Network Pharmacology in Research of Chinese Medicine Formula: Methodology, Application and Prospective

Qingfei oral liquid alleviates RSV-induced lung inflammation by promoting fatty-acid-dependent M1/M2 macrophage polarization via the Akt signaling pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Respiratory syncytial virus (RSV) is a common pathogen that causes lower respiratory tract disease in infants and the elderly, and no vaccination is presently available. Qingfei oral liquid (QF), a traditional Chinese medicine formula, has been shown in clinic to have anti-inflammatory properties.

AIM OF THE STUDY

The present study investigated whether QF can suppress RSV-induced lung inflammation in mice models via fatty acid-dependent macrophage polarization.

MATERIAL AND METHODS

BALB/c mice were given a low, medium, or high dose of QF intragastrically for four consecutive days following RSV infection. The lung inflammatory status was assessed using H&E staining and cytokine assays. The active components of QF and fatty acid metabolism were analyzed using ultra-high-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS). A lipid metabolism-related pathway was found through network pharmacology and molecular docking investigations. Western blotting assays were used to determine the levels of ATP-citrate lyase (ACLY), peroxisome proliferation-activated receptor alpha (PPAR), Akt protein kinase B and its phosphorylated form in Akt signaling. Flow cytometry was used to quantify the number of macrophage subtypes (M1/M2), and immunohistochemistry was used to examine the expression of inducible nitric oxide synthase (iNOS) and arginase-1 (Arg-1).

RESULTS

In the lung tissues of RSV-infected mice, QF suppressed the transcription of pro-inflammatory proteins such as interleukin-1 beta (IL-1β), tumor necrosis factor alpha (TNF-α), and interleukin-6 (IL-6), while increasing the level of anti-inflammatory factors such as interleukin-10 (IL-10). The alterations in metabolic enzyme activity mediated by Akt signaling were linked to QF's significant reduction in lung fatty acid accumulation. Lower ACLY expression and higher PPAR expression were found after QF treatment, showing that these two enzymes were downstream targets of Akt signaling, controlling fatty acid synthesis (FAS) and fatty acid oxidation (FAO), respectively. The reprogramming of fatty acid metabolism resulted in the polarization of macrophages from M1 to M2, with lower expression of iNOS and higher expression of Arg-1. Additionally, application of an Akt agonist (SC-79) reduced QF's anti-inflammatory effects by increasing FAS and decreasing macrophage polarization.

CONCLUSIONS

QF inhibited Akt-mediated FAS and polarized M1 to M2 macrophages, resulting in an anti-inflammatory impact.

Integrated network pharmacology and intestinal flora analysis to determine the protective effect of Xuanbai-Chengqi decoction on lung and gut injuries in influenza virus-infected mice

ETHNOPHARMACOLOGICAL RELEVANCE

Xuanbai-Chengqi decoction (XBCQ) is a traditional Chinese medicine (TCM) compound used in the treatment of pulmonary infection in China. Despite the popular usage of XBCQ, its underlying protective roles and the associated molecular mechanisms with the gut-lung axis in influenza remain unclear.

AIM OF THE STUDY

We aimed to explore the protective effects and the underlying mechanism of XBCQ efficacy on lung and intestine injuries induced by influenza A virus as well as to identify the main active components through integrated network pharmacology, intestinal flora analysis and pathway validation.

MATERIALS AND METHODS

The potential active components and therapeutic targets of XBCQ in the treatment of influenza were hypothesized through a series of network pharmacological strategies, including components screening, targets prediction and bioinformatics analysis. Inflammatory cytokines and pathway proteins were assayed to validate the results of network pharmacology. Then the mechanism of XBCQ alleviating lung and intestine injuries was further explored via intestinal flora analysis. The important role of Rhubarb in the formula was verified by removing Rhubarb.

RESULTS

XBCQ could significantly improve the survival rate in IAV-infected mice. The network pharmacology results demonstrated that JUN, mitogen-activated protein kinase (MAPK), and tumor necrosis factor (TNF) are the key targets of XBCQ that can be useful in influenza treatment as it contains the core components luteolin, emodin, and aloe-emodin, which are related to the pathways of TNF, T-cell receptor (TCR), and NF-κB. Verification experiments demonstrated that XBCQ could significantly alleviate the immune injury of the lungs and the gut of the mice, which is attributable to the inhibition of the release of inflammatory cytokines (such as TNF-α, IL-6, and IL-1β), the downregulation of the protein expression levels of Toll-like receptors-7 (TLR7), MyD88, and p-NF-κB65, and the reduction in the relative abundance of Enterobacteriaceae and Proteus, while an increase in that of Firmicutes and Lachnospiraceae. The overall protective role of XBCQ contributing to the treatment of the lungs and the gut was impaired when Rhubarb was removed from XBCQ.

CONCLUSIONS

Our results suggest that the efficacy of XBCQ is related to the inhibition of the immune injury and remodeling of the intestinal flora, wherein Rhubarb plays an important role, which cumulatively provide the evidence applicable for the treatment of viral pneumonia induced by a different respiratory virus with XBCQ.

Exploring the mechanisms of Gui Zhi Fu Ling Wan on varicocele via network pharmacology and molecular docking

Varicocele (VC) is a common urogenital disease that leads to a high risk of testicular pain or male infertility. The purpose of this research was to explore the molecular mechanism of the Gui Zhi Fu Ling Wan (GFW) in the treatment of VC. The main active ingredients and targets information of GFW were screened by Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, and the targets related to VC were determined by GeneCards, Online Mendelian Inheritance in Man (OMIM), and Disease Gene Network (DisGeNET) databases. The intersection of active ingredient targets and disease targets was selected to construct a protein-protein interaction (PPI) network through the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. Based on the use of CytoNCA plug-in to find the main targets, a 'component-target-disease' network was constructed by Cytoscape 3.8.2. Metascape was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of drug and disease targets. Molecular docking was employed to investigate the binding interaction between the main active components and core targets. A total of 76 active components of GFW were screened out. The main targets of the active components on VC were tumour protein p53 (TP53), tumour necrosis factor (TNF), hypoxia inducible factor 1 subunit alpha (HIF1A), interleukin-6 (IL-6), caspase 3 (CASP3), catalase (CAT), prostaglandin-endoperoxide synthase 2 (PTGS2), vascular endothelial growth factor A (VEGFA). The PI3K-Akt signalling pathway, HIF-1 signalling pathway, and apoptosis signalling pathway were mainly involved in the regulation of VC. The results of molecular docking showed that the binding potential and activity of the main active components and the core targets of GFW were good. We found that GFW could alleviate apoptosis, participate in venous vessel morphogenesis, and reduce oxidative stress in the treatment of VC. This study can provide a reference for subsequent clinical and scientific research experiments, which can be used to design new drugs and develop new therapeutic instructions to treat VC.

East Wind, West Wind: Toward the modernization of traditional Chinese medicine

Traditional Chinese medicine (TCM) has used herbal remedies for more than 2,000 years. The use of complimentary therapies has increased dramatically during the last years, especially in the West, and the incorporation and modernization of TCM in current medical practice is gaining momentum. We reflect on the main bottlenecks in the modernization of arcane Chinese herbal medicine: lack of standardization, safety concerns and poor quality of clinical trials, as well as the ways these are being overcome. Progress in these areas will facilitate the implementation of an efficacy approach, in which only successful clinical trials lead to the molecular characterization of active compounds and their mechanism of action. Traditional pharmacological methodologies will produce novel leads and drugs, and we describe TCM successes such as the discovery of artemisinin as well as many others still in the pipeline. Neurodegenerative diseases, such as Parkinson's and Alzheimer's disease, cancer and cardiovascular disease are the main cause of mortality in the Western world and, with an increasing old population in South East Asia, this trend will also increase in the Far East. TCM has been used for long time for treating these diseases in China and other East Asian countries. However, the holistic nature of TCM requires a paradigm shift. By changing our way of thinking, from "one-target, one-drug" to "network-target, multiple-component-therapeutics," network pharmacology, together with other system biology methodologies, will pave the way toward TCM modernization.

Network pharmacology and molecular docking reveal the mechanism of Angelica dahurica against Osteosarcoma

Osteosarcoma (OS) is a malignant bone tumor of mesenchymal origin. Angelica dahurica is a typical traditional Chinese herb. Angelica dahurica is used in the treatment of a variety of tumors. However, the studies of Angelica dahurica for OS have not been reported. To investigate Angelica dahurica's potential mechanism of action in the treatment of OS, we used network pharmacology and molecular docking methods in this study. Of which the network pharmacology includes the collection of active ingredients of Angelica dahurica, the collection of predicted targets of Angelica dahurica and predicted targets of OS, the analysis of therapeutic targets of Angelica dahurica, gene ontology (GO) enrichment, and Kyoto encyclopedia of genes and genomes (KEGG) enrichment. The Venn plot performance showed that there were 225 predicted targets of Angelica dahurica for the treatment of OS. The therapeutic targets enrichment analysis results showed that Angelica dahurica treated OS through multiple targets and pathways. Angelica dahurica could affect OS's proliferation, apoptosis, migration, infiltration, and angiogenesis through a signaling network formed by pivotal genes crosstalking numerous signaling pathways. In addition, molecular docking results showed that sen-byakangelicol, beta-sitosterol, and Prangenin, have a relatively high potential to become a treatment for patients with OS and improve 5-year survival in OS patients. We used network pharmacology and molecular docking methods to predict the active ingredients and significant targets of Angelica dahurica for the treatment of OS and, to a certain extent, elucidated the potential molecular mechanism of Angelica dahurica in the treatment of OS. This study provided a theoretical basis for Angelica dahurica in the treatment of OS.

Exploration of the Pharmacological Mechanism of Bufei Nashen Pill in Treating Chronic Obstructive Pulmonary Disease Using Network Pharmacology Integrated Molecular Docking

Objective: Based on network pharmacological analysis and molecular docking verification, the therapeutic mechanism of Bufei Nashen Pill (BFNSP) in treating chronic obstructive pulmonary disease (COPD) is discussed. Methods: First, the active ingredients and therapeutic targets of BFNSP were determined based on literature and the Chinese medicine system pharmacology database. Relevant targets of COPD were determined using GeneCard, Therapeutic Target Database and Online Mendelian Inheritance in Man (OMIM). The con-targets of BFNSP and COPD were then obtained through the Veen platform, which were implemented in Cytoscape to build “Drug-Ingredients-Potential Target network.” Target gene function enrichment analysis and signal pathway analysis were performed based on STRING database, Database for Annotation, Visualization, and Integrated Discovery, and Kyoto Encyclopedia of Genes and Genomes Pathway database. Finally, SYBYL 2.2.1 software was used to finish docking. Results: In the Drug-Ingredients-Potential Targets network, 172 active ingredients and 183 potential targets were found. Enrichment analysis showed that potential targets mainly involve biological functions such as inflammation, reactive oxygen, and immunity. Molecular docking showed that the active ingredients of BFNSP had preferential interaction with interleukin 6, mitogen-activated protein kinase 1, SRC, epidermal growth factor receptor, and matrix metalloproteinase-9. Conclusion: BFNSP can be used to treat COPD by the regulation of inflammation, immunity, and hypoxia tolerance.

