scholarly journals Prediction of the anti-inflammatory effects of bioactive components of a Hippocampus species-based TCM formulation on chronic kidney disease using network pharmacology

2021 ◽  
Vol 20 (11) ◽  
pp. 2355-2362
Author(s):  
Lingyu Zhang ◽  
Sitong Lu ◽  
Zhang Hu ◽  
Mingneng Liao ◽  
Chengpeng Li ◽  
...  
Keyword(s):  
Chronic Kidney Disease ◽  
Kidney Disease ◽  
Signaling Pathways ◽  
Target Genes ◽  
Scientific Evidence ◽  
Network Pharmacology ◽  
Bioactive Components ◽  
Active Components ◽  
Pathway Enrichment ◽  
Multiple Signaling

Purpose: To systematically study and predict the therapeutic targets and signaling pathways of Hippocampus (HPC) against chronic kidney disease (CKD) using network pharmacology.Methods: By combining database mining, literature searching, screening of disease targets, and network construction, the effects of various components of HPC on several proteins related to CKD were predicted and the active compounds were screened. Genes related to the selected compounds were linked using the SEA database. The correlation between CKD and genes was determined using OMIM, DisGenNet, and GeneCards databases. Pathway-enrichment analyses of overlapping genes were undertaken using online databases.Results: A total of 144 compounds in HPC were identified. Analyses of clusters suggest that the active components of HPC and the target genes against the inflammation caused by CKD were due to 10 compounds and 25 genes. Metascape results showed that these HPC targets are related to CKD inflammation.Conclusion: The active components of HPC and the target genes against CKD inflammation are involved in multiple signaling pathways, such as AGE-RAGE, TLR, TNF, and NF-κB. This work provides scientific evidence to support the clinical use of HPC against CKD.

Molecular Mechanism of The Effect of Huanglian Jiedu Decoction On Ulcerative Colitis Based On Network Pharmacology And Molecular Docking

2021 ◽  
Author(s):  
Jing Yang ◽  
Chao-Tao Tang ◽  
Ruiri Jin ◽  
Bixia Liu ◽  
Peng Wang ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Molecular Docking ◽  
Molecular Mechanism ◽  
Target Genes ◽  
Signal Pathway ◽  
Intestinal Barrier Function ◽  
Network Pharmacology ◽  
Bioactive Components ◽  
Ppi Network ◽  
Active Components

Abstract Huanglian jiedu decoction (HLJDD) is a heat-clearing and detoxifying agent composed of four kinds of Chinese herbal medicine. Previous studies have shown that HLJDD can improve the inflammatory response of ulcerative colitis (UC) and maintain intestinal barrier function. However, its molecular mechanism is not completely clear. In this study, we verified the bioactive components (BCI) and potential targets of HLJDD in the treatment of UC by means of network pharmacology and molecular docking, and constructed the pharmacological network and PPI network. Then the core genes were enriched by GO and KEGG. Finally, the bioactive components were docked with the key targets to verify the binding ability between them. A total of 54 active components related to UC were identified. Ten genes are considered to be very important to PPI network. Functional analysis showed that these target genes were mainly involved in the regulation of cell response to different stimuli, IL-17 signal pathway and TNF signal pathway. The results of molecular docking showed that the active components of HLJDD had good affinity with Hub gene. This study systematically elucidates the "multi-component, multi-target, multi-pathway" mechanism of anti-UC with HLJDD for the first time, suggesting that HLJDD or its active components may be candidate drugs for the treatment of ulcerative colitis.

scholarly journals Network Pharmacology‐Based Study on the Active Component and Mechanism of the Anti-Gastric-Cancer Effect of Herba Sarcandrae

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Li Han ◽  
Ying Han
Keyword(s):  
Gastric Cancer ◽  
Signaling Pathways ◽  
Signaling Pathway ◽  
Target Genes ◽  
Scientific Basis ◽  
Gene Expression Omnibus ◽  
Network Pharmacology ◽  
Chemical Components ◽  
Active Components ◽  
Pathway Network

Background. Herba Sarcandrae is used in the clinical practice of traditional Chinese medicine to deal with gastric cancer. However, there are few studies on its precise mechanism. Method. In this study, a network pharmacological approach was utilized to construct a molecular/target/pathway molecular regulatory network for the anti-gastric-cancer effect of Herba Sarcandrae. The active components of Herba Sarcandrae and their potential mechanisms were explored. Chemical components of the Herba Sarcandrae were identified through a database, and they were evaluated and screened based on oral bioavailability and drug similarity. Results. Genes related to gastric cancer were found in the Gene Expression Omnibus (GEO) database, and gene targets related to anti-gastric-cancer were chosen by comparison. Using annotation, visualization, and a comprehensive discovery database, the function and related pathways of target genes were analyzed and screened. Cytoscape software was utilized to construct a component/target/pathway network for the antitumor effect of Herba Sarcandrae. Finally, 6 drug ingredients and 29 target genes related to gastric cancer were detected. IL-17 signaling pathway, NF-kappa B signaling pathway, and other signaling pathways were significantly enriched. Many signaling pathways that directly act on tumors and indirect pathways inhibit the development of gastric cancer. Conclusion. This study provides a scientific basis for further elucidating the mechanism of the anti-gastric-cancer effect of Herba Sarcandrae.

