renal tubular apoptosis and suppress AKT and p53 phosphorylation. The effects of luteolin to reduce apoptosis may be mediated by inhibiting oxidative stress and downregulating the mitogen-activated protein kinase (MAPK) and p53 pathways. In general, we screened and analyzed the possible active components, therapeutic targets and pathways of P. frutescens for treating CKD. Our findings revealed that luteolin can reduce renal tubular epithelial cell apoptosis and may be the critical component of P. frutescens in the treatment of CKD. It provides references and direction for further research.

Idebenone-Activating Autophagic Degradation of α-Synuclein via Inhibition of AKT-mTOR Pathway in a SH-SY5Y-A53T Model of Parkinson's Disease: A Network Pharmacological Approach

Background

Parkinson's disease (PD) is the second most common neurodegenerative disease worldwide, which currently lacks disease-modifying therapy to slow down its progression. Idebenone, a coenzyme Q10 (CQ10) analogue, is a well-known antioxidant and has been used to treat neurological disorders. However, the mechanism of Idebenone on PD has not been fully elucidated. This study aims to predict the potential targets of Idebenone and explore its therapeutic mechanism against PD.

Method

We obtained potential therapeutic targets through database prediction, followed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Next, we constructed and analyzed a protein-protein interaction network (PPI) and a drug-target-pathway-disease network. A molecular docking test was conducted to identify the interactions between Idebenone and potential targets. Lastly, a PD cell line of SH-SY5Y overexpressing mutant α-synuclein was used to validate the molecular mechanism.

Result

A total of 87 targets were identified based on network pharmacology. The enrichment analysis highlighted manipulation of MAP kinase activity and the PI3K-AKT signaling pathway as potential pharmacological targets for Idebenone against PD. Additionally, molecular docking showed that AKT and MAPK could bind tightly with Idebenone. In the cell model of PD, Idebenone activated autophagy and promoted α-synuclein degradation by suppressing the AKT/mTOR pathway. Pretreating cells with chloroquine (CQ) to block autophagic flux could diminish the pharmacological effect of Idebenone to clear α-synuclein.

Conclusion

This study demonstrated that Idebenone exerts its anti-PD effects by enhancing autophagy and clearance of α-synuclein, thus providing a theoretical and experimental basis for Idebenone therapy against PD.

Computational Analysis Illustrates the Mechanism of Qingfei Paidu Decoction in Blocking the Transition of COVID-19 Patients from Mild to Severe Stage

BACKGROUND

The epidemic of SARS-CoV-2 has made COVID-19 a serious threat to human health around the world. The severe infections of SARS-CoV-2 are usually accompanied by higher mortality. Although the Qingfei Paidu Decoction (QFPDD) has been proved to be effective in blocking the transition of COVID-19 patients from mild to severe stage, its mechanism remains unclear.

OBJECTIVE

This study aims to explore the mechanism of QFPDD in blocking the transition of COVID-19 patients from mild to severe stage.

MATERIALS AND METHODS

In the process of screening active ingredients, oral bioavailability (OB) and drug likeness (DL) are key indicators, which can help to screen out pivotal compounds. Therefore, with the criteria of OB≥30% and DL≥0.18 , we searched active ingredients of QFPDD in the Traditional Chinese Medicine Systems Pharmacology (TCMSP, https://tcmspw.com/) by using its 21 herbs as keywords.

RESULTS

We filtered out 6 pivotal ingredients from QFPDD by using the bioinformatics method, namely quercetin, luteolin, berberine, hederagenin, shionone and kaempferol, which can inhibit the highly expressed genes (i.e. CXCR4, ICAM1, CXCL8, CXCL10, IL6, IL2, CCL2, IL1B, IL4, IFNG) in severe COVID-19 patients. By performing KEGG enrichment analysis, we found seven pathways, namely TNF signaling pathway, IL-17 signaling pathway, Toll-like receptor signaling pathway, NF-kappa B signaling pathway, HIF-1 signaling pathway, JAK-STAT signaling pathway, and Th17 cell differentiation, by which QFPDD could block the transition of COVID-19 patients from mild to severe stage.

CONCLUSION

QFPDD can prevent the deterioration of COVID-19 in the following mechanisms, i.e. inhibiting SARS-CoV-2 invasion and replication, anti-inflammatory and immune regulation, and repairing body damage. These results will be helpful for the prevention and treatment of COVID-19.