Curcumae longae Rhizoma (Jianghuang) extract reverses the 5-Fluoruracil resistance in colorectal cancer cells via TLR4/PI3K/Akt/mTOR pathway

OBJECTIVES

Intensive efforts have been made in the area of identifying drug resistance modulators from traditional Chinese medicine. Various natural plant extracts have been reported for their reversal effect of drug resistance in cancers. This study was to assess the reversal potential of Curcumae longae Rhizoma extract (CLRE) in 5-Fluorouracil (5-Fu) resistance to colon cancer and explore its underly mechanism.

METHODS

Increased concentrations of 5-Fu were used to culture SW480. A series of concentrations of CLRE were used to treat the 5-Fu resistant SW480 cells. WST-8 assay was used to detect the cell viability. Cell apoptosis was assessed by SuperView™ 488 Caspase-3 Assay Kit. The quantification of mentioned factors was archived by RT-qPCR. Network pharmacology analysis was used to explore the target of CLRE.

RESULTS

5-Fu resistant cell line (SW480/5-FuR) was established. The IC50 value of CLRE against SW480/5-FuR was 181.0 ± 14.12 µg/ml. CLRE can resensitize the SW480/5-FuR to 5-Fu by inhibiting cell growth. The combination treatment (CLRE+5-Fu) induced cell apoptosis via inhibition of bcl-2 and activation of caspase-3 and bax. Three active ingredients from CLRE were identified. TLR4 was targeted by these three ingredients and linked these ingredients to PI3K/Akt/mTOR pathway. The levels of TLR4, PI3K, AKT1, and mTORC1 mRNA were decreased when 5-Fu was combined with CLRE.

CONCLUSIONS

CLRE could reverse 5-Fu resistance in colon cancer by inactivating TLR4/PI3K/AKT/mTORC1 pathway. This finding might provide a molecular basis and a valuable direction for further clinical applications and research for treating 5-Fu resistant colon cancer.

Multiple anti-inflammatory mechanisms of Zedoary Turmeric Oil Injection against lipopolysaccharides-induced acute lung injury in rats elucidated by network pharmacology combined with transcriptomics

BACKGROUND

Prospects for the drug treatment of acute lung injury (ALI) is unpromising. Managing inflammation can prevent ALI from progressing and minimize further deterioration. Zedoary turmeric oil injection (ZTOI), a patented traditional Chinese medicine (TCM) that has been used against ALI, has shown significant anti-inflammatory effects. However, the mechanisms underlying these effects remain unclear.

PURPOSE

Elucidate the anti-inflammatory mechanism by which ZTOI acts against ALI in rats using an ingredients-targets-pathways (I-T-P) interaction network.

STUDY DESIGN AND METHODS

The key ingredients of ZTOI were characterized using UPLC-MS/MS combined with literature mining. The target profiles of each ingredient were established using drug-target databases. The anti-inflammatory activity of ZTOI against lipopolysaccharides (LPS)-induced rat ALI was validated using histopathology and inflammatory factor assessments. The therapeutic targets of ZTOI were screened by integrating transcriptomic results of lung tissues with protein-protein interaction (PPI) expansion. Using KEGG pathway enrichment, an I-T-P network was established to determine the essential interactions among ingredients, targets, and pathways of ZTOI against lung inflammation in ALI. Molecular docking and immunofluorescence staining were utilized to confirm the accuracy of the I-T-P network.

RESULTS

A total of 11 sesquiterpenes, whose target profiles may characterize the potential function of ZTOI, were identified as key ingredients. In the ALI rat model, ZTOI can alleviate lung inflammation by decreasing the levels of C-reactive protein, interleukin-6, interleukin-1β, and tumor necrosis factor α both in serum and lung tissues. Based on our biological samples, transcriptomics, PPI network expansion, and KEGG pathway enrichment, 11 ingredients, 174 targets, and 8 signaling pathways were linked in the I-T-P networks. From these results, ZTOI could be inferred to exert multiple anti-inflammatory effects against ALI through Toll-like receptor, NF-kappa B, RIG-I-like receptor, TNF, NOD-like receptor, IL-17, MAPK, and the Toll and Imd signaling pathways. In addition, two significantly regulated targets in the transcriptome, Usp18 and Map3k7, could be the essential anti-inflammatory targets of ZTOI.

CONCLUSION

By integrating network pharmacology with ingredient identification and transcriptomics, we show the multiple anti-inflammatory mechanisms by which ZTOI acts against ALI on an I-T-P level. This work also provides a methodological reference for related research into TCM.

Methodology of network pharmacology for research on Chinese herbal medicine against COVID-19: A review

Traditional Chinese medicine, as a complementary and alternative medicine, has been practiced for thousands of years in China and possesses remarkable clinical efficacy. Thus, systematic analysis and examination of the mechanistic links between Chinese herbal medicine (CHM) and the complex human body can benefit contemporary understandings by carrying out qualitative and quantitative analysis. With increasing attention, the approach of network pharmacology has begun to unveil the mystery of CHM by constructing the heterogeneous network relationship of "herb-compound-target-pathway," which corresponds to the holistic mechanisms of CHM. By integrating computational techniques into network pharmacology, the efficiency and accuracy of active compound screening and target fishing have been improved at an unprecedented pace. This review dissects the core innovations to the network pharmacology approach that were developed in the years since 2015 and highlights how this tool has been applied to understanding the coronavirus disease 2019 and refining the clinical use of CHM to combat it.

Integrated network pharmacology and metabolomics to reveal the mechanism of QiShenYiQi Dripping Pills (T101) against cardiac structural and functional abnormalities

Background: Heart failure (HF), the final stage of cardiovascular diseases, is a clinical syndrome of cardiac structural or functional abnormalities. QiShenYiQi Dripping Pills (T101), short for QSYQ (T101), showed effectiveness and safety in the treatment of HF according to modern pharmacological research and clinical studies, but the mechanism remains unclear. This study aims to clarify the mechanism of QSYQ (T101) in treating heart failure through the analysis to critical biomarkers, targets and pathways.

Materials and Methods: In this study, the efficacies of QSYQ (T101) in non-human primates and rodents were evaluated, and the mechanism was demonstrated by integrating network pharmacology and metabolomics analysis. Furthermore, the targets from network pharmacology and the metabolites from targeted metabolomics were jointly analyzed to screen the critical pathways.

Results: In rhesus monkeys with spontaneous chronic heart failure, nasogastric administration of QSYQ (T101) for 12 weeks caused profound improvement of systolic and diastolic function as evidenced by echocardiography detection. Consistently, QSYQ (T101) administration especially with higher dose lowered the blood pressure and improved the ventricular remodeling, collagen deposition and fibrosis markedly in Spontaneous Hypertension Rats (SHR) model. Computational prediction showed that QSYQ (T101) exhibited anti-HF effects possibly through HIF-1 signaling pathway, FoxO signaling pathway, TNF signaling pathway, PI3K-Akt signaling pathway and other enriched paths. Metabolomics analysis obtained 23 significantly altered metabolites, revealing that QSYQ (T101) significantly regulated the abnormal levels of fatty acids, carnitines, organic acids pyridines, nucleosides, which were mostly involved in myocardial energy metabolism related pathways.

Conclusion: Based on serum and myocardium metabolomics and network pharmacology, the present study revealed that the actions of QSYQ (T101) in treating HF depend on multi-components, multi-targets and multi-pathways.

Network pharmacology and molecular docking-based prediction of active compounds and mechanisms of action of Cnidii Fructus in treating atopic dermatitis

BACKGROUND

Atopic dermatitis (AD) is a common inflammatory skin disease that compromises the skin's barrier function and capacity to retain moisture. Cnidii Fructus (CF), the dried fruits of Cnidium monnieri, has long been used to treat atopic dermatitis (AD) in China. However, the anti-AD compounds and mechanisms of CF are not fully understood. In this study, we evaluated the active compounds and molecular targets of CF in treating AD.

METHODS

The Traditional Chinese Medicine Systems Pharmacology database was used to acquire information regarding the compounds that occur in the herb. Targets of these compounds were predicted using the SwissTargetPrediction website tool. AD-related genes were collected from the GeneCards database. Gene ontology (GO) enrichment analysis and KEGG pathway analysis of proteins that are targeted by active compounds of CF and encoded by AD-related genes were performed using Database for Annotation, Visualization, and Integrated Discovery Bioinformatics Resources. A "compound-target" network was constructed and analyzed using Cytoscape Software. Molecular docking was performed using BIOVIA Discovery Studio Visualizer and AutoDock Vina.

RESULTS

We identified 19 active compounds in CF, 532 potential targets for these compounds, and 1540 genes related to AD. Results of GO enrichment indicated that CF affects biological processes and molecular functions, such as inflammatory response and steroid hormone receptor activity, which may be associated with its anti-AD effects. KEGG pathway analyses showed that PI3K-Akt signaling, calcium signaling, Rap1 signaling, and cAMP signaling pathways are the main pathways involved in the anti-AD effects of CF. Molecular docking analyses revealed that the key active compounds in CF, such as (E)-2,3-bis(2-keto-7-methoxy-chromen-8-yl)acrolein, ar-curcumene, and diosmetin, can bind the main therapeutic targets AKT1, SRC, MAPK3, EGFR, CASP3, and PTGS2.

CONCLUSIONS

Results of the present study establish a foundation for further investigation of the anti-AD compounds and mechanisms of CF and provide a basis for developing modern anti-AD agents based on compounds that occur in CF.

The Mechanism of Crocetin Targeting Cardiovascular Disease Based on Network Pharmacology Constrained by Spectral Experiments

The network pharmacology under conditions is a recent development trend. We use network pharmacology methods to analyze the mechanism of crocetin (CRO) that regulates cardiovascular diseases. In this work, the spectral experimental data of CRO-Protein interaction is first time combined with constraint conditions to solve the problems of targeting redundancy and lack of verification. CRO targets and cardiovascular disease targets were obtained by the target database. The STRING platform was used for PPI analysis. The GO and KEGG pathways of the target were analyzed using the Metascape platform; The core functional targets of CRO were screened by molecular docking techniques and the spectra of CRO and human serum albumin (HSA). Under the collaborative constraint conditions, the core targets of CRO that regulate cardiovascular diseases are ADRA1A, ADRA1B, CHRM1, CHRM2, GABRA1, and PTGS2; This study incorporates spectroscopy and molecular docking as constraints into the network pharmacological analysis, which significantly improves the credibility of network pharmacological analysis compared with unconstrained conditions. This method provides theoretical references for the in-depth study of the mechanism between active substances and protein targets for other medicines in network pharmacology.

Advances in traditional Chinese medicine as adjuvant therapy for diabetic foot

Diabetes mellitus (DM) is a complex disease that often causes multiple systemic complications that have become a major international public health problem. Diabetic foot (DF) is one of the severe and frequent chronic complications of DM due to vascular lesions and neuropathy. DF ulcers (DFU) affect approximately 15% of people with DM and are the leading cause of death and disability. The prevalence and recurrence of DF are worrisome, and morbidity and mortality are also on the rise, which poses a substantial socioeconomic burden. Treating DF is difficult for clinicians and requires multidisciplinary cooperation, combining local and systemic therapy to reduce amputation and case-fatality rates. Traditional Chinese Medicine (TCM) has received extensive attention due to noticeable therapeutic effects and few adverse reactions. In recent years, research on DF treatment by TCM has been increasing, and further progress has been made. TCM includes oral medication, injectable preparations, and adjuvant therapy. This article reviews the relevant research on TCM-related adjuvant therapy for DF. We describe current progress in TCM in terms of external application, acupuncture, massage, acupoint injection, foot bath, fumigation, and moxibustion, as well as the mechanisms involved.