Investigating the Mechanism of Action of Frankincense against Drug-Induced Liver Injury Using Network Pharmacology and Molecular Docking

2021 ◽  
Vol 18 ◽  
Author(s):  
Yu-cheng Liao ◽  
Jing-wen Wang ◽  
Qian Yang ◽  
Wen-jun Wanga ◽  
Chao Zhao ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Liver Injury ◽  
Mechanism Of Action ◽  
Target Genes ◽  
Network Pharmacology ◽  
Active Components ◽  
Drug Induced ◽  
Drug Induced Liver Injury ◽  
Pathway Enrichment ◽  
Core Genes

Background: Frankincense has been used as a traditional medicine in many countries. It is an important herb with multiple targets and therapeutic effects including liver protection. However, its mechanism of action in drug-induced liver injury (DILI) remains unknown. Objective: The purpose of this work was to elucidate the active components, core genes, and molecular mechanism of frankincense in DILI through network pharmacology and molecular docking approaches. Method: The active components of frankincense and its target genes were obtained from the BATMAN-TCM database, and the DILI target genes were obtained from the GeneCards and DrugBank databases. Cytoscape was used to create the compound-shared gene target network. STRING and DAVID software were used to analyze key targets and pathway enrichment. Autodock Vina software was used for molecular docking. Results: Network analysis identified 16 compounds in frankincense and 103 target genes that are highly related to DILI. The core genes in the protein-protein interaction network are INS, IL6, TP53, TNF, SRC, PTGS2, IL1B, CAT, IL10, and IGF1. Furthermore, GO and KEGG pathway enrichment analyses indicated that the effect of frankincense on DILI is related to positive regulation of transcription from RNA polymerase II promoter and inflammatory response. Core pathways such as the HIF-1, TNF, FoxO, PI3K-Akt, and the sphingolipid signaling pathway are closely related to DILI. Conclusion: This study revealed the chemical constituents and pharmacological effects of frankincense and unveiled potential DILI healing targets. This study could provide insights for further development of drugs that specifically target DILI.

Exploration of  the mechanism of Ziyin Tongluo Formula on preventing and treating postmenopausal osteoporosis based on the network pharmacology

2020 ◽  
Author(s):  
Rong-Bin Chen ◽  
Ying-Dong Yang ◽  
Kai Sun ◽  
Shan Liu ◽  
Wei Guo ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Postmenopausal Osteoporosis ◽  
Target Genes ◽  
Interaction Network ◽  
Network Pharmacology ◽  
Regulation Of Transcription ◽  
Active Ingredients ◽  
Active Components ◽  
Kegg Pathways ◽  
Key Genes

Abstract Background Postmenopausal osteoporosis (PMOP) is a global chronic and metabolic bone disease that poses huge challenges to individuals and society. Previous studies have confirmed that Ziyin Tongluo Formula (ZYTLF) has a good clinical effect in the treatment of PMOP. However, the material basis and mechanism of ZYLTF against PMOP has not been thoroughly explained. Methods TCMSP, TCMID, and BATMAN-TCM databases were used to identify the active ingredients and their putative targets. Genes associated with PMOP were mined from GeneCards, OMIM, DisGeNET databases, and then mapped with the putative targets to obtain overlapping target genes. A network model of "herb-active ingredient-overlapping target genes" was constructed and a protein-protein interaction network of overlapping target genes was built and the key genes were selected based on the MCC algorithm. The key genes were imported to the DAVID database to performs GO and KEGG pathway enrichment analyses. Results Ninety-two active components of ZYTLF corresponded to 243 targets, with 129 target genes interacting with PMOP, and 50 key genes were selected. GO analysis results showed that biological process mainly included positive regulation of transcription, negative regulation of apoptosis, and cell components were mainly nucleus, cytoplasm, and molecular functions mainly included enzyme binding, protein binding and transcription factor binding. There were two main types of significant KEGG pathways in PMOP, hormone-related signaling pathways (estrogen, prolactin, thyroid hormone) and inflammation-related pathways (TNF, PI3K-Akt, MAPK ). Conclusions The underlying therapeutic mechanisms of ZYTLF action on PMOP maybe is that, the active ingredients such as quercetin, kaempferol, luteolin act on ESR1, TNF, IL6, MAPK8 and other key genes, which mainly enrich in estrogen, TNF, PI3K-Akt, MAPK and other signaling pathways.