Herb-drug interactions between androgenic Chinese herbal medicines and androgen receptor antagonist on tumor growth: Studies on two xenograft prostate cancer animal models

Our previous study revealed that Epimedii Folium (EF) and Codonopsis Radix (CNR) significantly promoted tumor growth on a subcutaneous mouse model of prostate cancer (PCa) via enhancing the mRNA and protein expressions of androgen receptor (AR), while Astragali Radix (AGR) inhibited tumor growth via suppressing the protein expression of AR. In the present study, we aimed to investigate the potential interactions between EF, CNR or AGR and AR antagonist (abiraterone acetate [ABI]) on the tumor growth using subcutaneous and orthotopic PCa mouse models. EF, CNR, AGR and ABI were intragastrically given to mice once every 2 days for 4 weeks. The pharmacokinetics of ABI were evaluated in the plasma of rats when combined with EF, CNR, or AGR. Our results demonstrated that EF or CNR could weaken the anti-tumor effects of ABI via increasing the AR expression involving activation of the PI3K/AKT and Rb/E2F pathways and decreasing the bioavailability of ABI, while AGR could enhance the anti-tumor effects of ABI through suppressing the AR expression via inhibiting the activations of PI3K/AKT and Rb/E2F pathways and increasing the bioavailability of ABI. These findings imply that cautions should be exercised when prescribing EF and CNR for PCa patients.

In vitro anti-bacterial activity and network pharmacology analysis of Sanguisorba officinalis L. against Helicobacter pylori infection

Background

Helicobacter pylori (H. pylori) infection has become an international public health problem, and antibiotic-based triple or quadruple therapy is currently the mainstay of treatment. However, the effectiveness of these therapies decreases due to resistance to multiple commonly used antibiotics. Sanguisorba officinalis L. (S. officinalis), a traditional Chinese medicine clinically used for hemostasis and treatment of diarrhea, has various pharmacological activities. In this study, in vitro antimicrobial activity was used for the preliminary evaluation of S. officinalis against H. pylori. And a pharmacology analysis approach was also utilized to elucidate its underlying mechanisms against H. pylori infection.

Methods

Micro-broth dilution method, agar dilution method, checkerboard assay, scanning electron microscopy (SEM), and transmission electron microscopy (TEM) were used for the assessment of anti-bacterial activity. Active ingredients screening, GO analysis, KEGG analysis, construction of PPI network, molecular docking, and RT-qPCR were used to elucidate the underlying pharmacological mechanisms of S. officinalis against H. pylori infection.

Results

The minimum inhibitory concentration (MIC) values of S. officinalis against multiple H. pylori strains including clinically isolated multi-drug resistant (MDR) strains were ranging from 160 to 320 µg/ml. These results showed that S. officinalis had additive interaction with four commonly used antibiotics and could exert antibacterial effect by changing the morphology of bacteria without developing drug resistance. Through network pharmacology analysis, 8 active ingredients in S. officinalis were screened out for subsequent studies. Among 222 putative targets of S. officinalis, 49 targets were identified as potential targets for treatment of H. pylori infection. And these 49 targets were significantly enriched in GO processes such as protein kinase B signaling, protein kinase activity, protein kinase binding, and KEGG pathways such as Pathways in cancer, MicroRNAs in cancer, and TNF signaling pathway. Protein-protein interaction analysis yielded 5 core targets (AKT1, VEGFA, EGFR, SRC, CCND1), which were validated by molecular docking and RT-qPCR.

Conclusions

Overall, this study confirmed the in vitro inhibitory activity of S. officinalis against H. pylori and explored the possible pharmacological mechanisms, laying the foundation for further research and clinical application.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13020-021-00442-1.

The Efficacy and Mechanism of Chinese Herbal Medicines in Lowering Serum Uric Acid Levels: A Systematic Review

Background. Chinese herbal medicines are widely used to lower serum uric acid levels. However, no systemic review summarizes and evaluates their efficacies and the underlying mechanisms of action. Objectives. To evaluate the clinical and experimental evidences for the effectiveness and the potential mechanism of Chinese herbal medicines in lowering serum uric acid levels. Methods. Four electronic databases PubMed, Wed of Science, the Cochrane Library and Embase were used to search for Chinese herbal medicines for their effects in lowering serum uric acid levels, dated from 1 January 2009 to 19 August 2020. For clinical trials, randomized controlled trials (RCTs) were included; and for experimental studies, original articles were included. The methodological quality of RCTs was assessed according to the Cochrane criteria. For clinical trials, a meta-analysis of continuous variables was used to obtain pooled effects. For experimental studies, lists were used to summarize and integrate the mechanisms involved. Results. A total of 10 clinical trials and 184 experimental studies were included. Current data showed that Chinese herbal medicines have promising clinical efficacies in patients with elevated serum uric acid levels (SMD: −1.65, 95% CI: −3.09 to −0.22; p = 0.024). There was no significant difference in serum uric acid levels between Chinese herbal medicine treatments and Western medicine treatments (SMD: −0.13, 95% CI: −0.99 to 0.74; p = 0.772). Experimental studies revealed that the mechanistic signaling pathways involved in the serum uric acid lowering effects include uric acid synthesis, uric acid transport, inflammation, renal fibrosis and oxidative stress. Conclusions. The clinical studies indicate that Chinese herbal medicines lower serum uric acid levels. Further studies with sophisticated research design can further demonstrate the efficacy and safety of these Chinese herbal medicines in lowering serum uric acid levels and reveal a comprehensive picture of the underlying mechanisms of action.

