scholarly journals Network pharmacology for the identification of phytochemicals in traditional Chinese medicine for COVID-19 that may regulate interleukin-6

2020 ◽  
Author(s):  
Chun Liang ◽  
Wenhao Niu ◽  
Feng Wu ◽  
Wenyue Cao ◽  
Zonggui Wu ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Binding Affinity ◽  
Ursolic Acid ◽  
Interleukin 6 ◽  
Chemical Constituents ◽  
Gene Clusters ◽  
Network Pharmacology ◽  
Biological Processes

Objective: “Three formulas and three medicines,” namely, Jinhua Qinggan Granule, Lianhua Qingwen Capsule, Xuebijing Injection, Qingfei Paidu Decoction, HuaShi BaiDu Formula, and XuanFei BaiDu Granule, were proven to be effective for coronavirus disease 2019 (COVID-19) treatment. This study aimed to identify the active chemical constituents of this traditional Chinese medicine (TCM) and investigate their mechanisms through interleukin-6 (IL-6) integrating network pharmacological approaches.Methods: We collected the compounds from all herbal ingredients of the previously mentioned TCM, but those that could downregulate IL-6 were screened through the network pharmacology approach. Then, we modeled molecular docking to evaluate the binding affinity between compounds and IL-6. Furthermore, we analyzed the biological processes and pathways of compounds. Lastly, we screened out the core genes of compounds through the construction of the protein-protein interaction network and the excavation of gene clusters of compounds.Results: The network pharmacology research showed that TCM could decrease IL-6 using several compounds, such as quercetin, ursolic acid, luteolin, and rutin. Molecular docking results showed that the molecular binding affinity with IL-6 of all compounds except γ-aminobutyric acid was < −5.0 kJ/mol, indicating the potential of numerous active compounds in TCM to directly interact with IL-6, leading to an anti-inflammation effect. Finally, Cytoscape 3.7.2 was used to topologize the biological processes and pathways of compounds, revealing potential mechanisms for COVID-19 treatment.Conclusion: These results indicated the positive effect of TCM on the prevention and rehabilitation of COVID-19 in at-risk people. Quercetin, ursolic acid, luteolin, and rutin could inhibit COVID-19 by downregulating IL-6.

scholarly journals Integrating Data Mining, Network Pharmacology, and Molecular Docking Verification to Investigate the Molecular Mechanism of Traditional Chinese Medicine Prescriptions for Treating Male Infertility

2021 ◽  
Author(s):  
Xue Bai ◽  
Yibo Tang ◽  
Qiang Li ◽  
Guimin Liu ◽  
Dan Liu ◽  
...  
Keyword(s):  
Data Mining ◽  
Molecular Docking ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Male Infertility ◽  
Signaling Pathway ◽  
Molecular Mechanism ◽  
Oxidant Stress ◽  
Estrogen Signaling ◽  
Network Pharmacology

Abstract Background: Male infertility (MI) affects almost 5% adult men worldwide, and 75% of these cases are unexplained idiopathic. There are limitations in the current treatment due to the unclear mechanism of MI, which highlight the urgent need for a more effective strategy or drug. Traditional Chinese Medicine (TCM) prescriptions have been used to treat MI for thousands of years, but their molecular mechanism is not well defined. Methods: Aiming at revealing the molecular mechanism of TCM prescriptions on MI, a comprehensive strategy integrating data mining, network pharmacology, and molecular docking verification was performed. Firstly, we collected 289 TCM prescriptions for treating MI from National Institute of TCM Constitution and Preventive Medicine for 6 years. Then, Core Chinese Materia Medica (CCMM), the crucial combination of TCM prescriptions, was obtained by the TCM Inheritance Support System from China Academy of Chinese Medical Sciences. Next, the components and targets of CCMM in TCM prescriptions and MI-related targets were collected and analyzed through network pharmacology approach.Results: The results showed that the molecular mechanism of TCM prescriptions for treating MI are regulating hormone, inhibiting apoptosis, oxidant stress and inflammatory. Estrogen signaling pathway, PI3K-Akt signaling pathway, HIF-1 signaling pathway, and TNF signaling pathway are the most important signaling pathways. Molecular docking experiments were used to further validate network pharmacology results. Conclusions: This study not only discovers CCMM and the molecular mechanism of TCM prescriptions for treating MI, but may be helpful for the popularization and application of TCM treatment.