Network Pharmacology-Based Exploration on the Intervention of Qinghao Biejia Decoction on the Inflammation-Carcinoma Transformation Process of Chronic Liver Disease via MAPK and PI3k/AKT Pathway

Chronic liver disease(CLD) is a slow-developing and long-term disease that can cause serious damage to the liver. Thus far, it has been associated with viral hepatitis, non-alcoholic fatty liver disease(NAFLD), alcoholic liver disease(ALD), hepatic fibrosis(HF), liver cirrhosis (LC), and liver cancer. Qinghao Biejia Decoction (QBD) is a classic ancient Chinese herbal prescription with strong immune-enhancing, anti-inflammatory, and anti-tumor effects. In this study, we used a network pharmacology approach to investigate the molecular mechanisms of QBD in the inflammation-carcinoma transformation process of chronic liver disease. Two key drug targets, MAPK1 and PIK3CA, were screened using network pharmacology and molecular docking techniques, revealing dihydroartemisinin, artesunate, 12-O-Nicotinoylisolineolone, caffeic acid, and diincarvilone A as active ingredients involved in QBD mechanisms. The main signaling pathways involved were the PI3K-AKT signaling pathway and MAPK signaling pathway. In summary, our results indicated that QBD affects the inflammatory transformation of chronic liver disease through MAPK1 and PIK3CA and signaling pathways MAPK and PI3K/AKT. These data provide research direction for investigating the mechanisms underlying the inflammation-carcinoma transformation process in QBD for chronic liver disease.

Exploring the mechanism of Buyang Huanwu Decoction in the treatment of spinal cord injury based on network pharmacology and molecular docking

Buyang Huanwu Decoction, a traditional Chinese medicine decoction, is widely used to treat spinal cord injury in China. However, the underlying mechanism of this decoction in treating spinal cord injury is unclear. This study used network pharmacology and molecular docking to examine the pharmacological mechanism of Buyang Huanwu Decoction in prevention and treatment of spinal cord injury. The active compounds and target genes of Buyang Huanwu Decoction were collected from the Traditional Chinese Medicine Systems Pharmacology and the SwissTargetPrediction Database. The network diagram of "traditional Chinese medicine compound target" was constructed by Cytoscape software. Genetic data of spinal cord injury were obtained by GeneCards database. According to the intersection of Buyang Huanwu Decoction's targets and disease targets, the core targets were searched. The protein-protein interaction network were constructed using the STRING and BisoGenet platforms. Meanwhile, gene ontology enrichment and Kyoto encyclopedia of genes, and genome pathway were performed on the intersection targets by Metascape. Molecular docking technology was adopted to verify the combination of main components and core targets. A total of 109 active compounds and 5440 prediction targets were screened from 7 Chinese herbal medicines of Buyang Huanwu Decoction, with 98 active components and 49 related prediction targets being strongly linked to Spinal Cord Injury. By studying protein-protein interaction network, a total of 8 core proteins were identified, primarily interleukin-6, tumor protein P53, epidermal growth factor receptor, and others. Positive regulation of kinase activity regulation of reaction to inorganic chemicals are the basic biological processes. Buyang Huanwu Decoction cures Spinal Cord Injury primarily by moderating immunological inflammation, apoptosis, and oxidative stress, which involves the cancer pathway, the HIF-1 signaling pathway, the p53 signaling pathway, the MAPK signaling pathway, and so on. The results of molecular docking demonstrated that the primary components could attach to the target protein effectively. Finally, the mechanism of Buyang Huanwu Decoction in the treatment of spinal cord injury through multicomponent, multitarget, and multichannel was deeply explored. And it offers new ideas and directions for future research on the mechanism of the treatment of spinal cord injury.

Integrative pharmacology reveals the mechanisms of Erzhi Pill, a traditional Chinese formulation, against diabetic cardiomyopathy

ETHNOPHARMACOLOGICAL RELEVANCE

Erzhi Pill (EZP) is a traditional Chinese prescription that has marked effects in treating type 2 diabetes mellitus and diabetic nephropathy. However, its underlying pharmacological mechanisms in the treatment of diabetic cardiomyopathy (DCM), remain to be elucidated.

AIM OF THE STUDY

This study aimed to apply an integrative pharmacological strategy to systematically evaluate the pharmacological effects and molecular mechanisms of EZP, and provide a solid theoretical basis for the clinical application of EZP in the treatment of DCM.

MATERIALS AND METHODS

In this study, the potential targets and key pathways of EZP were predicted and validated using network pharmacology and molecular docking, respectively. Changes in cardiac metabolites and major metabolic pathways in rat heart samples were examined using ¹H-nuclear magnetic resonance (NMR) metabolomics. Finally, biochemical analysis was conducted to detect the protein expression levels of key pathways.

RESULTS

We found that EZP decreased fasting blood glucose (FBG), triglycerides (TG), total cholesterol (TC), and low-density lipoprotein (LDL) levels, increased high-density lipoprotein (HDL) levels in the serum, and alleviated the morphological abnormalities of the heart tissue in diabetic rats. Furthermore, EZP effectively restored superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), caspase-3, caspase-8, and caspase-9 activity levels, as well as the levels of reactive oxygen species (ROS), malondialdehyde (MDA), B-cell lymphoma (Bcl)-2, and Bcl-2-associated X protein (Bax) in the heart tissue. Network pharmacology prediction results indicated that the mechanism of EZP in treating DCM was closely related to apoptosis, oxidative stress, and the HIF-1, PI3K-Akt, and FoxO signaling pathways. In addition, ¹H-NMR metabolomics confirmed that EZP primarily regulated both energy metabolism and amino acid metabolism, including the tricarboxylic acid (TCA) cycle, ketone bodies metabolism, glutamine and glutamate metabolism, glycine metabolism, and purine metabolism. Finally, immunohistochemistry results indicated that EZP reduced the expression levels of p-AMPK, p-PI3K, p-Akt, and p-FoxO3a proteins, in the heart tissue of DCM rats.

CONCLUSION

The results confirmed that the overall therapeutic effect of EZP in the DCM rat model is exerted via inhibition of oxidative stress and apoptosis, alongside the regulation of energy metabolism and amino acid metabolism, as well as the AMPK and PI3K/Akt/FoxO3a signaling pathways. This study provides an experimental basis for the use of EZP in DCM treatment.

Scopolin obtained from Smilax china L. against hepatocellular carcinoma by inhibiting glycolysis: A network pharmacology and experimental study

ETHNOPHARMACOLOGICAL RELEVANCE

Smilax china L. is a well-known traditional medicinal plant. In China, it is a common anti-cancer drug that has been inherited for thousands of years. Some in vitro and in vivo studies have confirmed its potential lipid-lowering, anti-inflammatory and anti-ovarian cancer effects. However, there is no research on the material basis and mechanism of the rhizome of Smilax china L. against hepatocellular carcinoma.

AIM OF THE STUDY

To explore the material basis and mechanism of scopolin from Smilax china L. against hepatocellular carcinoma.

METHODS

The potential targets and active components of Smilax china L. against hepatocellular carcinoma were screened by transcriptomics, network pharmacology and molecular docking. Microscale Thermophoresis (MST) detection was used to verify the affinity of small molecule compounds with potential proteins and protein-protein interaction. The Extract from HepG2 cells was used to measure the expression of glycolysis-related proteins, glucose consumption and lactate production. The expression of apoptosis-related factors and glycolysis-related proteins in vivo was detected by immunohistochemistry.

RESULTS

The glycolysis-related proteins glucose-6-phosphate isomerase (GPI), glycerol-3-phosphate dehydrogenase, mitochondrial (GPD2) and phosphoglycerate kinase 2 (PGK2) screened by transcriptomics, network pharmacology showed strongly binding with scopolin by molecular docking. MST detection has also verified the affinity of scopolin with GPI and GPD2. It was the first time found that Heat shock protein HSP 90-alpha (Hsp90α) bound strongly to GPI and GPD2 in the worldwide, while scopolin was able to affect the interaction between Hsp90α and GPD2. In vitro and in vivo experiments further demonstrated that scopolin may play an anti-cancer role by affecting the stability of tumor-associated proteins. The results showed that scopolin obtained from Smilax china L. could regulate the expression of GPI, GPD2 and PGK2 and inhibit the interaction of protein-protein, reduce the energy metabolism of tumor tissue, thereby inhibit tumor growth.

CONCLUSION

Scopolin obtained from Smilax china L. plays the role of anti-hepatocellular carcinoma by regulating the expression of glycolysis proteins GPI, GPD2 and PGK2. Scopolin could affect the interaction between Hsp90α and GPD2 may provide a novel potential treatment direction for hepatocellular carcinoma.

Network Pharmacology-Based Analysis on the Potential Biological Mechanisms of Yinzhihuang Oral Liquid in Treating Neonatal Hyperbilirubinemia

Objective

Neonatal hyperbilirubinemia is caused by the excessive production of bilirubin and decreased excretion ability in the neonatal period. It leads to a concentration of blood bilirubin that exceeds a certain threshold. Yinzhihuang oral liquid (YZH) is a traditional Chinese medicine mixture used in the treatment of neonatal hyperbilirubinemia in China. This article systematically explores the pharmacological mechanisms by which YZH acts in the treatment of neonatal hyperbilirubinemia through network pharmacology at the molecular level.

Methods

We adopted the method of network pharmacology, which includes active component prescreening, target gene prediction, gene enrichment analysis, and network analysis.

Results

According to the network pharmacological analysis, 8 genes (STAT3, AKT1, MAPK14, JUN, TP53, MAPK3, ESR1, and RELA) may be targets of YZH in the treatment of neonatal hyperbilirubinemia. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that YZH may regulate antioxidation, modulate lipid metabolism, and have anti-infective properties.

Conclusion

In this study, the pharmacological action and molecular mechanisms of YZH were predicted as a whole. It was found that YZH is a promising drug for treating oxidative stress due to bilirubin, as it reduces immunosuppression and helps to eliminate virus infection.

The mechanism of the anti-inflammatory effect of Oldenlandia diffusa on arthritis model rats: a quantitative proteomic and network pharmacologic study

BACKGROUND

In China, Oldenlandia diffusa (OD) has been prescribed as a therapeutic herb for rheumatoid arthritis (RA). We previously conducted a preliminary study of the anti-inflammatory effect of OD, and the purpose of this study is to further investigate its mechanism.

METHODS

We performed a quantitative proteomic analysis of synovium, identified the differentially expressed proteins, and performed bioinformatics analyses. With the help of network pharmacology, we aimed to find the key synovial proteins which OD or its key compound might influence. To verify the result, liquid chromatography-mass spectrometry (LC-MS) was applied to quantify and qualify the absorbable potential compounds of OD. The anti-inflammatory effect was evaluated by morphological, histopathological, and cytokine analyses. Target proteins were observed by immunohistochemistry (IHC) and enzyme-linked immunosorbent assay (ELISA).