scholarly journals Application of Network Pharmacology to Elucidate The Potential Mechanism of Finger Citron Against Obesity

2020 ◽  
Author(s):  
Zhen Wu ◽  
Yujiao Yang ◽  
Yao Wei ◽  
Xu-guang Hu
Keyword(s):  
Molecular Docking ◽  
Signaling Pathways ◽  
Target Genes ◽  
Chinese Herbs ◽  
Network Pharmacology ◽  
Potential Mechanism ◽  
Active Components ◽  
Docking Analysis ◽  
Treatment Of Obesity ◽  
Molecular Docking Analysis

Abstract Background: Finger citron (FS) is one of many traditional Chinese herbs that have been used to treat obesity. However, the active components and potential targets of FS in improving obesity remain unclear. Methods：The aim of this study was to elucidate the pharmacological effects and mechanisms of FS on obesity using network pharmacology analysis. We used network pharmacology to determine the active components, potential targets and mechanisms in the treatment of obesity.Results：We identified 25 active ingredients of FS such as diosmetin, hesperidin and sitosterol-alpha1 with important biological effect. A total of 258 key targets were screened, containing TNF，NOS2, MAPK8 which were found to be enriched in 27 signaling pathways, such as apoptosis, TNF, PPAR and AKT1, and Insulin resistance signaling pathways. Moreover, molecular docking analysis showed that the main ingredients were tightly bound to the core targets, further confirming the effects of weight loss. Conclusion: Based on network pharmacology and molecular docking analysis, our study provides insights into the potential mechanism of FS in ameliorating obesity after screening for associated key target genes and signaling pathways. These findings further provide a theoretical basis for further pharmacological research into the potential mechanism of FS in treating obesity.

scholarly journals A network pharmacology approach to explore the mechanism of HuangZhi YiShen Capsule for treatment of diabetic kidney disease

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Xue-Feng Zhou ◽  
Wei-E Zhou ◽  
Wen-Jing Liu ◽  
Min-Jing Luo ◽  
Xia-Qing Wu ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Kidney Disease ◽  
Signaling Pathways ◽  
Diabetic Kidney Disease ◽  
Target Genes ◽  
Chemical Constituents ◽  
Mendelian Inheritance ◽  
Network Pharmacology ◽  
Active Compounds ◽  
Diabetic Kidney

Abstract Background and Objective HuangZhi YiShen Capsule (HZYS) is a Chinese patent herbal drug that protects kidney function in diabetic kidney disease (DKD) patients. However, the pharmacologic mechanisms of HZYS remain unclear. This study would use network pharmacology to explore the pharmacologic mechanisms of HZYS. Methods Chemical constituents of HZYS were obtained through the Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) and literature search. Potential targets of HZYS were identified by using the TCMSP and the SwissTarget Prediction databases. DKD-related target genes were collected by using the Online Mendelian Inheritance in Man, Therapeutic Target Database, GeneCards, DisGeNET, and Drugbank databases. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out to further explore the mechanisms of HZYS in treating DKD. Molecular docking was conducted to verify the potential interactions between the prime compounds and the hub genes. Results 179 active compounds and 620 target genes were obtained, and 571 common targets were considered potential therapeutic targets. The top 10 main active compounds of HZYS were heparin, quercetin, kaempferol, luteolin, methyl14-methylpentadecanoate, methyl (Z)-11-hexadecenoate, 17-hydroxycorticosterone, 4-pregnene-17α, 20β, 21-triol-3, 11-dione, wogonin, and hydroxyecdysone. Hub signaling pathways by which HZYS treating DKD were PI3K-Akt, MAPK, AGE-RAGE in diabetic complications, TNF, and apoptosis. The top 10 target genes associated with these pathways were IL6, MAPK1, AKT1, RELA, BCL2, JUN, MAPK3, MAP2K1, CASP3, and TNF. Quercetin and Luteolin were verified to have good binding capability with the hub potential targets IL6, MAPK1, AKT1 through molecular docking. Conclusion HZYS appeared to treat DKD by regulating the inflammatory, oxidative stress, apoptotic, and fibrosis signaling pathways. This study provided a novel perspective for further research of HZYS.