scholarly journals Study on the Mechanism of Baimai Ointment in the Treatment of Osteoarthritis Based on Network Pharmacology and Molecular Docking with Experimental Verification

2021 ◽  
Vol 12 ◽  
Author(s):  
Yingyin Zhu ◽  
Wanling Zhong ◽  
Jing Peng ◽  
Huichao Wu ◽  
Shouying Du
Keyword(s):  
Molecular Docking ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Signaling Pathway ◽  
Molecular Mechanism ◽  
Animal Experiments ◽  
Tibetan Medicine ◽  
Blue Staining ◽  
Network Pharmacology ◽  
Enzyme Linked Immunosorbent Assay

Purpose: The external preparation of the Tibetan medicine formula, Baimai ointment (BMO), has great therapeutic effects on osteoarthritis (OA). However, its molecular mechanism remains almost elusive. Here, a comprehensive strategy combining network pharmacology and molecular docking with pharmacological experiments was adopted to reveal the molecular mechanism of BMO against OA.Methods: The traditional Chinese medicine for systems pharmacology (TCMSP) database and analysis platform, traditional Chinese medicine integrated database (TCMID), GeneCards database, and DisGeNET database were used to screen the active components and targets of BMO in treating OA. A component–target (C-T) network was built with the help of Cytoscape, and the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment through STRING. Autodock Tools which was used to dock the key components and key target proteins was analyzed. Animal experiments were performed to verify the key targets of BMO. Hematoxylin–eosin and toluidine blue staining were used to observe the pathology of joints. Protein expression was determined using enzyme-linked immunosorbent assay.Results: Bioactive compounds and targets of BMO and OA were screened. The network analysis revealed that 17-β-estradiol, curcumin, licochalone A, quercetin, and glycyrrhizic acid were the candidate key components, and IL6, tumor necrosis factor (TNF), MAPK1, VEGFA, CXCL8, and IL1B were the candidate key targets in treating OA. The KEGG indicated that the TNF signaling pathway, NF-κB signaling pathway, and HIF-1 signaling pathway were the potential pathways. Molecular docking implied a strong combination between key components and key targets. The pathology and animal experiments showed BMO had great effects on OA via regulating IL6, TNF, MAPK1, VEGFA, CXCL8, and IL1B targets. These findings were consistent with the results obtained from the network pharmacology approach.Conclusion: This study preliminarily illustrated the candidate key components, key targets, and potential pathways of BMO against OA. It also provided a promising method to study the Tibetan medicine formula or external preparations.

Exploring the mechanisms of Drynariae Rhizoma on treating memory impairment through network pharmacology

2021 ◽  
Author(s):  
Wangmi Liu ◽  
Jiayan Wu
Keyword(s):  
Molecular Docking ◽  
Nerve Growth Factor ◽  
Chinese Medicine ◽  
Growth Factor ◽  
Traditional Chinese Medicine ◽  
Memory Impairment ◽  
Network Pharmacology ◽  
Active Compounds ◽  
Major Health Problem ◽  
Nerve Growth

Abstract Background Memory impairment continues to be a major health problem and increases with age, especially in the elderly population worldwide. However, a causal mechanism has not been clearly identified. Currently, an interaction between bone and brain, the so-called “bone-brain crosstalk,” has emerged. We used a network pharmacology approach to explore the potential mechanisms of Drynariae Rhizoma (DR), a traditional Chinese medicine for fracture treatment, for therapeutic intervention of human conditions associated with memory impairment. Methods The Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform was used to screen out the active compounds of DR, and the targets of the active compounds were predicted using PharmMapper. Targets related to memory impairment were downloaded from the DisGeNET database. The compound-target network and protein-protein interaction network were built by NetworkAnalyst and Cytoscape software. Gene ontology analysis and Reactome pathway enrichment analysis were performed using NetworkAnalyst. SYBYL-X software was used to perform molecular docking simulation. Results Our study demonstrated that DR had 7 active compounds. There were 60 target genes related to these active compounds as well as to memory impairment. Signalling by nerve growth factor was among the top 3 enriched Reactome terms. Akt1 was an important signalling hub gene belonging to signalling by nerve growth factor pathway. Molecular docking results showed that the one of the active compounds, xanthogalenol, exhibited acceptable affinities to Akt1. Conclusion This study demonstrated the molecular mechanism that DR may alleviate memory impairment via regulation of Akt1 and signalling by nerve growth factor pathway. These results offer new ideas in searching for novel strategies for the treatment of memory impairment.