RESULTS

MMP3 and CAV1 were identified as 2 of the differentially expressed proteins in RA synovium, and might be influenced by quercetin, the active compound of OD. MMP3 might be altered through atherosclerosis signaling, while CAV1 might be altered through caveolar-mediated endocytosis signaling. According to our verification, quercetin was identified as the absorbed and effective compound of OD, and it could exert an anti-inflammatory effect on the collagen-induced arthritis (CIA) model, including serum cytokine expression, synovial hyperplasia and lymphocyte infiltration, articular cartilage lesion. Quercetin could also down-regulate the synovial expression of MMP3 and CAV1, and could exert better effects at a high dose.

CONCLUSIONS

Quercetin was the main active compound of OD in the treatment of RA. OD might alleviate inflammatory responses in CIA rats by suppressing the expression of MMP3 and CAV1 through quercetin, and at a high dose, quercetin could exert a better anti-inflammatory effect.

Study on the Potential Mechanism of Semen Strychni against Myasthenia Gravis Based on Network Pharmacology and Molecular Docking with Experimental Verification

Background

Semen Strychni (SS) is an effective Chinese medicine formula for treating myasthenia gravis (MG) in clinics. Nonetheless, its molecular mechanism is largely unknown.

Objective

Using network pharmacology, molecular docking, and experimental validation, we aim to identify the therapeutic effect of SS on MG and its underlying mechanism.

Methods

The main ingredients of SS and their targets and potential disease targets for MG were extracted from public databases. The protein-protein interaction (PPI) network was constructed using the STRING 11.0 database, and Cytoscape was used to identify the hub targets. In addition, Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to identify molecular biological processes and signaling pathways. Then, AutoDock Via conducted molecular docking. The experimental autoimmune myasthenia gravis (EAMG) model in female Lewis rats, quantitative real-time polymerase chain reaction (qRT-PCR), Western blot, and enzyme-linked immunosorbent assay (ELISA) were performed to confirm the effect and mechanism of SS on MG.

Results

The following active compounds and hub targets were identified by screening and analyzing: isobrucine, vomicine, (S)-stylopine, strychnine, brucine-N-oxide, brucine and AKT1, MAPK1, MAPK14, CHRM1, ACHE, and CHRNA4. KEGG enrichment analyses indicated that the cholinergic synapse and neuroactive ligand-receptor interaction signaling pathway may be necessary. The results of molecular docking revealed that the main active ingredients bind well to the hub targets. In vivo experiments proved that SS could improve the weight loss and Lennon scores in the EAMG model. Experiments in molecular biology showed that SS could treat MG by affecting the cholinergic synapse through the respective antibody, receptor, and key enzymes in the cholinergic pathway.

Conclusion

This study provided a preliminary overview of the active constituents, primary targets, and potential pathways of SS against MG. SS ameliorated EAMG by regulating the cholinergic synaptic junction.

Exploring the Protective Effects and Mechanism of Huaji Jianpi Decoction against Nonalcoholic Fatty Liver Disease by Network Pharmacology and Experimental Validation

This paper was designed to predict the mechanisms of the active components of Huaji Jianpi Decoction (HJJPD) against nonalcoholic fatty liver disease (NAFLD) based on network pharmacology-combined animal experiments. The candidate compounds of HJJPD and its relative targets were obtained from TCMSP and PharmMapper web server, and the intersection genes for NAFLD were discerned using OMIM, GeneCards, and DisGeNET. Then, the target protein-protein interaction (PPI) and component-target-pathway networks were constructed. Moreover, gene function annotation (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to study the potential signaling pathways associated with HJJPD’s effect on NAFLD. Molecular docking simulation was preformed to validate the binding affinity between potential core components and key targets. Eventually, the candidate targets, the possible pathway, and the mechanism of HJJPD were predicted by the network pharmacology-based strategy, followed by experimental validation in the NAFLD mice model treated with HJJPD. A total of 55 candidate compounds and 36 corresponding genes were identified from HJJPD that are associated with activity against NAFLD, and then the network of them was constructed. Inflammatory response and lipid metabolism-related signaling pathways were identified as the critical signaling pathways mediating the therapeutic effect of the active bioactive ingredients on NAFLD. Compared with the model group, the liver wet weight, liver/body ratio, the levels of total cholesterol (TC), triglyceride (TG), aspartate aminotransferase (AST), alanine aminotransferase (ALT), and high-density lipoprotein (HDL) in serum in the HJJPD low-dose (17.52 g/kg·d), medium-dose (35.04 g/kg·d), and high-dose (70.07 g/kg·d) groups significantly decreased ( $P<0.05$ ). Light microscope observation shows that HJJPD could control the degree of lipid denaturation of the mouse liver tissue to a great extent. RT-qPCR results show that the mRNA expression levels of peroxisome proliferative activated receptor gamma (PPARG), tumor necrosis factor-α (TNF-α), antiserine/threonine protein kinase 1 (AKT1), and prostaglandin-endoperoxide synthase (PTGS2) in the liver tissues of the three HJJPD groups (17.52 g/kg·d, 35.04 g/kg·d, and 70.07 g/kg·d) were significantly lower than those in the model group ( $P<0.05$ ). HJJPD can exert its effect by inhibiting hepatic steatosis and related mRNA expression and decreasing the levels of other liver-related indexes. This study suggested that HJJPD exerted its effect on NAFLD by modulating multitargets with multicompounds through multipathways. It also demonstrated that the network pharmacology-based approach might provide insights for understanding the interrelationship between complex diseases and interventions of HJJPD.

Mechanism of Shishiwei Wendan Decoction in the Prevention and Treatment of Lung Adenocarcinoma Using Network Pharmacology and Molecular Docking

Objective

This study used network pharmacology and molecular docking technology to elucidate the mechanism of action of Shishiwei Wendan Decoction against lung adenocarcinoma.

Methods

By using the world's largest TCM System Pharmacology Database and Analysis Technology Platform (TCMSP) system to conduct in-depth mining analysis and data collection of the main active components of the medicinal components in Shishiwei Wendan Decoction and using the human gene card database (GeneCards), Human Mendelian Inheritance Online System (OMIM), and Human Disease-Related Gene and Mutation Information Database (DisGeNET) to collect the pathogenic targets of lung adenocarcinoma and build a PPI network; for the core drug targets, use GO enrichment analysis and KEGG pathway analysis; use Cytoscape software to build relevant network maps; and use AutoDock to achieve molecular docking.

Results

Shishiwei Wendan Decoction screened 144 active ingredients and 384 drug targets; 7680 lung adenocarcinoma disease targets were obtained, including 380 targets for Shishiwei Wendan Decoction in the treatment of lung adenocarcinoma. GO enrichment analysis demonstrated 2,299 downstream genes, and key target genes were closely related to nutrient levels, membrane rafts, and protein serine/threonine kinase activity; KEGG functional enrichment analysis yielded 179 related pathways, including tumor necrosis factor signaling pathway which is related to the target gene. Molecular docking showed that the core active ingredients and key targets could be well combined.

Conclusion

Through the network pharmacology analysis and molecular docking experiments of Shishiwei Wendan Decoction against lung adenocarcinoma, it is found that Shishiwei Wendan Decoction has multidimensional effects on the treatment of lung adenocarcinoma, and it is the first Shiwei Wendan Decoction to treat lung adenocarcinoma. Decoction in the treatment of lung adenocarcinoma provides biointellectual support and the oretical support.

Traditional chinese medicine to prevent and treat diabetic erectile dysfunction

Diabetic erectile dysfunction (DED) is one of the most common complications of diabetes mellitus. However, current therapeutics have no satisfactory effect on DED. In recent years, traditional Chinese medicine (TCM) has shown good effects against DED. By now, several clinical trials have been conducted to study the effect of TCM in treating DED; yet, the underlying mechanism is not fully investigated. Therefore, in this review, we briefly summarized the pathophysiological mechanism of DED and reviewed the published clinical trials on the treatment of DED by TCM. Then, the therapeutic potential of TCM and the underlying mechanisms whereby TCM exerts protective effects were summarized. We concluded that TCM is more effective than chemical drugs in treating DED by targeting multiple signaling pathways, including those involved in oxidation, apoptosis, atherosclerosis, and endothelial function. However, the major limitation in the application of TCM against DED is the lack of a large-scale, multicenter, randomized, and controlled clinical trial on the therapeutic effect, and the underlying pharmaceutical mechanisms also need further investigation. Despite these limitations, clinical trials and further experimental studies will enhance our understanding of the mechanisms modulated by TCM and promote the widespread application of TCM to treat DED.

Decoding the Mechanism of CheReCunJin Formula in Treating Sjögren's Syndrome Based on Network Pharmacology and Molecular Docking

Background

Sjögren's syndrome (SS) is a chronic autoimmune disease characterized by progressive oral and ocular dryness that correlates poorly with autoimmune damage to the glands. CheReCunJin (CRCJ) formula is a prescription formulated according to the Chinese medicine theory for SS treatment.

Objective

This study aimed to explore the underlying mechanisms of CRCJ against SS.

Methods

The databases, including Traditional Chinese Medicine System Pharmacology, Encyclopedia of Traditional Chinese Medicine, Bioinformatics Analysis Tool for the molecular mechanism of Traditional Chinese Medicine, and Traditional Chinese Medicine Integrated Databases, obtained the active ingredients and predicted targets of CRCJ. Then, DrugBank, Therapeutic Target Database, Genecards, Comparative Toxicogenomics Database, and DisGeNET disease databases were used to screen the predicted targets of SS. Intersected targets of CRCJ and SS were visualized by using Venn diagrams. The overlapping targets were uploaded to the protein-protein interaction network analysis search tool. Cytoscape 3.8.2 software constructed a "compound-targets-disease" network. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes analyses characterized potential targets' biological functions and pathways. AutoDock Vina 1.1.2 software was used to research and verify chemical effective drug components and critical targets.

Results

From the database, we identified 878 active components and 2578 targets of CRCJ, and 827 SS-related targets. 246 SS-related genes in CRCJ were identified by intersection analysis, and then ten hub genes were identified as crucial potential targets from PPI, including ALB, IL-6, TNF, INS, AKT1, IL1B, VEGFA, TP53, JUN, and TLR4. The process of CRCJ action against SS was mainly involved in human cytomegalovirus infection and Th17 cell differentiation, as well as the toll-like receptor signaling and p53 signaling pathways. Molecular docking showed that the bioactive compounds of CRCJ had a good binding affinity with hub targets.

Conclusions

The results showed that CRCJ could activate multiple pathways and treat SS through multiple compounds and targets. This study lays a foundation for better elucidation of the molecular mechanism of CRCJ in the treatment of SS, and also provides basic guidance for future research on Chinese herbal compounds.