Identification of Antitumor Active Constituents in Polygonatum sibiricum Flower by UPLC-Q-TOF-MSE and Network Pharmacology

We aimed to investigate the material basis and mechanisms underlying the antitumor activity of Polygonatum sibiricum flower by ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS^E). A compound-protein interaction network for cancer was constructed to identify potential drug targets, and then the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was conducted to elucidate the pathways involved in the antitumor activity of P. sibiricum flower. Subsequently, molecular docking was performed to determine whether the identified proteins are a target of the compounds of P. sibiricum flower. Sixty-four compounds were identified in P. sibiricum flower. Among these, 35 active constituents and 72 corresponding targets were found to be closely associated with the antitumor activity of P. sibiricum flower. By constructing and analyzing the compound-target-pathway network, five key compounds and 10 key targets were obtained. The five key compounds were wogonin, rhamnetin, dauriporphine, chrysosplenetin B, and 5-hydroxyl-7,8-panicolin. The 10 key targets were PIK3CG, AKT1, PTGS1, PTGS2, MAPK14, CCND1, TP53, GSK3B, NOS2, and SCN5A. In addition, 34 antitumor-related pathways were identified using the KEGG pathway analysis. To further verify the results of network pharmacology screening, molecular docking was performed with the five key compounds and the top three targets based on degree ranking, namely, PIK3CG, AKT1, and PTGS2; the results of molecular docking were consistent with those of network pharmacology. P. sibiricum flower can exert its antitumor activity via multicomponent, multitarget, and multichannel mechanisms of action. In this study, we identified the antitumor active constituents of P. sibiricum flower and their potential mechanisms of action.

Homotherapy for heteropathy active components and mechanisms of Qiang-Huo-Sheng-Shi decoction for treatment of rheumatoid arthritis and osteoarthritis

Qiang-Huo-Sheng-Shi decoction (QHSSD), a classic traditional Chinese herbal formula, which has been reported to be effective in rheumatoid arthritis (RA) and osteoarthritis (OA). However, the concurrent targeting mechanism of how the aforementioned formula is valid in the two distinct diseases OA and RA, which represents the homotherapy-for-heteropathy principle in traditional Chinese medicine (TCM), have not yet been clarified. In the present study, network pharmacology was adopted to analyze the potential molecular mechanism, and therapeutic effective components of QHSSD on both OA and RA. A total of 153 active ingredients in QHSSD were identified, 142 of which associated with 59 potential targets for the two diseases were identified. By constructing the protein-protein interaction network and the compound-target-disease network, 72 compounds and 10 proteins were obtained as the hub targets of QHSSD against OA and RA. The hub genes of ESR1, PTGS2, PPARG, IL1B, TNF, MMP2, IL6, CYP3A4, MAPK8, and ALB were mainly involved in osteoclast differentiation, the NF-κB and TNF signaling pathways. Moreover, molecular docking results showed that the screened active compounds had a high affinity for the hub genes. This study provides new insight into the molecular mechanisms behind how QHSSD presents homotherapy-for-heteropathy therapeutic efficacy in both OA and RA. For the first time, a two-disease model was linked with a TCM formula using network pharmacology to identify the key active components and understand the common mechanisms of its multi-pathway regulation. This study will inspire more innovative and important studies on the modern research of TCM formulas.