scholarly journals Study on the Sleep-Improvement Effects of Hemerocallis citrina Baroni in Drosophila melanogaster and Targeted Screening to Identify Its Active Components and Mechanism

Foods ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 883
Author(s):  
Yuxuan Liang ◽  
Riming Huang ◽  
Yongchun Chen ◽  
Jing Zhong ◽  
Jie Deng ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
High Resolution Mass Spectrometry ◽  
Sleep Time ◽  
Network Pharmacology ◽  
Dependent Manner ◽  
Bioactive Components ◽  
Active Components ◽  
Edible Plant ◽  
Hemerocallis Citrina ◽  
Ultrahigh Performance Liquid Chromatography

Hemerocallis citrina Baroni (HC) is an edible plant in Asia, and it has been traditionally used for sleep-improvement. However, the bioactive components and mechanism of HC in sleep-improvement are still unclear. In this study, the sleep-improvement effect of HC hydroalcoholic extract was investigated based on a caffeine-induced insomnia model in Drosophila melanogaster (D. melanogaster), and the ultrahigh-performance liquid chromatography coupled with electrospray ionization quadrupole Orbitrap high-resolution mass spectrometry (UHPLC-ESI-Orbitrap-MS) and network pharmacology strategy were further combined to screen systematically the active constituents and mechanism of HC in sleep-improvement. The results suggested HC effectively regulated the number of nighttime activities and total sleep time of D. melanogaster in a dose-dependent manner and positively regulated the sleep bouts and sleep duration of D. melanogaster. The target screening suggested that quercetin, luteolin, kaempferol, caffeic acid, and nicotinic acid were the main bioactive components of HC in sleep-improvements. Moreover, the core targets (Akt1, Cat, Ple, and Sod) affected by HC were verified by the expression of the mRNA of D. melanogaster. In summary, this study showed that HC could effectively regulate the sleep of D. melanogaster and further clarifies the multi-component and multi-target features of HC in sleep-improvement, which provides a new insight for the research and utilization of HC.

scholarly journals Mechanism of protective effect of xuan-bai-cheng-qi decoction on LPS-induced acute lung injury based on an integrated network pharmacology and RNA-sequencing approach

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huahe Zhu ◽  
Shun Wang ◽  
Cong Shan ◽  
Xiaoqian Li ◽  
Bo Tan ◽  
...  
Keyword(s):  
Acute Lung Injury ◽  
Lung Injury ◽  
Rna Sequencing ◽  
Target Genes ◽  
Mammalian Target Of Rapamycin ◽  
Network Pharmacology ◽  
Protective Mechanism ◽  
Rna Seq ◽  
Active Components ◽  
Integrated Network

AbstractXuan-bai-cheng-qi decoction (XCD), a traditional Chinese medicine (TCM) prescription, has been widely used to treat a variety of respiratory diseases in China, especially to seriously infectious diseases such as acute lung injury (ALI). Due to the complexity of the chemical constituent, however, the underlying pharmacological mechanism of action of XCD is still unclear. To explore its protective mechanism on ALI, firstly, a network pharmacology experiment was conducted to construct a component-target network of XCD, which identified 46 active components and 280 predicted target genes. Then, RNA sequencing (RNA-seq) was used to screen differentially expressed genes (DEGs) between ALI model rats treated with and without XCD and 753 DEGs were found. By overlapping the target genes identified using network pharmacology and DEGs using RNA-seq, and subsequent protein–protein interaction (PPI) network analysis, 6 kernel targets such as vascular epidermal growth factor (VEGF), mammalian target of rapamycin (mTOR), AKT1, hypoxia-inducible factor-1α (HIF-1α), and phosphoinositide 3-kinase (PI3K) and gene of phosphate and tension homology deleted on chromsome ten (PTEN) were screened out to be closely relevant to ALI treatment. Verification experiments in the LPS-induced ALI model rats showed that XCD could alleviate lung tissue pathological injury through attenuating proinflammatory cytokines release such as tumor necrosis factor (TNF)-α, interleukin (IL)-6, and IL-1β. Meanwhile, both the mRNA and protein expression levels of PI3K, mTOR, HIF-1α, and VEGF in the lung tissues were down-regulated with XCD treatment. Therefore, the regulations of XCD on PI3K/mTOR/HIF-1α/VEGF signaling pathway was probably a crucial mechanism involved in the protective mechanism of XCD on ALI treatment.

scholarly journals The Underlying Mechanism of Chinese Herb of Regulating Marrow in the Treatment of  Osteonecrosis of the Femoral Head Based on Network Pharmacology and Molecular Docking