The Evaluation of Xiaozeng Qianggu Tablets for Treating Postmenopausal Osteoporosis via up-Regulated Autophagy

Objective. Postmenopausal osteoporosis (PMOP) is a common age-associated disease in the life course. Clinically, Xiaozeng Qianggu Tablets (XQT) have a potent therapeutic effect on the PMOP. However, the bioactive components and the mechanism of XQT underlying the PMOP treatment were unclear and it should be explored to discover the scientific connotation in traditional medical practice. Methods. The components in XQT were identified by UPLC-Q-TOF/MS. The animal model of PMOP was established by surgical ovariectomy in the female Sprague-Dawley rats. After treatment of XQT, the therapeutic effect was assessed by the determination of bone metabolism biomarkers in serum and histopathological examination. The effect of XQT on the autophagy and bone micro-situation were tested using western blot, RT-qPCR, and transmission electron microscope. Results. There were 27 compounds identified in XQT, including catalpol, monotropein, verbascoside, cryptochlorogenic acid, 5,7-dihydroxychromone 7-rutinoside, biorobin, and so on. The bone metabolism markers (alkaline phosphatase, bone alkaline phosphatase, procollagen type I intact N-terminal propeptide, cross-linked carboxy-terminal telopeptide of type I collagen, and tartrate-resistant acid phosphatase) were significantly increased in the PMOP rats and reversed by XQT administration. Moreover, the width of bone trabeculae and the ratio of the area of calcium deposition to bone trabeculae were also improved after treating the middle dose of XQT. Meanwhile, the bone micro-structure was improved by XQT. The mRNA and protein expression of unc-51 like kinase 1, beclin-1, and microtubule-associated protein 1B-light chain 3 in PMOP rats were down-regulated and up-regulated by XQT administration. Conclusions. The compounds in XQT, including catalpol, monotropein, verbascoside cryptochlorogenic acid, and so on, were valuable for further pharmacy evaluation. The pathological changes and bone micro-structure were improved by XQT, and the down-regulated autophagy level was also restored, which suggested a potent effect of XQT on treating PMOP, corresponding to its clinic use.

One of the active ingredients in Paeoniae Radix Alba functions as JAK1 inhibitor in rheumatoid arthritis

Objective: We aimed to explore and verify the mechanism underlying the action of the active ingredients of Paeoniae Radix Alba (PRA) in the treatment of rheumatoid arthritis (RA).

Methods: The protein targets of PRA’s six active ingredients and RA were identified. Then, the intersection of the two groups was studied. The drug–target network was constructed, visualized, and analyzed by Cytoscape software. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were performed to analyze these genes. Furthermore, we validated our predictions of the potential targets through a docking study. Finally, the anti-inflammatory effect of Palbinone (PB), one of the active ingredients of PRA, was tested by conducting in vitro and in vivo studies.

Results: Six active ingredients of PRA were identified, and 103 overlapping genes were discovered. Functional enrichment analysis indicated that the genes are mostly enriched in IL-17 signaling pathway, Th17 cell differentiation, and the FoxO, ErbB, and TNF signaling pathways. 10 hub genes and two gene cluster modules were identified by Cytoscape. Molecular docking analysis proved that PB was able to bind to the ATP binding site of Janus kinase (JAK)1, thereby acting as a potential inhibitor of JAK1. In vitro and in vivo studies demonstrated that PB exerts its anti-inflammatory role via the inhibition of JAK1.

Conclusion: We constructed a multitarget pharmacological network of PRA in RA treatment. PB, one of the active compounds of PRA, was demonstrated to be a promising inhibitor of JAK1.

Identification of Interleukin-1-Beta Inhibitors in Gouty Arthritis Using an Integrated Approach Based on Network Pharmacology, Molecular Docking, and Cell Experiments

Background

This study aimed to investigate the molecular mechanism of Tongfengding capsule (TFDC) in treating immune-inflammatory diseases of gouty arthritis (GA) and interleukin-1-beta (IL-1β) inhibitors by using network pharmacology, molecular docking, and cell experiments.

Methods

In this study, the compounds of TFDC and the potential inflammatory targets of GA were obtained from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), Online Mendelian Inheritance in Man (OMIM), and GeneCards databases. The TFDC-GA-potential targets interaction network was accomplished by the STRING database. The TFDC-active compound-potential target-GA network was constructed using Cytoscape software. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to further explore the GA mechanism and therapeutic effects of TFDC. Quantitative real-time PCR (qPCR) was used to verify whether the TFDC inhibited IL-1β in GA. Molecular docking technology was used to analyze the optimal effective compounds from the TFDC for docking with IL-1β.

Result

133 active compounds and 242 targets were screened from the TFDC, and 25 of the targets intersected with GA inflammatory targets, which were considered as potential therapeutic targets. Network pharmacological analysis showed that the TFDC active compounds such as quercetin, stigmasterol, betavulgarin, rutaecarpine, naringenin, dihydrochelerythrine, and dihydrosanguinarine had better correlation with GA inflammatory targets such as PTGS2, PTGS1, NOS2, SLC6A3, HTR3A, PPARG, MAPK14, RELA, MMP9, and MMP2. The immune-inflammatory signaling pathways of the active compounds for treating GA are IL-17 signaling pathway, TNF signaling pathway, NOD-like receptor signaling pathway, NF-kappa B signaling pathway, Toll-like receptor signaling pathway, HIF-1 signaling pathway, etc. The TFDC reduced IL-1β mRNA expression in GA by qPCR. Molecular docking results suggested that rutaecarpine was the most appropriate natural IL-1β inhibitor.

Conclusion

Our findings provide an essential role and bases for further immune-inflammatory studies on the molecular mechanisms of TFDC and IL-1β inhibitors development in GA.

Potential molecular mechanisms of Ermiao san in the treatment of hyperuricemia and gout based on network pharmacology with molecular docking

A network pharmacology integrated molecular docking strategy was used to predict the underlying molecular mechanism of Ermiao san in the treatment of hyperuricemia and gout. Traditional Chinese medicine systems pharmacology (TCMSP) database and analysis platform were used to screen out the active compounds and their targets of Ermiao san. The disease target genes related to hyperuricemia (HUA) and gout were obtained by searching CTD, DisGeNET, DrugBank, GeneCards, OMIM, TTD, and PharmGKB databases with "Hyperuricemia" and "Gout" as keywords, respectively. The potential targets of Ermiao san in the treatment of HUA and gout were screened through a Venn diagram. The protein-protein interaction network was constructed using Cytoscape software. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were then conducted. Finally, some compounds and core targets were selected for molecular docking verification by Autodock Vina and Pymol software. Forty-six active compounds, such as quercetin, wogonin and beta-sitosterol, etc were identified. Ermiao san plays a therapeutic role in HUA and gout regulating various biological processes, cellular compounds, and molecular functions. The core targets of Ermiao san for treating HUA and gout are AT1 (namely Protein Kinase Bα), interleukin-1 beta, prostaglandin-endoperoxide synthase 2, JUN, etc. And the key pathways are nuclear factor-κB, interleukin-17 and tumor necrosis factor. The results of molecular docking analyses suggested that active compounds of Ermiao san could bind well to the core protein receptors. Ermiao san has a synergistic mechanism of multiple compounds, multiple targets, and multiple pathways in the treatment of HUA and gout, which provides a good theoretical basis for the clinical application.

Integrated metabolomics and network pharmacology to reveal the mechanisms of Guizhi-Fuling treatment for myocardial ischemia

Myocardial ischemia is a cardio-physiological condition caused by a decrease in blood perfusion to the heart, resulting in reduced oxygen supply and abnormal myocardial energy metabolism. Guizhi-Fuling (GZFL) is effective in treating Myocardial ischemia. However, its mechanism of action remains unclear and requires further exploration. we hope to reveal the mechanisms of GZFL treating Myocardial ischemia by integrating metabolomics and network pharmacology. In this study, myocardial metabolomic analysis was first performed using GC-MS to discover the potential mechanism of action of GZFL on myocardial ischemia. Then, network pharmacology was used to analyze key pathways and construct a pathway-core target network. Molecular docking was used to validate core targets in network pharmacological signaling pathways. Finally, western blots were used to verify core targets of metabolomics and network pharmacology integrated pathways as well as key targets in signaling pathways. As a result, we identified 22 important biomarkers of GZFL for the treatment of myocardial ischemia. Most of these metabolites were restored by modulation after GZFL treatment. Based on the network pharmacology, 297 targets of GZFL in the treatment of myocardial ischemia were obtained. The further comprehensive analysis focused on 3 key targets, including Tyrosine hydroxylase (TH), myeloperoxidase (MPO), and phosphatidylinositol 3-kinases (PIK3CA), and their associated metabolites and pathways. Compared with the model group, the protein expression levels of TH, MPO and PIK3CA were decreased in GZFL. Therefore, the mechanism of GZFL for treating myocardial ischemia may be to inhibit myocardial inflammatory factors, reduce myocardial inflammation, and restore endothelial function, while regulating norepinephrine release and uric acid concentration.

Network pharmacology-based investigation and experimental validation of the mechanism of scutellarin in the treatment of acute myeloid leukemia

Background: It has been demonstrated that scutellarin, a natural flavone compound from Scutellaria lateriflora and Scutellaria barbata, exerts selective cytotoxicity against a range of cancer cells. However, the underlining mechanism of scutellarin on acute myeloid leukemia (AML) remains elusive.

Methods: In this study, the combination of network pharmacology and experimental verification was performed to identify the pharmacological mechanisms of scutellarin for AML therapy. The public databases, such as PharmMapper, UniProt, OMIM, GeneCards, DrugBank and PharmGkb database, were used to sceen the potential targets of scutellarin and AML. The protein-protein interaction (PPI), gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were conducted to uncover the mechanism of scutellarin in the treatment of AML. Finally, the network pharmacological results were further confirmed by in vitro and in vivo experiments.

Results: First and foremost, we totally obtained 289 target genes for scutellarin and 10998 disease targets for AML. 253 overlapping genes were preliminarily considered the potential targets of scutellarin for AML treatment. The results of PPI network analysis, GO analysis and KEGG pathway enrichment demonstrated that the anti-AML effect of scutellarin may focused on MAPK signaling pathway. Furthermore, the cytologic tests suggested that scutellarin can inhibit AML cells proliferation through the mediation of JNK/Caspase-3 pathway. Meanwhile, pretreatment with the JNK inhibitor SP600125 rescued scutellarin-induced apoptosis. Similarly, scutellarin obviously suppressed subcutaneous xenograft growth in nude mice via regulating the JNK/Caspase-3 signaling pathway.

Conclusion: In this study, we integrated network pharmacology-based prediction and experimental validation and revealed the importance of the JNK pathway in scutellarin-mediated AML treatment.

Mechanisms of Intervertebral Disc Degeneration Treatment with Deer Antlers Based on Network Pharmacology and Molecular Docking

Background

With the aging of the population, the prevalence of IVDD increases preoperatively. How to better treat IVDD has become an important clinical issue. Deer antlers proved to have a great effect on the treatment of IVDD in many studies, but the molecular mechanism has not been clarified.

Objective

To investigate the molecular mechanism and target of deer antlers in the treatment of IVDD.

Methods

Compounds from deer antlers were collected and targets were predicted using HERB, TCMSP, TCMID, SwissADME, and SwissTargetPrediction. Collection of disease targets for IVDD was done using GeneCards, TTD, DrugBank, DisGeNET, and OMIM. Cytoscape 3.7.2, AutoDock Vina (v1.1.2), and R software were used for data analysis and the construction of network diagrams.

