scholarly journals The Advantages of Connectivity Map Applied in Traditional Chinese Medicine

2021 ◽  
Vol 12 ◽  
Author(s):  
Huimin Jiang ◽  
Cheng Hu ◽  
Meijuan Chen
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Molecular Mechanisms ◽  
Modern Science ◽  
Biological Database ◽  
Network Pharmacology ◽  
Connectivity Map ◽  
New Era ◽  
Functional Relationships

Amid the establishment and optimization of Connectivity Map (CMAP), the functional relationships among drugs, genes, and diseases are further explored. This biological database has been widely used to identify drugs with common mechanisms, repurpose existing drugs, discover the molecular mechanisms of unknown drugs, and find potential drugs for some diseases. Research on traditional Chinese medicine (TCM) has entered a new era in the wake of the development of bioinformatics and other subjects including network pharmacology, proteomics, metabolomics, herbgenomics, and so on. TCM gradually conforms to modern science, but there is still a torrent of limitations. In recent years, CMAP has shown its distinct advantages in the study of the components of TCM and the synergetic mechanism of TCM formulas; hence, the combination of them is inevitable.

scholarly journals A Network Pharmacology-Based Study on the Anti-Lung Cancer Effect of Dipsaci Radix

2020 ◽  
Vol 2020 ◽  
pp. 1-9 ◽  
Author(s):  
Jiayan Wu ◽  
Shengkun Hong ◽  
Xiankuan Xie ◽  
Wangmi Liu
Keyword(s):  
Lung Cancer ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Interaction Network ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Hub Genes ◽  
Active Compounds

Objective. Dipsaci Radix (DR) has been used to treat fracture and osteoporosis. Recent reports have shown that myeloid cells from bone marrow can promote the proliferation of lung cancer. However, the action and mechanism of DR has not been well defined in lung cancer. The aim of the present study was to define molecular mechanisms of DR as a potential therapeutic approach to treat lung cancer. Methods. Active compounds of DR with oral bioavailability ≥30% and drug-likeness index ≥0.18 were obtained from the traditional Chinese medicine systems pharmacology database and analysis platform. The potential target genes of the active compounds and bone were identified by PharmMapper and GeneCards, respectively. The compound-target network and protein-protein interaction network were built by Cytoscape software and Search Tool for the Retrieval of Interacting Genes webserver, respectively. GO analysis and pathway enrichment analysis were performed using R software. Results. Our study demonstrated that DR had 6 active compounds, including gentisin, sitosterol, Sylvestroside III, 3,5-Di-O-caffeoylquinic acid, cauloside A, and japonine. There were 254 target genes related to these active compounds as well as to bone. SRC, AKT1, and GRB2 were the top 3 hub genes. Metabolisms and signaling pathways associated with these hub genes were significantly enriched. Conclusions. This study indicated that DR could exhibit the anti-lung cancer effect by affecting multiple targets and multiple pathways. It reflects the traditional Chinese medicine characterized by multicomponents and multitargets. DR could be considered as a candidate for clinical anticancer therapy by regulating bone physiological functions.

scholarly journals Potential Molecular Mechanisms of Chaihu-Shugan-San in Treatment of Breast Cancer Based on Network Pharmacology

2020 ◽  
Vol 2020 ◽  
pp. 1-9 ◽  
Author(s):  
Kunmin Xiao ◽  
Kexin Li ◽  
Sidan Long ◽  
Chenfan Kong ◽  
Shijie Zhu
Keyword(s):  
Breast Cancer ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Molecular Mechanisms ◽  
Endocrine Resistance ◽  
Protein Domain ◽  
Network Pharmacology ◽  
Complementary And Alternative Therapy ◽  
Cell Substrate ◽  
Catabolic Process

Breast cancer is one of the most common cancers endangering women’s health all over the world. Traditional Chinese medicine is increasingly recognized as a possible complementary and alternative therapy for breast cancer. Chaihu-Shugan-San is a traditional Chinese medicine prescription, which is extensively used in clinical practice. Its therapeutic effect on breast cancer has attracted extensive attention, but its mechanism of action is still unclear. In this study, we explored the molecular mechanism of Chaihu-Shugan-San in the treatment of breast cancer by network pharmacology. The results showed that 157 active ingredients and 8074 potential drug targets were obtained in the TCMSP database according to the screening conditions. 2384 disease targets were collected in the TTD, OMIM, DrugBank, GeneCards disease database. We applied the Bisogenet plug-in in Cytoscape 3.7.1 to obtain 451 core targets. The biological process of gene ontology (GO) involves the mRNA catabolic process, RNA catabolic process, telomere organization, nucleobase-containing compound catabolic process, heterocycle catabolic process, and so on. In cellular component, cytosolic part, focal adhesion, cell-substrate adherens junction, and cell-substrate junction are highly correlated with breast cancer. In the molecular function category, most proteins were addressed to ubiquitin-like protein ligase binding, protein domain specific binding, and Nop56p-associated pre-rRNA complex. Besides, the results of the KEGG pathway analysis showed that the pathways mainly involved in apoptosis, cell cycle, transcriptional dysregulation, endocrine resistance, and viral infection. In conclusion, the treatment of breast cancer by Chaihu-Shugan-San is the result of multicomponent, multitarget, and multipathway interaction. This study provides a certain theoretical basis for the treatment of breast cancer by Chaihu-Shugan-San and has certain reference value for the development and application of new drugs.