Systems pharmacology-based approach for dissecting the mechanisms of pyrazine components in Maotai liquor

Maotai liquor is a typical representative of sauce aroma-style flavor liquors and has been considered to be a precious cultural heritage of the oriental spirit culture. Aroma components are largely responsible for the characteristic aroma of liquor. Pyrazine compound is one of the most important categories of aroma components that affect the flavor of Maotai liquor. However, limited information is available regarding the systemic analysis of pyrazine compounds, especially the pharmacological effects of bioactive pyrazine components. Therefore, in the current study, a systemic analysis approach was provided by integrating absorption, distribution, metabolism, and excretion (ADME) screening, target identification, pharmacological evaluation and pathway analysis to explore the pharmacological mechanism of pyrazine compounds in Maotai liquor. As a result, 17 pyrazine components with adequate pharmacokinetic properties were filtered out using ADME models. Thirty eight potential targets of these active compounds were identified through target prediction. The pharmacological evaluation was proposed to uncover the pharmacological effect of pyrazine compounds in Maotai liquor from the holistic perspective. Finally, the pharmacological effects of the pathways perturbed by potential targets were interpreted based on the pathway analysis. Our study lays the foundation for formulating a comprehensive understanding of the pyrazine compounds in Maotai liquor, which would contribute to the development of Chinese liquor.

Enhancing and Complementary Mechanisms of Synergistic Action of Acori Tatarinowii Rhizoma and Codonopsis Radix for Alzheimer's Disease Based on Systems Pharmacology

Materials and Methods

In this study, a systems pharmacology-based strategy was used to elucidate the synergistic mechanism of Acori Tatarinowii Rhizoma and Codonopsis Radix for the treatment of AD. This novel systems pharmacology model consisted of component information, pharmacokinetic analysis, and pharmacological data. Additionally, the related pathways were compressed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and the organ distributions were determined in the BioGPS bank.

Results

Sixty-eight active ingredients with suitable pharmacokinetic profiles and biological activities were selected through ADME screening in silico. Based on 62 AD-related targets, such as APP, CHRM1, and PTGS1, systematic analysis showed that these two herbs were mainly involved in the PI3K-Akt signaling pathway, MAPK signaling pathway, neuroactive ligand-receptor interaction, and fluid shear stress and atherosclerosis, indicating that they had a synergistic effect on AD. However, ATR acted on the KDR gene, while CR acted on IGF1R, MET, IL1B, and CHUK, showing that they also had complementary effects on AD. The ingredient contribution score involved 29 ingredients contributing 90.14% of the total contribution score of this formula for AD treatment, which emphasized that the effective therapeutic effects of these herbs for AD were derived from both ATR and CR, not a single herb. Organ distribution showed that the targets of the active ingredients were mainly located in the whole blood, the brain, and the muscle, which are associated with AD.

Conclusions

In sum, our findings suggest that the systems pharmacology methods successfully revealed the synergistic and complementary mechanisms of ATR and CR for the treatment of AD.

A system-level investigation into the pharmacological mechanisms of flavor compounds in liquor

Maotai-flavor liquor, one of the world's most famous natural fermentation food products plays a significant role in traditional Chinese culture and people's daily lives for a long time due to its good taste. However, the pharmacological activities of flavor compounds in Maotai liquor have not been fully elucidated. In answering this question, a system-level analysis was developed by combining in silico ADME evaluation, multi-target prediction, GO enrichment analysis, network pharmacology technology, pathway analysis, as well as experimental verification to elucidate the pharmacological effects of flavor compounds in Maotai liquor. Finally, 55 active compounds and 80 targets were identified to interpret the pharmacological effect of the flavor compounds. Moreover, the key active compounds were verified by in vitro experiments to validate the reliability of our approaches. Our study provides a novel integrated strategy to comprehensively understand the pharmacological activities of complex components in Maotai liquor. PRACTICAL APPLICATIONS: We proposed an integrative strategy by systems pharmacology to investigate the potential active compounds and their related targets, as well as to understand the potential pharmacological mechanism of flavor compounds in Maotai liquor. The present work will not only shed light on the mechanism of active compounds in Maotai liquor at the system level, but also provide a novel approach for discovery of the active compounds that may benefit human health.

A Systems Pharmacology Approach for Identifying the Multiple Mechanisms of Action for the Rougui-Fuzi Herb Pair in the Treatment of Cardiocerebral Vascular Diseases