Results

A total of 5 active compounds from deer antlers were screened and 104 therapeutic targets were predicted. A total of 1023 IVDD disease targets were collected. Subsequently, PPI network prediction analysis was performed for disease and treatment targets, and 112 core targets were collected after screening. After obtaining the core target, we used the clusterProfiler software package of R software to carry out GO and KEGG enrichment analyses for the core target and plot the bubble maps. According to the GO enrichment results, the main biological processes of IVDD treatment by deer antlers lie in the rhythmic process, mRNA catabolic process, and G1/S transition of the mitotic cell cycle. KEGG results were mainly related to the PI3K-Akt signaling pathway, thyroid hormone signaling pathway, and Notch signaling pathway. Molecular docking results showed that estrone had the best docking results on ESR1.

Conclusion

Deer antlers are rich in various compounds that can prevent the development of IVDD by upregulating the PI3K-Akt signaling pathway and Notch signaling pathway. Its key compounds estradiol and estrone can reduce the inflammatory response and oxidative stress in tissues and organs, thus slowing down the progression of IVDD. Estrone, the active compound in deer antlers, was found by molecular docking to have good results against ESR1, the target of the disease, which may be a potential site for drug therapy.

Network pharmacology provides a systematic approach to understanding the treatment of ischemic heart diseases with traditional Chinese medicine

BACKGROUND

The field of network pharmacology showed significant development. The concept of network pharmacology has many similarities to the philosophy of traditional Chinese medicine (TCM), making it suitable to understand the action mechanisms of TCM in treating complex diseases, such as ischemic heart diseases (IHDs).

PURPOSE

This review summarizes the representative applications of network pharmacology in deciphering the mechanism underlying the treatment of IHDs with TCM.

METHODS

In this report, we used "ischemic heart disease" OR "coronary heart disease" OR "coronary artery disease" OR "myocardial ischemia" AND ("network pharmacology" OR "systematic pharmacology") as keywords to search for publications from PubMed, the Web of Science, and Google Scholar databases and then analyzed the representative research reports that summarized and validated the active components and targets network of TCM in improving IHDs to show the advantages and deficiencies of network pharmacology applied in TCM research.

RESULTS

The network pharmacology research indicated that HGF, PGF, MMP3, INSR, PI3K, MAPK1, SRC, VEGF, VEGFR-1, NO, eNOS, NO3, IL-6, TNF-α, and more are the main targets of TCM. Apigenin, 25S-macrostemonoside P, ginsenosides Re, Rb3, Rg3, SheXiang XinTongNing, colchicine, dried ginger-aconite decoction, Suxiao Xintong dropping pills, Ginseng-Danshen drug pair and Shenlian and more are the active ingredients, extracts, and formulations of TCM to ameliorate IHDs. These active compounds, extract, and formulations of TCM treat IHDs by delaying ventricular remodeling, reducing myocardial fibrosis, decreasing reactive oxygen species, regulating myocardial energy metabolism, ameliorating inflammation, mitigating apoptosis, and many other aspects.

CONCLUSIONS

The network pharmacology supplies a novel research exemplification for understanding the treatment of IHDs with TCM. However, the application of network pharmacology in TCM studies is still at a superficial level. By rational combining artificial intelligence technology and network pharmacology, molecular biology, metabolomics, and other advanced theories and technologies, and systematically studying the metabolic process and the network among products, targets, and pathways of TCM from the clinical perspective may be a potential development trend in network pharmacology.

Study on the mechanism of Ginseng-Gegen for mesenteric lymphadenitis based on network pharmacology

BACKGROUND

This study aimed to determine the main active ingredients of the Ginseng-Gegen (Panax Ginseng-Radix Puerariae) drug pair, to predict relevant action targets, and to establish a network of "drug-active ingredients-targets", to ultimately explore the mechanism of Ginseng-Gegen in the treatment of mesenteric lymphadenitis.

METHODS

The Traditional Chinese Medicine Systems Pharmacology (TCMSP) platform was used to screen the chemical constituents of Ginseng-Gegen, and the active ingredient targets were retrieved by UniProt database. The databases of GeneCards and the Online Mendelian Inheritance in Man (OMIM) were applied to search for mesenteric lymphadenitis-related targets. Cytoscape software was used to construct the network of active ingredient-action targets. The biological functions of the targets were analyzed in the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database.

RESULTS

A total of 26 potential active ingredients of the Ginseng-Gegen drug pair were screened, with 128 drug-related targets and 255 mesenteric lymphadenitis-related targets. After matching, 23 potential targets were obtained for treating mesenteric lymphadenitis. Among them, MOL012297 (puerarin), MOL005344 (ginsenoside Rh2), and MOL000358 (beta-sitosterol) were linked to 3 or more key target genes. They were supposed to be important ingredients of Ginseng-Gegen in the treatment of mesenteric lymphadenitis.

CONCLUSIONS

Ginseng-Gegen is related to oxidative stress and inflammation, and it is a part of the nuclear factor κB (NF-κB) signaling pathway, tumor necrosis factor (TNF) signaling pathway, and the advanced glycation end products/receptor for advanced glycation end products (AGE-RAGE) signaling pathway. These biological processes and signaling pathways may be potential mechanisms of Ginseng-Gegen for treating mesenteric lymphadenitis.

Active Compounds Screening and Hepatoprotective Mechanism of Shuganning Injection Based on Network Pharmacology and Experimental Validation

Objective: The study aimed to analyze the core active compounds and the potential mechanism of Shuganning injection (SGNI) through network pharmacology with biological experiments. Methods: Active compounds and targets of SGNI were screened from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and Targetnet database, whereas the liver disease-related targets were identified through the Genecards and Online Mendelian Inheritance in Man databases. The “compound-target” and “protein-protein interaction” networks construction, core target identification, and pathway enrichment were then performed. Finally, the exploration of the mechanism of action for SGNI against acetaminophen (APAP)-induced liver injury in the HepaRG cells and validation of three identified protein targets was also carried out through western blot assay, including tumor protein p53 (p53, TP53), transcription factor Jun (Jun), and Caspase 3 (CASP3). Results: The result showed that a total of 312 active compounds of SGNI and 408 liver disease-related targets, as well as 131 core targets were revealed through databases, such as prostaglandin G/H synthase 1, prostaglandin G/H synthase 2, and nuclear factor NF-kappa B (NF-kB) p65 subunit (RELA). The core targets of SGNI were involved in regulating hepatitis B signaling pathway, NF-kB signaling pathway, Toll-like receptor signaling pathway, and tumor necrosis factor (TNF) signaling pathway. Moreover, results of molecular docking in this study indicated that chlorogenic acid, geniposide, baicalin, indirubin, and ganoderic acid A could act on RELA, JUN, TP53, TNF, CASP3, Caspase 8 (CASP8) and nuclear factor NF-kB p105 subunit (NFKB1). Similarly, results of western blot revealed that SGNI reduced the expression of p53, Jun, and Caspase 3 proteins in HepaRG cells as compared with the APAP group ( P < 0.01 or P < 0.05). Conclusion: The present study verified the therapeutic effects and mechanism of SGNI on liver diseases and pointed out new directions for further research.

Integrated RNA-sequencing and network pharmacology approach reveals the protection of Yiqi Huoxue formula against idiopathic pulmonary fibrosis by interfering with core transcription factors

BACKGROUND

Idiopathic pulmonary fibrosis (IPF) is a refractory disease. Therefore, developing effective therapies for IPF is the need of the hour.

PURPOSE

Yiqi Huoxue Formula (YQHX) is an herbal formula comprising three herbal medicines: Ligusticum chuanxiong Hort. (Chuanxiong Rhizoma, CR), Panax notoginseng (Burk.) F. H. Chen (Notoginseng Radix Et Rhizoma, NR) and Panax ginseng C. A. Mey. (Ginseng Radix Et Rhizoma, GR). This study aims to determine the anti-pulmonary fibrosis effect of YQHX and explore its mechanism of action.

STUDY

Design and Methods: The chemical components in the GR, CR and NR extracts were identified by High Performance Liquid Chromatography. A TGF-β1-induced myofibroblast cell model was used to test the anti-fibrosis effect of GR, CR, NR and YQHX. RNA-sequencing was used to identify the differentially expressed genes (DEGs) after YQHX treatment. Subsequently, gene enrichment analysis and key transcription factors (TFs) prediction for YQHX-regulated DEGs was performed. The active constituents of GR, CR and NR were obtained from the Traditional Chinese Medicine Database and Analysis Platform. Targets of the active constituents were predicted using the similarity ensemble approach search server and Swiss Target Prediction tool. YQHX-targeted key TFs that transcribed the DEGs were screened out. Then, the effect of YQHX on the bleomycin-induced pulmonary fibrosis mouse model was studied. Finally, one of the predicted TFs, STAT3, was selected to validate the prediction accuracy.

RESULTS

Seven, two, and five compounds were identified in the GR, CR, and NR extracts, respectively. YQHX and its constituents-GR, CR and NR-inhibited the expression of fibrotic markers, including α -SMA and fibronectin, indicating that YQHX inhibited TGF-β1-induced myofibroblast activation. RNA-sequencing identified 291 genes that were up-regulated in the TGF-β1 group but down-regulated after YQHX treatment. In total, 55 key TFs that transcribed YQHX-regulated targets were predicted. A regulatory network of 24 active ingredients and 232 corresponding targets for YQHX was established. Among YQHX's predicted targets, 20 were TFs. On overlapping YQHX-targeted TFs and DEGs' key TFs, six key TFs, including HIF1A, STAT6, STAT3, PPARA, DDIT3 and AR, were identified as the targets of YQHX. Additionally, YQHX alleviated bleomycin-induced pulmonary fibrosis in a mouse model by inhibiting the phosphorylation of STAT3 in the lungs of pulmonary fibrosis mice.

CONCLUSIONS

This study provides pharmacological support for the use of YQHX in the treatment of IPF. The potential mechanism of action of YQHX is speculated to involve the modulation of core TFs and inhibition of pathogenetic gene expressions in IPF.

Metabolomics Combined with Network Pharmacology-Based Strategy to Reveal the Underlying Mechanism of Zhenhuang Submicron Emulsion in Treating Oropharyngeal Mucositis Complications of Radiation Therapy for Head and Neck Cancer

Introduction

Head and neck tumors account for more than 6% of all cancers. The primary treatment for tumors of the head and neck is radiation therapy, which can induce oropharyngeal mucositis as a side effect. At present, there is no widely available therapeutic for the treatment of oropharyngeal mucositis in clinical practice. Based on the traditional prescription Liushen Wan, the pathogenesis and pathology, we developed a new Chinese medicine prescription and made Zhenhuang submicron emulsion (ZHSE) spray, which has an efficacious therapeutic effect for oropharyngeal mucositis. However, its mechanism is unclear.

Methods

This research explored the mechanism behind the modulatory effects of ZHSE by a strategy of metabolomics and network pharmacology. Multivariate data analyses, including unsupervised principal component analysis (PCA) and supervised orthogonal partial least squares discriminant analysis (OPLS-DA), were performed. Potential biomarkers were identified depending on the mass-charge ratio of the selected compound. Statistical and pathway enrichment analysis was performed in the KEGG pathway database. Network pharmacology combining metabolomic analyses was conducted to illustrate the key targets and pathways.