scholarly journals Network Pharmacology Analysis to Identify Phytochemicals in Traditional Chinese Medicines That May Regulate ACE2 for the Treatment of COVID-19

2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Wenhao Niu ◽  
Feng Wu ◽  
Haiming Cui ◽  
Wenyue Cao ◽  
YuChieh Chao ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Gallic Acid ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Peroxisome Proliferator ◽  
Active Components ◽  
Peroxisome Proliferator Activated Receptor ◽  
Effective Components

“Three formulas and three medicines,” which include Jinhua Qinggan granule, Lianhua Qingwen capsule/granule, Xuebijing injection, Qingfei Paidu decoction, HuaShiBaiDu formula, and XuanFeiBaiDu granule, have been proven to be effective in curbing coronavirus disease 2019 (COVID-19), according to the State Administration of Traditional Chinese Medicine. The aims of this study were to identify the active components of “Three formulas and three medicines” that can be used to treat COVID-19, determine their mechanism of action via angiotensin-converting enzyme 2 (ACE2) by integrating network pharmacological approaches, and confirm the most effective components for COVID-19 treatment or prevention. We investigated all the compounds present in the aforementioned herbal ingredients. Compounds that could downregulate the transcription factors (TFs) of ACE2 and upregulate miRNAs of ACE2 were screened via a network pharmacology approach. Hepatocyte nuclear factor 4 alpha (HNF4A), peroxisome proliferator-activated receptor gamma (PPARG), hsa-miR-2113, and hsa-miR-421 were found to regulate ACE2. Several compounds, such as quercetin, decreased ACE2 expression by regulating the aforementioned TFs or miRNAs. After comparison with the compounds present in Glycyrrhiza Radix et Rhizoma, quercetin, glabridin, and gallic acid present in the herbal formulas and medicines were found to alter ACE2 expression. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were used to search for possible molecular mechanisms of these compounds. In conclusion, traditional Chinese medicine (TCM) plays a pivotal role in the prevention and treatment of COVID-19. Quercetin, glabridin, and gallic acid, the active components of recommended TCM formulas and medicines, can inhibit COVID-19 by downregulating ACE2.

scholarly journals Utilizing network pharmacology to explore the underlying mechanism of Radix Salviae in diabetic retinopathy

2019 ◽  
Vol 14 (1) ◽  
Author(s):  
Chun-Li Piao ◽  
Jin-Li Luo ◽  
De Jin ◽  
Cheng Tang ◽  
Li Wang ◽  
...  
Keyword(s):  
Diabetic Retinopathy ◽  
Chinese Medicine ◽  
Growth Factor ◽  
Traditional Chinese Medicine ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Pathway Enrichment ◽  
Underlying Mechanisms

Abstract Introduction Radix Salviae (Dan-shen in pinyin), a classic Chinese herb, has been extensively used to treat diabetic retinopathy in clinical practice in China for many years. However, the pharmacological mechanisms of Radix Salviae remain vague. The aim of this study was to decrypt the underlying mechanisms of Radix Salviae in the treatment of diabetic retinopathy using a systems pharmacology approach. Methods A network pharmacology-based strategy was proposed to elucidate the underlying multi-component, multi-target, and multi-pathway mode of action of Radix Salviae against diabetic retinopathy. First, we collected putative targets of Radix Salviae based on the Traditional Chinese Medicine System Pharmacology database and a network of the interactions among the putative targets of Radix Salviae and known therapeutic targets of diabetic retinopathy was built. Then, two topological parameters, “degree” and “closeness certainty” were calculated to identify the major targets in the network. Furthermore, the major hubs were imported to the Database for Annotation, Visualization and Integrated Discovery to perform a pathway enrichment analysis. Results A total of 130 nodes, including 18 putative targets of Radix Salviae, were observed to be major hubs in terms of topological importance. The results of pathway enrichment analysis indicated that putative targets of Radix Salviae mostly participated in various pathways associated with angiogenesis, protein metabolism, inflammatory response, apoptosis, and cell proliferation. The putative targets of Radix Salviae (vascular endothelial growth factor, matrix metalloproteinases, plasminogen, insulin-like growth factor-1, and cyclooxygenase-2) were recognized as active factors involved in the main biological functions of treatment, which implied that these were involved in the underlying mechanisms of Radix Salviae on diabetic retinopathy. Conclusions Radix Salviae could alleviate diabetic retinopathy via the molecular mechanisms predicted by network pharmacology. This research demonstrates that the network pharmacology approach can be an effective tool to reveal the mechanisms of traditional Chinese medicine from a holistic perspective.