scholarly journals Integrated Analysis of the Mechanisms of Da-Chai-Hu Decoction in Type 2 Diabetes Mellitus by a Network Pharmacology Approach

2020 ◽  
Vol 2020 ◽  
pp. 1-21 ◽  
Author(s):  
Beida Ren ◽  
Ling Tan ◽  
Yiliang Xiong ◽  
Wenting Ji ◽  
Jie Mu ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Type 2 Diabetes Mellitus ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Network Pharmacology ◽  
Integrated Analysis ◽  
Biological Processes ◽  
Active Components

Background. The incidence of type 2 diabetes mellitus (T2DM) has increased year by year, which not only seriously affects people’s quality of life, but also imposes a heavy economic burden on the family, society, and country. Currently, the pathogenesis, diagnosis, and treatment of T2DM are still unclear. Therefore, exploration of a precise multitarget treatment strategy is urgent. Here, we attempt to screen out the active components, effective targets, and functional pathways of therapeutic drugs through network pharmacology with taking advantages of traditional Chinese medicine (TCM) formulas for multitarget holistic treatment of diseases to clarify the potential therapeutic mechanism of TCM formulas and provide a systematic and clear thought for T2DM treatment. Methods. First, we screened the active components of Da-Chai-Hu Decoction (DCHD) by absorption, distribution, metabolism, excretion, and toxicity (ADME/T) calculation. Second, we predicted and screened the active components of DCHD and its therapeutic targets for T2DM relying on the Traditional Chinese Medicine Systems Pharmacology Analysis Platform (TCMSP database) and Text Mining Tool (GoPubMed database), while using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to obtain T2DM targets. Third, we constructed a network of the active component-target, target-pathway of DCHD using Cytoscape software (http://cytoscape.org/,ver.3.5.1) and then analyzed gene function, related biological processes, and signal pathways through the DAVID database. Results. We screened 77 active components from 1278 DCHD components and 116 effective targets from 253 ones. After matching the targets of T2DM, we obtained 38 important targets and 7 core targets were selected through further analysis. Through enrichment analysis, we found that these important targets were mainly involved in many biological processes such as oxidative stress, inflammatory reaction, and apoptosis. After analyzing the relevant pathways, the synthetic pathway for the treatment of T2DM was obtained, which provided a diagnosis-treatment idea for DCHD in the treatment of T2DM. Conclusions. This article reveals the mechanism of DCHD in the treatment of T2DM related to inflammatory response and apoptosis through network pharmacology, which lays a foundation for further elucidation of drugs effective targets.

scholarly journals A Network Pharmacology to Explore the Mechanism of Calculus Bovis in the Treatment of Ischemic Stroke

2021 ◽  
Vol 2021 ◽  
pp. 1-20
Author(s):  
Fangchen Liu ◽  
Ling Li ◽  
Jian Chen ◽  
Ying Wu ◽  
Yongbing Cao ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Second Messengers ◽  
Mapk Signaling ◽  
Network Pharmacology ◽  
Analysis Tool ◽  
Biological Processes ◽  
Hub Genes ◽  
Stroke Treatment

Background. Calculus Bovis is a valuable Chinese medicine, which is widely used in the clinical treatment of ischemic stroke. The present study is aimed at investigating its target and the mechanism involved in ischemic stroke treatment by network pharmacology. Methods. Effective compounds of Calculus Bovis were collected using methods of network pharmacology and using the Bioinformatics Analysis Tool for Molecular Mechanism of Traditional Chinese Medicine (BATMAN-TCM) and the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Potential compound targets were searched in the TCMSP and SwissTargetPrediction databases. Ischemic stroke-related disease targets were searched in the Drugbank, DisGeNet, OMIM, and TTD databases. These two types of targets were uploaded to the STRING database, and a network of their interaction (PPI) was built with its characteristics calculated, aiming to reveal a number of key targets. Hub genes were selected using a plug-in of the Cytoscape software, and Gene Ontology (GO) biological processes and pathway enrichment analyses of Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted using the clusterProfiler package of R language. Results. Among 12 compounds, deoxycorticosterone, methyl cholate, and biliverdin were potentially effective components. A total of 344 Calculus Bovis compound targets and 590 ischemic stroke targets were found with 92 overlapping targets, including hub genes such as TP53, AKT, PIK2CA, MAPK3, MMP9, and MMP2. Biological functions of Calculus Bovis are associated with protein hydrolyzation, phosphorylation of serine/threonine residues of protein substrates, peptide bond hydrolyzation of peptides and proteins, hydrolyzation of intracellular second messengers, antioxidation and reduction, RNA transcription, and other biological processes. Conclusion. Calculus Bovis may play a role in ischemic stroke by activating PI3K-AKT and MAPK signaling pathways, which are involved in regulating inflammatory response, cell apoptosis, and proliferation.