Results

Critical metabolic pathways were investigated, 56f biomarkers were enriched and key metabolites such as linoleic acid, 9,10-epoxyoctadecenoic acid, acetoacetic acid and citric acid were identified. A complex network of “compound-target-potential metabolite” interactions was drawn to illuminate the regulation of chemical constituents on key metabolites. These findings manifest that ZHSE regulates endogenous metabolite disorders during the treatment of oropharyngeal mucositis by various constituents, interacting with multiple targets associated with inflammation and pain.

Conclusion

In this work, we determined several critical biomarkers and metabolic pathways and identified the possible regulatory mechanism by which ZHSE functions in the treatment of oropharyngeal mucositis. This study provides a new perspective on integrating metabolomics and network pharmacology for exploring improved therapy for head and neck tumors based on the traditional classic prescription of LSW.

Combining Network Pharmacology with Experimental Validation to Elucidate the Mechanism of Salvianolic Acid B in Treating Diabetic Peripheral Neuropathy

Background. Salvianolic acid B (Sal B) is a bioactive component of Radix Salviae, which has antiinflammation and antiapoptotic activity in diabetic complications. However, the molecular mechanism of action of Sal B on diabetic peripheral neuropathy (DPN) is unknown. This study was designed to identify a mechanism for Sal B in the treatment of DPN by using a pharmacology network, molecular docking, and in vitro experiments. Methods. Sal B and DPN-related targets from Gene Cards and OMIM platforms were retrieved and screened. Then, an analysis of possible targets with STRING and Cytoscape software was conducted. KEGG signaling pathways were determined using the R software. Subsequently, the binding capacity of Sal B to target proteins was analyzed by molecular docking and in vitro experiments. Results. A total of 501 targets related to Sal B and 4662 targets related to DPN were identified. Among these targets, 108 intersection targets were shared by Sal B and DPN. After topological and cluster analysis, 11 critical targets were identified, including p38MAPK. KEGG analysis revealed that the AGE-RAGE signaling pathway likely plays an important role in Sal B action on DPN. The p38MAPK protein is a key target in the AGE-RAGE signaling pathway. Molecular docking results suggested that Sal B and p38MAPK have excellent binding affinity (<−5 kcal/mol). The in vitro experiments revealed that Sal B downregulates the expressions of p-P38MAPK, inflammatory cytokines, and apoptosis targets, which are upregulated by hyperglycemia. Conclusion. Sal B may alter DPN by inhibiting inflammation and apoptosis activated by p38MAPK.

Pharmacological Mechanism of Zuojin Pill for Gastroesophageal Reflux Disease: A Network Pharmacology Study

Background. Although Zuojin Pill (ZJP) is widely used in China as a traditional prescription to treat gastroesophageal reflux disease (GERD), its exact mechanism of action is still unknown. Therefore, we employed network pharmacology (NP), molecular docking (MD), and molecular dynamics simulation (MDS) to investigate the pharmacological mechanisms of ZJP against GERD. Methods. Active compounds and target genes corresponding to ZJP and target genes related to GERD were identified through analysis of publicly available datasets. Subsequently, the obtained data were subjected to further network pharmacological analysis to explore the potential key active compounds, core target genes, and biological processes (BPs) associated with the effect of ZJP against GERD. Finally, the prediction results of NP were validated by MD, and MDS of the optimal core protein-ligand for each component obtained by MD were performed using Gromacs 2020 software. Results. Twelve active components of ZJP were identified to act on 82 target genes associated with GERD, and ZJP might exert an anti-GERD effect through the regulation of BPs such as reactive oxygen species (ROS) metabolism, response to oxidative stress (OS), and ROS, as well as the activation of signaling pathways such as apoptosis, p53 signaling, chemical carcinogenesis-ROS, and HIF-1 signaling pathways. Furthermore, quercetin, kaempferol, and coptisine, the three key components of ZJP were shown to stably bond with the 14 core target genes, including AKT1, MMP2, TP53, EGFR, JUN, CASP3, CXCL8, HIF1α, IL-1β, MYC, PPARG, MMP9, PTGS2, and FOS. Results from MDS showed that PPARG-quercetin and MMP2-quercetin bound more stably. Conclusions. The findings suggest that ZJP alleviates the symptoms of GERD and improves the prognosis by regulating ROS metabolism, thereby reducing the secretion of proinflammatory cytokines like IL-1β, COX-2, CXCL8, and MMPs, regulating the expression of oncogenes such as JUN and FOS, and maintaining the normal expression of tumor suppressor genes such as TP53 and MYC. However, whether the effect of this modulation of ROS metabolism is positive or negative needs to be further verified by pharmacological experiments.

Network Pharmacology, Molecular Docking, and Experimental Validation to Unveil the Molecular Targets and Mechanisms of Compound Fuling Granule to Treat Ovarian Cancer

Background

Compound fuling granule (CFG) is a traditional Chinese medicine formula that is used for more than twenty years to treat ovarian cancer (OC) in China. However, the underlying processes have yet to be completely understood. This research is aimed at uncovering its molecular mechanism and identifying possible therapeutic targets.

Methods

Significant genes were collected from Therapeutic Target Database and Database of Gene-Disease Associations. The components of CFG were analyzed by LC-MS/MS, and the active components of CFG were screened according to their oral bioavailability and drug-likeness index. The validated targets were extracted from PharmMapper and PubChem databases. Venn diagram and STRING website diagrams were used to identify intersection targets, and a protein-protein interaction network was prepared using STRING. The ingredient-target network was established using Cytoscape. Molecular docking was performed to visualize the molecule-protein interactions using PyMOL 2.3. Enrichment and pathway analyses were performed using FunRich software and Reactome pathway, respectively. Experimental validations, including CCK-8 assay, wound-scratch assay, flow cytometry, western blot assay, histopathological examination, and immunohistochemistry, were conducted to verify the effects of CFG on OC cells.

Results

A total of 56 bioactive ingredients of CFG and 185 CFG-OC-related targets were screened by network pharmacology analysis. The potential therapeutic targets included moesin, glutathione S-transferase kappa 1, ribonuclease III (DICER1), mucin1 (MUC1), cyclin-dependent kinase 2 (CDK2), E1A binding protein p300, and transcription activator BRG1. Reactome analysis showed 51 signaling pathways (P < 0.05), and FunRich revealed 44 signaling pathways that might play an important role in CFG against OC. Molecular docking of CDK2 and five active compounds (baicalin, ignavine, lactiflorin, neokadsuranic acid B, and deoxyaconitine) showed that baicalin had the highest affinity to CDK2. Experimental approaches confirmed that CFG could apparently inhibit OC cell proliferation and migration in vitro; increase apoptosis; decrease the protein expression of MUC1, DICER1, and CDK2; and suppress the progression and distant metastasis of OC in vivo. DICER1, a tumor suppressor, is essential for microRNA synthesis. Our findings suggest that CFG may impair the production of miRNAs in OC cells.

Conclusion

Based on network pharmacology, molecular docking, and experimental validation, the potential mechanism underlying the function of CFG in OC was explored, which supplies the theoretical groundwork for additional pharmacological investigation.

Network Pharmacology and Molecular Docking-Based Mechanism Study to Reveal Antihypertensive Effect of Gedan Jiangya Decoction

Primary hypertension is understood as a disease with diverse etiology, a complicated pathological mechanism, and progressive changes. Gedan Jiangya Decoction (GJD), with the patent publication number CN114246896A, was designed to treat primary hypertension. It contains six botanical drugs; however, the underlying mechanism is uncertain. We utilized network pharmacology to predict the active components, targets, and signaling pathways of GJD in the treatment of primary hypertension. We also investigated the potential molecular mechanism using molecular docking and animal experiments. The Traditional Chinese Medicine System Pharmacology Database and Analysis Platform (TCMSP), the Protein Database (UniProt), and a literature review were used to identify the active components and related targets of GJD's pharmacological effects. The GeneCards, Online Mendelian Inheritance in Man (OMIM), Therapeutic Target Database (TTD), and DrugBank databases were utilized to identify hypertension-related targets. Based on a Venn diagram of designed intersection targets, 214 intersection targets were obtained and 35 key targets for the treatment of hypertension were determined using the STRING data platform and Cytoscape software. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of key targets revealed that the relevant molecular action pathways of GJD in the treatment of hypertension include the Toll-like receptor, MAPK, PI3K-Akt, and renin-angiotensin signaling pathways. A GJD active ingredient-key target-pathway connection diagram was created using Cytoscape software, and 11 essential active components were selected. Molecular docking was then used to verify the binding activity of key targets and key active ingredients in GJD to treat primary hypertension. The results of this study indicate that AGTR1, AKT1 with puerarin, EDNRA with tanshinone IIA, MAPK14 with daidzein, MAPK8 with ursolic acid, and CHRM2 with cryptotanshinone had high binding activity to the targets with active components, whereas AGTR1 was selected as target genes verified by our experiment. HPLC was utilized to identify the five active ingredients. Experiments in high-salt rats demonstrated that GJD might decrease the expression of AGTR1 in the kidney and thoracic aorta while increasing the expression of eNOS by preventing the activation of the renin-angiotensin pathway, thereby reducing lowering systolic and diastolic blood pressure.

Study on the mechanism of anti-hepatic fibrosis of Glycyrrhiza Uralensis-Salvia miltiorrhiza prescription based on serum and urine metabolomics and network pharmacology

Hepatic fibrosis (HF) is a kind of chronic epidemic liver disease. Glycyrrhiza Uralensis and Salvia Miltiorrhiza (GUSM), traditional Chinese medicine, has the obvious clinical treatment of liver fibrosis. This study aimed to investigate the mechanisms of GUSM against HF by an integrated strategy combining untargeted metabolomics with network pharmacology. The results showed that GUSM prescription can improve the morphology and structure of liver tissue, inhibit the proliferation of collagen fibers and reducing the inflammatory response of the liver and so on. Endogenous metabolites and HF-related potential biomarkers in serum and urine were detected by ultra-high-performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF/MS). The metabolic pathways were enriched by MetaboAnalyst. GUSM prescription showed an antifibrotic effect on rats by regulating metabolic pathways, mainly pentose and glucuronate interconversions and arachidonic acid metabolism. Network pharmacology was then applied to find 42 overlapping targets of GUSM-HF. Quercetin was found to be the main active component and STAT3 was the main active target in GUSM prescription. Molecular docking showed high affinities between quercetin and STAT3. Therefore, GUSM has protective effects on HF by regulating the metabolism and different signaling pathways. The work also shows that the metabolomic and network pharmacology methods are promising tools to gain insight into the efficacy and mechanism research of traditional Chinese medicines.

Potential Mechanisms of Shu Gan Jie Yu Capsule in the Treatment of Mild to Moderate Depression Based on Systemic Pharmacology and Current Evidence

Background

Shu Gan Jie Yu (SGJY) capsule has a good effect on relieving depressive symptoms in China. However, the mechanism of action is still unclear. Therefore, systemic pharmacology and molecular docking approaches were used to clarify its corresponding antidepressant mechanisms.