2021 ◽  
Author(s):  
Xiaojian Wang ◽  
Rui Wang ◽  
Ting Xu ◽  
Hongting Jin ◽  
Peijian Tong ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Chinese Medicine ◽  
Signaling Pathway ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Chinese Herbs ◽  
Network Pharmacology ◽  
Active Components ◽  
Pathway Enrichment

Abstract Background The lesion of marrow is a crucial factor in orthopedic diseases, which is recognized by orthopedics-traumatology expert from "Zhe-School of Chinese Medicine". The Chinese herbs of regulating marrow has been widely used to treat osteonecrosis of the femoral head (ONFH) in China, while the interaction mechanisms were still elucidated. Thus, we conducted this study to explore the underlying mechanism of the five highest-frequency Chinese herbs of regulating marrow(HF-CHRM) in the treatment of ONFH with the aid of network pharmacology(NP) and molecular docking(MD). Methods The active components and potential targets of HF-CHRM were obtained through several online databases, such as Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP), UniProt database. The gene targets related to ONFH were collected with the help of the OMIM and GeneCards disease-related databases. The "drug- component-target-disease" network and protein-protein interaction(PPI) network of the drug and disease intersecting targets were constructed by using Cytoscape software and the STRING database. R software was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The MD of critical components and targets was carried out using Autodock Vina and Pymol to validate the binding affinity. Results A total of 54 active components, 1074 drug targets and 195 gene targets were obtained. There were 1219 ONFH related targets. 39 drug and disease intersection targets(representative genes: IL6, TP53, VEGFA, ESR1, IL1B) were obtained and considered potential therapeutic targets. 1619 items were obtained by the GO enrichment analysis, including 1517 biological processes, 10 cellular components and 92 molecular functions, which is mainly related to angiogenesis, bone and lipid metabolism and inflammatory reaction. The KEGG pathway enrichment analysis revealed 119 pathways, including AGE-RAGE signaling pathway, PI3K-Akt signaling pathway and IL-17 signaling pathway. MD results showed that quercetin, wogonin, and kaempferol active components had good affinity with IL6, TP53, and VEGFA core proteins. Conclusion The HF-CHRM can treat ONFH by multi-component, multi-target, and multi-pathway comprehensive action.

Discussing the Mechanism of Dahuang Huanglian Xiexin Decoction in the Treatment of Type 2 Diabetes Mellitus via Network Pharmacology and Molecular Docking

2021 ◽  
Author(s):  
Xi Cen ◽  
Yan Wang ◽  
LeiLei Zhang ◽  
XiaoXiao Xue ◽  
Yan Wang ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Molecular Docking ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Overlapping Genes ◽  
Potential Mechanism ◽  
Active Components ◽  
The Core ◽  
Core Genes

Abstract BackgroundType 2 diabetes mellitus (T2DM) is regarded as Pi Dan disease in traditional Chinese medicine (TCM). Dahuang Huanglian Xiexin Decoction (DHXD), a classical TCM formula, has been used for treating Pi Dan disease in clinic, its pharmacological mechanism has not been elucidated. MethodsThis study used network pharmacological analysis and molecular docking approach to explore the mechanism of DHXD on T2DM. Firstly, the compounds in DHXD were obtained from TCMSP and TCMID databases, the potential targets were determined based on TCMSP and UniProt databases. Next, Genecards, Digenet and UniProt databases were used to identify the targets of T2DM. Then, the protein-protein interaction (PPI) network was established with overlapping genes of T2DM and compounds, and the core targets in the network were identified and analyzed. Then, the David database was used for GO and KEGG enrichment analysis. Finally, the target genes were selected and the molecular docking was completed by Autodock software to observe the binding level of active components with target genes.ResultsA total of 397 related components and 128 overlapping genes were identified. After enrichment analysis, it was found that HIF-1, TNF, IL-17 and other signaling pathways, as well as DNA transcription, gene expression, apoptosis and other cellular biological processes had the strongest correlation with the treatment of T2DM by DHXD, and most of them occurred in the extracellular space, plasma membrane and other places, which were related to enzyme binding and protein binding. In addition, 42 core genes of DHXD, such as VEGFA, TP53 and MAPK1, were considered as potential therapeutic targets, indicating the potential mechanism of DHXD on T2DM. Finally, the results of molecular docking showed that HIF-1 pathway had strong correlation with the target genes INSR and GLUT4, quercetin and berberine had the strongest binding power with them respectively.ConclusionThis study summarized the main components of DHXD in the treatment of T2DM, identified the core genes and pathways, and systematically analyzed the interaction of related targets, trying to lay the foundation for clarifying the potential mechanism of DHXD on T2DM, so as to carry out further research in the future.

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