scholarly journals Network Pharmacology Deciphering Mechanisms of Volatiles of Wendan Granule for the Treatment of Alzheimer’s Disease

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Jun-feng Liu ◽  
An-na Hu ◽  
Jun-feng Zan ◽  
Ping Wang ◽  
Qiu-yun You ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Molecular Mechanisms ◽  
Senile Dementia ◽  
Quality Standard ◽  
Network Pharmacology ◽  
Gamma Aminobutyric Acid ◽  
Integrated Network

Objective. To explore the mechanisms of the volatiles of Wendan granule (WDG) for the treatment of Alzheimer’s disease, network pharmacology method integrating absorption, distribution, metabolism, and excretion (ADME) screening, target fishing, network constructing, pathway analysing, and correlated diseases prediction was applied. Methods. Twelve small molecular compounds of WDG were selected as the objects from 74 volatiles with the relative abundances above 2 %, and their ADME parameters were collected from Traditional Chinese Medicine Systems Pharmacology platform (TCMSP), and the corresponding targets, genes, pathways, and diseases were predicted according to the data provided by TCMSP, DrugBank, Uniport, and the Database for Annotation, Visualization, and Integrated Discovery (DAVID). Then the related pathways and correlation analysis were explored by the Kyoto Encyclopedia and Genomes (KEGG) database. Finally, the networks of compound target, target pathway, and pathway disease of WDG were constructed by Cytoscape software. Results. Twelve compounds interacted with 49 targets, of which top three targets were gamma-aminobutyric acid receptor subunit alpha-1 (GABRA1), prostaglandin G/H synthase 2 (PGHS-2), and sodium-dependent noradrenaline transporter. Interestingly, these targets were highly associated with depression, insomnia, and Alzheimer’s disease that mainly corresponded to mental and emotional illnesses. Conclusion. The integrated network pharmacology method provides precise probe to illuminate the molecular mechanisms of the main volatiles of WDG for relieving senile dementia related syndromes, which will also facilitate the application of traditional Chinese medicine as an alternative or supplementary to conventional treatments of AD, as well as follow-up studies such as upgrading the quality standard of clinically applied herbal medicine and novel drug development.

scholarly journals The Mechanisms of Yinchensini Decoction in Treating Hepatitis B were Explored by Network Pharmacology and Existing Literatures

2021 ◽  
Author(s):  
Xun Zhang ◽  
Xudong Liu ◽  
Xingqiu Liang ◽  
Xia Liu ◽  
Jian Liang
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Hepatitis B ◽  
Molecular Mechanisms ◽  
Mapk Signaling ◽  
Research Strategy ◽  
Network Pharmacology ◽  
Experimental Conditions ◽  
Combined Application ◽  
Chemokine Signaling

Abstract As one of the classic traditional Chinese medicine prescriptions for treating hepatitis B and its related diseases, Yinchensini Decoction has been widely accepted after the thousands of years of spread. However, until now, the underlying molecular mechanisms are remained unclear. Therefore, this study adopts the method of network pharmacology to explore the mechanisms of Yinchensini Decoction in the treatment of hepatitis B. Due to the limitation of experimental conditions, we finally decided to verify the explored mechanisms in the way of existing literatures. The components and related targets of Yinchensini Decoction were screened by the TCMSP database, the targets were converted into gene symols through uniform ID conversion in the Uniprot database. The gene targets of hepatitis B were screened out through the GeneCards database, the gene targets of Yinchensini Decoction for the treatment of hepatitis B were obtained by intersecting the gene targets of Yinchensini Decoction with those of hepatitis B. The STRING database was used to analyze the protein-protein interaction of the intersecting genes, and the metascape database was used to analyze the Gene Ontology and the KEGG pathway of the intersecting genes. Cytoscape3.8.2 was used for mapping various networks and for the specific analysis of various networks. The results show that: quercetin, kaempferol, beta-sitosterol, naringenin, Licochalcone a are the main active ingredients of the Yinchensini Decoction in the treatment of hepatitis B. The main gene targets of these components are TP53, TNF, IFNG, IL6, IL10, MYC, IKBKB, BCL2, STAT1, CHUK. The main mechanisms of these components are MAPK signaling, PI3K signaling, TGFB signaling, JAK-STAT signaling, TLR signaling, RLR signaling, IFN Signaling, chemokine signaling, cell cycle, apoptosis, transcription. In addition, through the analysis of relevant data in the network, about the specific disease of hepatitis B, the herbs in Yinchensini Decoction are ranked according to their importance: yinchen > gancao > ganjiang, fuzi, which are very consistent with the concept of the traditional Chinese medicine theory. Finally, the mechanisms of Yinchensini Decoction through network pharmacology in the treatment of hepatitis B were verified by the relevant literatures. To sum up, the combined application of network pharmacology and relevant literatures validation provides a new practical research strategy for the study of the mechanisms of complex traditional Chinese medicine prescriptions or extremely dangerous substances.