Methods

Traditional Chinese Medicine Database and Analysis Platform (TCMSP), the Encyclopedia of Traditional Chinese Medicine (ETCM), and Swiss Target Prediction servers were used to screen and predict the bioactive components of the SGJY capsule and their antidepressive targets. Mild to moderate depression (MMD) related genes were obtained from GeneCards and DisGeNET databases. A network of bioactive components-therapeutic targets of the SGJY capsule was established by STRING 11.5 and Cytoscape 3.9.0 software. Gene function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed by utilizing Database for Annotation, Visualization, and Integrated Discovery (DAVID) platform. Active components were taken to dock with the hypothetical proteins by iGEMDOCK and SwissDock, and the docking details were visually displayed by UCSF Chimera software. Then, the related research literature of the SGJY capsule was reviewed, summarized, sorted, and analyzed, including experimental evidence and clinical experience.

Results

Seven active components and 45 intersection targets were included in the study. PPI network had genuinely uncovered the potential therapeutic targets, such as AKT1, HSP90AA1, ESR1, EGFR, and PTGS2. KEGG pathway analysis showed that the mechanism of the SGJY capsule on MMD was mainly involved in the PI3K-Akt signaling pathway.

Conclusions

In this study, we have successfully predicted the biochemically active constituents, potential therapeutic targets, and comprehensively predicted the related drug-gene interaction of the SGJY capsule for treating MMD and provided a basis for subsequent experiments.

Network Pharmacology and Molecular Docking Validation to Reveal the Pharmacological Mechanisms of Kangai Injection against Colorectal Cancer

Background

Kangai injection is a traditional Chinese medicine (TCM) mixed by extracts from astragalus, ginseng, and kurorinone with modern technology. It is a commonly used antitumor injection in China, but the mechanism of Kangai injection in the treatment of colorectal cancer (CRC) is still unclear. The purpose of this study is to explore the mechanism of Kangai injection against CRC using network pharmacology and molecular docking technology.

Methods

Targets of Kangai injection in CRC were predicted by SwissTargetPrediction and DisGeNET databases. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed by using the DAVID database. A component-disease-target gene-pathway network was constructed by Cytoscape 3.8.0 software.

Results

114 overlapping targets of Kangai injection and CRC were used to construct a PPI network, and the top 10 hub targets of Kangai injection were rated from high to low as TP53, VEGFA, EGFR, TNF, ESR1, STAT3, HSP90AA1, HDAC1, AR, and MMP9. The ingredient-target-disease interactive network was constructed, which included 22 compounds and 114 overlapping targets with 161 nodes and 707 edges. Entries of enrichment analysis were obtained based on P value (<0.05), which included 19 of GO-MF, 217 of GO-BP, 8 of GO-CC, and 13 KEGG. Molecular docking analysis showed that Kangai injection strongly interacted with top 10 hub target proteins.

Conclusion

Network pharmacology intuitively showed the multicomponent, multiple targets, and multiple pathways of Kangai injection in the treatment of CRC. The molecular docking experiment verified that compounds of Kangai injection had good binding ability with top 10 hub target proteins as well.

Potential Mechanisms of Biejiajian Pill in the Treatment of Diabetic Atherosclerosis Based on Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation

Background

Biejiajian pill (BJJP), a classical traditional Chinese formula, has been reported that it has an effective treatment for diabetic atherosclerosis in recent years, but its underlying mechanisms remain elusive. The study aimed to explore the potential mechanisms of BJJP on diabetic atherosclerosis by integrating network pharmacology, molecular docking, and molecular dynamics simulation.

Methods

The active components of BJJP were collected by TCMSP and TCMID, and then the potential targets were obtained from the SwissTargetPrediction database. The targets related to diabetic atherosclerosis were identified from the GeneCards and OMIM databases. The intersection of the potential targets regulated by active components of BJJP and the targets of diabetic atherosclerosis were common targets, which were visualized by the Venn diagram. The common targets were imported into the STRING database to construct a protein-protein interaction (PPI) network. The network of “Medicine-Compound-Target” was constructed with Cytoscape 3.7.1 software. GO functional enrichment analysis and KEGG pathway enrichment analysis were performed using the DAVID database and visualized through bioinformatics. The intersecting targets were input into Cytoscape 3.7.1 software, and the Network Analyzer tool was employed to screen out the key targets. Then molecular docking was used to verify the binding affinity between the active compounds and the key targets, and molecular dynamics simulation was used to investigate the stability of the binding models.

Results

A total of 81 active components, 186 targets of BJJP, and 4041 targets of diabetic atherosclerosis were obtained. Furthermore, 121 overlapping targets were identified. GO functional enrichment analysis revealed that these targets were correlated with the oxidation-reduction process, negative regulation of apoptotic process, inflammatory response, and other biological processes. The results of the KEGG pathway enrichment analysis showed that the common targets mainly participated in proteoglycans in cancer, PPAR signaling pathway, adherens junction, insulin resistance, HIF-1 signaling pathway, PI3K-Akt signaling pathway, etc. The results of molecular docking confirmed that the core active components in BJJP could bind well to the key targets. Results from molecular dynamics simulation showed that the binding energies of AKT1-Luteolin, MMP9-quercetin, and MMP9-luteolin complexes were −28.93 kJ·mol⁻¹, −37.12 kJ·mol⁻¹, and −62.91 kJ·mol⁻¹, respectively.

Conclusion

The study revealed that BJJP is characterized as multicomponent, multitarget, and multipathway to treat diabetic atherosclerosis, which is helpful to provide ideas and a basis for pharmacological research and clinical application in the future.

Investigation of the mechanism of the anti-cancer effects of Astragalus propinquus Schischkin and Pinellia pedatisecta Schott (A&P) on melanoma via network pharmacology and experimental verification

Melanoma is a commonly malignant cutaneous tumor in China. Astragalus propinquus Schischkin and Pinellia pedatisecta Schott (A&P) have been clinically used as adjunctive drugs in the treatment of malignant melanoma. However, the effect and mechanism of A&P on melanoma have yet to be explored. The current investigation seeks to characterize the active components of A&P and their potential roles in treating malignant melanoma using network pharmacology and in vitro and in vivo experiments. We first used the traditional Chinese medicine systems pharmacology (TCMSP) database and high-performance liquid chromatography-mass spectrometry (HPLC-MS/MS) to identify a total of 13 effective compounds within A&P. 70 common genes were obtained by matching 487 potential genes of A&P with 464 melanoma-related genes, and then we built up protein-protein interaction (PPI) network of these 70 genes, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The results revealed that A&P might influence the pathobiology of melanoma through the PI3K/Akt pathway. Molecular docking also confirmed that higher content of ingredients in A&P, including hederagenin, quercetin, beta-sitosterol and stigmasterol, had a strong binding activity (affinity < −5 kcal/mol) with the core targets AKT1, MAPK3 and ESR1. Furthermore, we confirmed A&P could inhibit melanoma cells proliferation and induce cells apoptosis through suppressing the PI3K/Akt signaling pathway by in vitro and in vivo xenograft model experiments. These findings indicate that A&P may function as a useful therapy for melanoma through the PI3K/Akt pathway.

Investigating the multi-target therapeutic mechanism of Guihuang formula on Chronic Prostatitis

ETHNOPHARMACOLOGICAL RELEVANCE

Chronic prostatitis (CP) is a complex, intractable and prevalent urological disorder in men with no effective treatment. Guihuang formula (GHF) is a traditional Chinese medicine compound that is advantageous as a CP treatment, but its aetiology is poorly understood. Research and exploration of the mechanism of GHF will help the development of a potentially valuable drug for CP and provide deeper insight into CP.

AIM OF THE STUDY

To examine and further clarify the multi-target therapeutic mechanism of GHF on CP.

MATERIALS AND METHODS

The chemical components in GHF were identified using UPLC-Q/TOF-MS. The active components and potential targets of GHF for the treatment of CP were screened and analyzed using network pharmacology and molecular docking. We constructed a CP rat model to investigate the therapeutic effect of GHF on CP and verify the influence of key targets and core pathways based on the results of network pharmacology.

RESULTS

A total of 143 ingredients were identified in GHF using UPLC-Q/TOF-MS, and 111 potential targets for GHF of CP were predicted. The "drug-ingredient-target-pathway" network was constructed and in compliance with the "Jun-Chen-Zuo-Shi" principle. GHF significantly reduced the prostate index, alleviated histological damage in the prostate, decreased CD3⁺ T cells and CD45⁺ leukocyte infiltration in the prostate, downregulated the expression of the proinflammatory cytokines IL-1β, IL-6, IL-18, COX-2, MCP-1 and TNF-α, decreased ROS levels and alleviated the production of MDA accompanied by an increase of SOD and GSH-PX levels. Meanwhile, GHF suppressed apoptosis in macrophages, downregulated the mRNA levels of PI3K, AKT and P65 NF-κB and inhibited the phosphorylation of the PI3K, AKT and P65 NF-κB.

CONCLUSION

A network pharmacology and experimental validation-based strategy was used to elucidate the underlying "multicomponent, multitarget, and multipathway" mode of action of GHF against CP. We verified that GHF inhibited oxidative stress and inflammatory response, suppressed apoptosis in macrophages, inhibited the activation of the inflammation-related PI3K/AKT/NF-κB pathway in CP rat. These findings extend the conventional views of "one drug hits one target", and offer novel insights and indication paradigm for the future discovery on the multi-target therapeutic mechanism of traditional Chinese medicine compound.

Mechanisms of Qing-Gan Li-Shui Formulation in Ameliorating Primary Open Angle Glaucoma: An Analysis Based on Network Pharmacology

Objective

In this study, we investigated the mechanism of Qing-Gan Li-Shui formulation (QGLSF) in treating primary open glaucoma (POAG) by network pharmacology and in vitro experiments.

Methods

The active pharmaceutical ingredients (APIs) of GLQSF (prepared with Prunella vulgaris, Kudzu root, Plantago asiatica, and Lycium barbarum) were obtained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and Yet Another Traditional Chinese Medicine database (YATCM). The targets of POAG were screened out with GeneCards, OMIM, PharmGKB, Therapeutic Target Database (TTD), and DrugBank databases. The Venny platform was used to summarize the core targets. Topological analysis was performed using Cytoscape3.8.0. A protein-protein interaction network was plotted by STRING online. The key targets were subjected to GO and KEGG enrichment analyses. Finally, the effects of APIs were verified by a model of chloride hexahydrate (CoCl₂)-induced retinal ganglion cells-5 (RGC-5).

Results

The main APIs were selected as quercetin (Que) by network pharmacology. Nine clusters of QGLSF targets were obtained by the PPI network analysis, including AKT-1, TP53, and JUN. KEGG enrichment analysis showed that these targets were mainly involved in the AGE-RAGE signaling pathway. By in vitro experiments, Que promoted cell proliferation. The secretion of AKT-1, TP53, JUN, AGE, and RAGE in the cell culture supernatant decreased, as shown by ELISA. The mRNA levels of AKT-1, TP53, JUN, and RAGE decreased, as shown by RT-PCR. QGLSF may employ the AGE-RAGE signaling pathway to counter POAG.

Conclusion

This study preliminarily elucidates the efficacy and mechanism of QGLSF in the treatment of POAG.