Cardiocerebral vascular diseases (CCVDs) are the main reasons for high morbidity and mortality all over the world, including atherosclerosis, hypertension, myocardial infarction, stroke, and so on. Chinese herbs pair of the Cinnamomum cassia Presl (Chinese name, rougui) and the Aconitum carmichaelii Debx (Chinese name, fuzi) can be effective in CCVDs, which is recorded in the ancient classic book Shennong Bencao Jing, Mingyibielu and Thousand Golden Prescriptions. However, the active ingredients and the molecular mechanisms of rougui-fuzi in treatment of CCVDs are still unclear. This study was designed to apply a system pharmacology approach to reveal the molecular mechanisms of the rougui-fuzi anti-CCVDs. The 163 candidate compounds were retrieved from Traditional Chinese Medicine System Pharmacology Database and Analysis Platform (TCMSP). And 84 potential active compounds and the corresponding 42 targets were obtained from systematic model. The underlying mechanisms of the therapeutic effect for rougui-fuzi were investigated with gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Then, component-target-disease (C-T-D) and target-pathway (T-P) networks were constructed to further dissect the core pathways, potential targets, and active compounds in treatment of CCVDs for rougui-fuzi. We also constituted protein-protein in interaction (PPI) network by the reflect target protein of the crucial pathways against CCVDs. As a result, 21 key compounds, 8 key targets, and 3 key pathways were obtained for rougui-fuzi. Afterwards, molecular docking was performed to validate the reliability of the interactions between some compounds and their corresponding targets. Finally, UPLC-Q-Exactive-MS^E and GC-MS/MS were analyzed to detect the active ingredients of rougui-fuzi. Our results may provide a new approach to clarify the molecular mechanisms of Chinese herb pair in treatment with CCVDs at a systematic level.

A New Strategy for Identifying Mechanisms of Drug-drug Interaction Using Transcriptome Analysis: Compound Kushen Injection as a Proof of Principle

Drug-drug interactions (DDIs), especially with herbal medicines, are complex, making it difficult to identify potential molecular mechanisms and targets. We introduce a workflow to carry out DDI research using transcriptome analysis and interactions of a complex herbal mixture, Compound Kushen Injection (CKI), with cancer chemotherapy drugs, as a proof of principle. Using CKI combined with doxorubicin or 5-Fu on cancer cells as a model, we found that CKI enhanced the cytotoxic effects of doxorubicin on A431 cells while protecting MDA-MB-231 cells treated with 5-Fu. We generated and analysed transcriptome data from cells treated with single treatments or combined treatments and our analysis showed that opposite directions of regulation for pathways related to DNA synthesis and metabolism which appeared to be the main reason for different effects of CKI when used in combination with chemotherapy drugs. We also found that pathways related to organic biosynthetic and metabolic processes might be potential targets for CKI when interacting with doxorubicin and 5-Fu. Through co-expression analysis correlated with phenotype results, we selected the MYD88 gene as a candidate major regulator for validation as a proof of concept for our approach. Inhibition of MYD88 reduced antagonistic cytotoxic effects between CKI and 5-Fu, indicating that MYD88 is an important gene in the DDI mechanism between CKI and chemotherapy drugs. These findings demonstrate that our pipeline is effective for the application of transcriptome analysis to the study of DDIs in order to identify candidate mechanisms and potential targets.

Systems Pharmacology-Based Method to Assess the Mechanism of Action of Weight-Loss Herbal Intervention Therapy for Obesity

Obesity is a multi-factorial chronic disease that has become a serious, prevalent, and refractory public health challenge globally because of high rates of various complications. Traditional Chinese medicines (TCMs) as a functional food are considered to be a valuable and readily available resource for treating obesity because of their better therapeutic effects and reduced side effects. However, their "multi-compound" and "multi-target" features make it extremely difficult to interpret the potential mechanism underlying the anti-obesity effects of TCMs from a holistic perspective. An innovative systems-pharmacology approach was employed, which combined absorption, distribution, metabolism, and excretion screening and multiple target fishing, gene ontology enrichment analysis, network pharmacology, and pathway analysis to explore the potential therapeutic mechanism of weight-loss herbal intervention therapy in obesity and related diseases. The current study provides a promising approach to facilitate the development and discovery of new botanical drugs.

Synergistic mechanisms of Sanghuang-Danshen phytochemicals on postprandial vascular dysfunction in healthy subjects: A network biology approach based on a clinical trial

With the increased risk of cardiovascular disease, the use of botanicals for vascular endothelial dysfunction has intensified. Here, we explored the synergistic mechanisms of Sanghuang–Danshen (SD) phytochemicals on the homeostatic protection against high-fat-induced vascular dysfunction in healthy subjects, using a network biology approach, based on a randomised crossover clinical trial. Seventeen differential markers identified in blood samples taken at 0, 3 and 6 h post-treatment, together with 12SD phytochemicals, were mapped onto the network platform, termed the context-oriented directed associations. The resulting vascular sub-networks illustrated associations between 10 phytochemicals with 32 targets implicated in 143 metabolic/signalling pathways. The three key events included adhesion molecule production (ellagic acid, fumaric acid and cryptotanshinone; VCAM-1, ICAM-1 and PLA2G2A; fatty acid metabolism), platelet activation (ellagic acid, protocatechuic acid and tanshinone IIA; VEGFA, APAF1 and ATF3; mTOR, p53, Rap1 and VEGF signalling pathways) and endothelial inflammation (all phytochemicals, except cryptotanshinone; 29 targets, including TP53 and CASP3; MAPK and PI3K-Akt signalling pathways, among others). Our collective findings demonstrate a potential of SD to protect unintended risks of vascular dysfunction in healthy subjects, providing a deeper understanding of the complicated synergistic mechanisms of signature phytochemicals in SD.