scholarly journals Molecular Targets and Pathways Contributing to the Effects of Wenxin Keli on Atrial Fibrillation Based on a Network Pharmacology Approach

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Yujie Zhang ◽  
Xiaolin Zhang ◽  
Xi Zhang ◽  
Yi Cai ◽  
Minghui Cheng ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Clinical Symptoms ◽  
Chemical Constituents ◽  
Molecular Targets ◽  
Network Pharmacology ◽  
Systems Pharmacology

Background. Atrial fibrillation (AF) is the most common sustained arrhythmia and is associated with high rates of mortality and morbidity. The traditional Chinese medicine Wenxin Keli (WXKL) can effectively improve clinical symptoms and is safe for the treatment of AF. However, the active substances in WXKL and the molecular mechanisms underlying its effects on AF remain unclear. In this study, the bioactive compounds in WXKL, as well as their molecular targets and associated pathways, were evaluated by systems pharmacology. Materials and Methods. Chemical constituents and potential targets of WXKL were obtained via the Traditional Chinese Medicine Systems Pharmacology (TCMSP). The TTD, DrugBank, DisGeNET, and GeneCards databases were used to collect AF-related target genes. Based on common targets related to both AF and WXKL, a protein interaction network was generated using the STRING database. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGGs) pathway enrichment analyses were performed. Network diagrams of the active component-target and protein-protein interactions (PPIs) were constructed using Cytoscape. Results. A total of 30 active ingredients in WXKL and 219 putative target genes were screened, including 83 genes identified as therapeutic targets in AF; these overlapping genes were considered candidate targets for subsequent analyses. The effect of treating AF was mainly correlated with the regulation of target proteins, such as IL-6, TNF, AKT1, VEGFA, CXCL8, TP53, CCL2, MMP9, CASP3, and NOS3. GO and KEGG analyses revealed that these targets are associated with the inflammatory response, oxidative stress reaction, immune regulation, cardiac energy metabolism, serotonergic synapse, and other pathways. Conclusions. This study demonstrated the multicomponent, multitarget, and multichannel characteristics of WXKL, providing a basis for further studies of the mechanism underlying the beneficial effects of WXKL in AF.

scholarly journals A Network Pharmacology Approach to Explore the Mechanisms of Artemisiae scopariae Herba for the Treatment of Chronic Hepatitis B

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Asi He ◽  
Wei Wang ◽  
Yang Xia ◽  
Xiaoping Niu
Keyword(s):  
Chronic Hepatitis ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Hepatitis B ◽  
Signaling Pathway ◽  
Chronic Hepatitis B ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Network Pharmacology ◽  
Active Components

Background. As a traditional Chinese medicine, Artemisiae scopariae Herba (ASH) is used to treat various liver diseases. The purpose of this study was to explore the mechanisms of ASH for treating chronic hepatitis B (CHB) using a network pharmacological method. Methods. Bioactive ingredients and related targets of ASH were obtained from Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. Gene names of targets were extracted from UniProt database. Differentially expressed genes (DEGs) of CHB were obtained from microarray dataset GSE83148. The intersect genes between DEGs and target genes were annotated using clusterProfiler package. The STRING database was used to obtain a network of protein-protein interactions. Cytoscape 3.7.2 was used to construct the “ingredient-gene-pathway” (IGP) network. Molecular docking studies were performed using Autodock vina. Results. A total of 13 active components were extracted from TCMSP database. Fifteen intersect genes were obtained between 183 target genes and 403 DEGs of GSE83148. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results showed that ASH against CHB mainly involved in toll-like receptor signaling pathway, cellular senescence, hepatitis B, and chemokine signaling pathway. We screened one hub compound, five core targets, and four key pathways from constructed networks. The docking results indicated the strong binding activity between quercetin and AKT1. Conclusions. This study provides potential molecular mechanisms of ASH against CHB based on exploration of network pharmacology.

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