Systematic Analysis of the Pharmacological Effects of Alcoholic Components in Maotai

Maotai liquor is one of the most famous traditional Chinese distilled liquor enjoyed by many people all over the world for its unique production method, impressive liquor quality, and soy sauce-like and roasted aroma style. It is known that aroma characteristics of liquor mainly depend on the aroma compounds. Alcohols as one of the most important categories of aroma components have been determined in Maotai liquor. However, the systemic analysis of alcoholic compounds in liquor is limited, especially the active alcoholic components and their pharmacological effects. Therefore, in this study, a systemic analysis method was proposed by combining in silico absorption, distribution, metabolism, and excretion (ADME) evaluation, target fishing, network pharmacology technology, pathway analysis, and experimental verification to interpret the pharmacological mechanism of alcoholic compounds in Maotai liquor. Finally, 15 compounds with favorable pharmacokinetic profiles were screened through in silico ADME models. Thirty-eight related targets of these active compounds were identified by target prediction method. The network pharmacology and pathway analysis were developed to clarify the pharmacological effect of alcoholic compounds in Maotai liquor at the system and pathway level. Moreover, the key active compounds were validated by in vitro experiments that verified the effectiveness of our methods. Our study provides a novel approach to systematically analyze the pharmacological effect of alcoholic compounds in Maotai liquor, which would be beneficial for promoting the in-depth study of various liquors. PRACTICAL APPLICATION: Maotai liquor is popularly enjoyed in the world for a very long time. However, the systemic analysis of compounds in liquor is limited. Our systematic analysis approach was developed to explore the bioactive ingredients and their related target proteins as well as the pharmacological effects of Maotai liquor. This will provide a new method to understand the pharmacological mechanisms of compounds in various liquors at the systems level, so as to promote the development of liquors and to increase the public awareness of science about alcohol consumption.

Systems pharmacology reveals the unique mechanism features of Shenzhu Capsule for treatment of ulcerative colitis in comparison with synthetic drugs

In clinic, both synthetic drugs and Shenzhu Capsule (SZC), one kind of traditional Chinese medicines (TCMs), are used to treat ulcerative colitis (UC). In our study, a systems pharmacology approach was employed to elucidate the chemical and mechanism differences between SZC and synthetic drugs in treating UC. First, the compound databases were constructed for SZC and synthetic drugs. Then, the targets of SZC were predicted with on-line tools and validated using molecular docking method. Finally, chemical space, targets, and pathways of SZC and synthetic drugs were compared. Results showed that atractylenolide I, atractylone, kaempferol, etc., were bioactive compounds of SZC. Comparison of SZC and synthetic drugs showed that (1) in chemical space, the area of SZC encompasses the area of synthetic drugs; (2) SZC can act on more targets and pathways than synthetic drugs; (3) SZC can not only regulate immune and inflammatory reactions but also act on ulcerative colitis complications (bloody diarrhea) and prevent UC to develop into colorectal cancer whereas synthetic drugs mainly regulate immune and inflammatory reactions. Our study could help us to understand the compound and mechanism differences between TCM and synthetic drugs.

A Systems-Level Analysis of Mechanisms of Platycodon grandiflorum Based on A Network Pharmacological Approach

Platycodon grandiflorum (PG) is widely used in Asia for its various beneficial effects. Although many studies were conducted to understand the molecular mechanisms of PG, it is still unclear how the combinations of multiple ingredients work together to exert its therapeutic effects. The aim of the present study was to provide a comprehensive review of the systems-level mechanisms of PG by adopting network pharmacological analysis. We constructed a compound⁻target⁻disease network for PG using experimentally validated and machine-leaning-based prediction results. Each target of the network was analyzed based on previously known pharmacological activities of PG. Gene ontology analysis revealed that the majority of targets were related to cellular and metabolic processes, responses to stimuli, and biological regulation. In pathway enrichment analyses of targets, the terms related to cancer showed the most significant enrichment and formed distinct clusters. Degree matrix analysis for target⁻disease associations of PG suggested the therapeutic potential of PG in various cancers including hepatocellular carcinoma, gastric cancer, prostate cancer, small-cell lung cancer, and renal cell carcinoma. We expect that network pharmacological approaches will provide an understanding of the systems-level mechanisms of medicinal herbs and further develop their therapeutic potentials.

Prediction Methods of Herbal Compounds in Chinese Medicinal Herbs

Chinese herbal medicine has recently gained worldwide attention. The curative mechanism of Chinese herbal medicine is compared with that of western medicine at the molecular level. The treatment mechanism of most Chinese herbal medicines is still not clear. How do we integrate Chinese herbal medicine compounds with modern medicine? Chinese herbal medicine drug-like prediction method is particularly important. A growing number of Chinese herbal source compounds are now widely used as drug-like compound candidates. An important way for pharmaceutical companies to develop drugs is to discover potentially active compounds from related herbs in Chinese herbs. The methods for predicting the drug-like properties of Chinese herbal compounds include the virtual screening method, pharmacophore model method and machine learning method. In this paper, we focus on the prediction methods for the medicinal properties of Chinese herbal medicines. We analyze the advantages and disadvantages of the above three methods, and then introduce the specific steps of the virtual screening method. Finally, we present the prospect of the joint application of various methods.

Systems Pharmacology-Based Approach of Connecting Disease Genes in Genome-Wide Association Studies with Traditional Chinese Medicine

Traditional Chinese medicine (TCM) originated in ancient China has been practiced over thousands of years for treating various symptoms and diseases. However, the molecular mechanisms of TCM in treating these diseases remain unknown. In this study, we employ a systems pharmacology-based approach for connecting GWAS diseases with TCM for potential drug repurposing and repositioning. We studied 102 TCM components and their target genes by analyzing microarray gene expression experiments. We constructed disease-gene networks from 2558 GWAS studies. We applied a systems pharmacology approach to prioritize disease-target genes. Using this bioinformatics approach, we analyzed 14,713 GWAS disease-TCM-target gene pairs and identified 115 disease-gene pairs with q value < 0.2. We validated several of these GWAS disease-TCM-target gene pairs with literature evidence, demonstrating that this computational approach could reveal novel indications for TCM. We also develop TCM-Disease web application to facilitate the traditional Chinese medicine drug repurposing efforts. Systems pharmacology is a promising approach for connecting GWAS diseases with TCM for potential drug repurposing and repositioning. The computational approaches described in this study could be easily expandable to other disease-gene network analysis.

Integrated Modules Analysis to Explore the Molecular Mechanisms of Phlegm-Stasis Cementation Syndrome with Ischemic Heart Disease

Background: Ischemic heart disease (IHD) has been the leading cause of death for several decades globally, IHD patients usually hold the symptoms of phlegm-stasis cementation syndrome (PSCS) as significant complications. However, the underlying molecular mechanisms of PSCS complicated with IHD have not yet been fully elucidated. Materials and Methods: Network medicine methods were utilized to elucidate the underlying molecular mechanisms of IHD phenotypes. Firstly, high-quality IHD-associated genes from both human curated disease-gene association database and biomedical literatures were integrated. Secondly, the IHD disease modules were obtained by dissecting the protein-protein interaction (PPI) topological modules in the String V9.1 database and the mapping of IHD-associated genes to the PPI topological modules. After that, molecular functional analyses (e.g., Gene Ontology and pathway enrichment analyses) for these IHD disease modules were conducted. Finally, the PSCS syndrome modules were identified by mapping the PSCS related symptom-genes to the IHD disease modules, which were further validated by both pharmacological and physiological evidences derived from published literatures. Results: The total of 1,056 high-quality IHD-associated genes were integrated and evaluated. In addition, eight IHD disease modules (the PPI sub-networks significantly relevant to IHD) were identified, in which two disease modules were relevant to PSCS syndrome (i.e., two PSCS syndrome modules). These two modules had enriched pathways on Toll-like receptor signaling pathway (hsa04620) and Renin-angiotensin system (hsa04614), with the molecular functions of angiotensin maturation (GO:0002003) and response to bacterium (GO:0009617), which had been validated by classical Chinese herbal formulas-related targets, IHD-related drug targets, and the phenotype features derived from human phenotype ontology (HPO) and published biomedical literatures. Conclusion: A network medicine-based approach was proposed to identify the underlying molecular modules of PSCS complicated with IHD, which could be used for interpreting the pharmacological mechanisms of well-established Chinese herbal formulas (e.g., Tao Hong Si Wu Tang, Dan Shen Yin, Hunag Lian Wen Dan Tang and Gua Lou Xie Bai Ban Xia Tang). In addition, these results delivered novel understandings of the molecular network mechanisms of IHD phenotype subtypes with PSCS complications, which would be both insightful for IHD precision medicine and the integration of disease and TCM syndrome diagnoses.

Systems-level mechanisms of action of Panax ginseng: a network pharmacological approach

Panax ginseng has been used since ancient times based on the traditional Asian medicine theory and clinical experiences, and currently, is one of the most popular herbs in the world. To date, most of the studies concerning P. ginseng have focused on specific mechanisms of action of individual constituents. However, in spite of many studies on the molecular mechanisms of P. ginseng, it still remains unclear how multiple active ingredients of P. ginseng interact with multiple targets simultaneously, giving the multidimensional effects on various conditions and diseases. In order to decipher the systems-level mechanism of multiple ingredients of P. ginseng, a novel approach is needed beyond conventional reductive analysis. We aim to review the systems-level mechanism of P. ginseng by adopting novel analytical framework-network pharmacology. Here, we constructed a compound-target network of P. ginseng using experimentally validated and machine learning-based prediction results. The targets of the network were analyzed in terms of related biological process, pathways, and diseases. The majority of targets were found to be related with primary metabolic process, signal transduction, nitrogen compound metabolic process, blood circulation, immune system process, cell-cell signaling, biosynthetic process, and neurological system process. In pathway enrichment analysis of targets, mainly the terms related with neural activity showed significant enrichment and formed a cluster. Finally, relative degrees analysis for the target-disease association of P. ginseng revealed several categories of related diseases, including respiratory, psychiatric, and cardiovascular diseases.

System Pharmacology-Based Dissection of the Synergistic Mechanism of Huangqi and Huanglian for Diabetes Mellitus

The rapidly increasing diabetes mellitus (DM) is becoming a major global public health issue. Traditional Chinese medicine (TCM) has a long history of the treatment of DM with good efficacy. Huangqi and Huanglian are one of the most frequently prescribed herbs for DM, and the combination of them occurs frequently in antidiabetic formulae. However, the synergistic mechanism of Huangqi (Radix Astragali) and Huanglian (Rhizoma Coptidis) has not been clearly elucidated. To address this problem, a feasible system pharmacology model based on chemical, pharmacokinetic and pharmacological data was developed via network construction approach to clarify the synergistic mechanisms of these two herbs. Forty-three active ingredients of Huangqi (mainly astragalosides and isoflavonoids) and Huanglian (primarily isoquinoline alkaloids) possessing favorable pharmacokinetic profiles and biological activities were selected, interacting with 50 DM-related targets to provide potential synergistic therapeutic actions. Systematic analysis of the constructed networks revealed that these targets such as GLUT2, NOS2, PTP1B, and IGF1R were mainly involved in PI3K-Akt signaling pathway, insulin resistance, insulin signaling pathway, and HIF-1 signaling pathway, and were mainly located in retina, pancreatic islet, smooth muscle, immunity-related organ tissues, and whole blood. The contribution index of every active ingredient also indicated five compounds, including berberine (BBR), astragaloside IV (AIV), quercetin, palmatine, and astragalus polysaccharides, as the principal components of this herb combination. These results successfully explained the polypharmcological and synergistic mechanisms underlying the efficiency of Huangqi and Huanglian for the treatment of DM and its complications.

How impaired efficacy happened between Gancao and Yuanhua: Compounds, targets and pathways

As recorded in Traditional Chinese Medicine (TCM) theory, Gancao (Glycyrrhizae Radix et Rhizoma) could weaken the pharmacological effect or increase the toxicity of Yuanhua (Genkwa Flos). However, the theory has been suspected due to lack of evidence. Here, we investigate whether Gancao could weaken Yuanhua’s diuretic effect, if so, which chemicals and which targets may be involved. Results showed that Yuanhua exerted diuretic effect through down-regulating renal AQP 2, without electrolyte disturbances such as K⁺ loss which has been observed as side-effect of most diuretics. Gancao had no diuretic effect, but could impair Yuanhua’s diuretic effect through up-regulating renal AQP 2. Glycyrrhetinic acid (GRA) in Gancao could up-regulate AQP 2 and counteract the AQP 2 regulation effect of Yuanhuacine (YHC) and Ginkwanin (GKW) in Yuanhua. Network pharmacology method suggested that YHC, GKW and GRA could bind to MEK1/FGFR1 protein and influence ERK-MAPK pathway, which was verified by Western blotting. This study supports TCM theory and reminds that more attention should be paid to the safety and efficacy problems induced by improper combination between herbs. Moreover, we suggested that promising diuretics with less side effects can be developed from Chinese Medicines such as Yuanhua.