scholarly journals Investigation of the Mechanism of Zishen Yutai Pills on Polycystic Ovary Syndrome: A Network Pharmacology and Molecular Docking Approach

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Yingyin Chen ◽  
Xinyi Chai ◽  
Ying Zhao ◽  
Xinqian Yang ◽  
Caiting Zhong ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Polycystic Ovary Syndrome ◽  
Target Genes ◽  
Polycystic Ovary ◽  
Network Pharmacology ◽  
Analysis Tool ◽  
Ovary Syndrome

Background. Zishen Yutai Pills (ZSYTP) is a prescription based on traditional Chinese medicine used to treat kidney-deficient pattern in traditional Chinese medicine. It is also widely used clinically for the treatment of polycystic ovary syndrome (PCOS) with positive results. This study aims to explore the potential pharmacological mechanism of ZSYTP for the treatment of PCOS by a network pharmacology approach. Methods. Compounds were collected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform and Bioinformatics Analysis Tool for Molecular mechanism of Traditional Chinese Medicine and TCM Database@ Taiwan, and the corresponding targets were retrieved from PubChem, Swiss Target Prediction, STITCH, and DrugBank. Meanwhile, PCOS targets were retrieved from the GeneCards database, the Online Mendelian Inheritance in Man database, National Center for Biotechnology Information Database, and DrugBank. Subsequently, multiple network construction and gene enrichment analyses were conducted with Cytoscape 3.8.2 software. Based on the previous results in the study, molecular docking simulations were done. Results. 205 active compounds and 478 ZSYTP target genes were obtained after screening by ADME consideration. 1881 disease-related targets were obtained after removing duplicates. 148 intersection target genes between drug and disease targets were isolated. Gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes analysis highlighted multiple gene functions and different signaling pathways to treat PCOS. Further molecular docking demonstrated the practicality of in vivo action of ZSYTP to a certain extent. Conclusions. It is possible that the pharmacological effect of ZSYTP on PCOS is linked to the hypoxia-inducible factor 1 (HIF-1) signaling pathway, improving insulin resistance, the variation on gene expression such as RNA splicing, and regulation of mRNA metabolic process. This study paves the way for further research investigating its mechanisms.

scholarly journals Exploring anti-nonalcoholic fatty liver disease mechanism of Gardeniae Fructus by combining an animal model with network pharmacology and molecular docking

2020 ◽  
Author(s):  
Lin Li ◽  
Lihua Lu ◽  
Zhong-yan Tang ◽  
Zhengxiang Xia
Keyword(s):  
Animal Model ◽  
Molecular Docking ◽  
Surface Plasmon Resonance ◽  
Liver Disease ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Fatty Liver Disease ◽  
Target Protein ◽  
Network Pharmacology ◽  
Nonalcoholic Fatty Liver

Abstract Background Gardeniae Fructus (GF), a traditional Chinese medicine in clinic for the treatment of nonalcoholic fatty liver disease (NAFLD). However, the mechanisms of action of GF was still margin. To explore the efficacy and mechanism of action of GF for the treatment of NAFLD, we proposed a strategy combined in vivo efficacy verification, network pharmacology analysis, molecular docking, and validity assay of target protein. Methods Firstly, an animal model induced by the high fat diet feed was established, then orally administrated with GF, the mRNA expression levels of lipogenesis was performed by RT-PCR, the liver tissue specimens were stained by hematoxylin and eosin (H&E), then observed by light microscopy. Secondly, network pharmacology studies clarified the relationship among the active constituents, target protein, and pathways, and then explored by the molecular docking. Finally, validity assay of target protein was performed in surface plasmon resonance (SPR) test. Results GF protected against NAFLD in rats. Network pharmacology showed that quercetin, oleanolic acid, and geniposide, targeted on PPARα, PPARγ, and CA2 genes, through regulating PPAR, AMPK, and cGMP-PKG signal pathways, to protect against NAFLD. And the Conclusion GF could alleviate NAFLD through the molecular mechanisms explored by network pharmacology, molecular docking, and surface plasmon resonance, those method can be effective tools to clarify the mechanisms of actions of traditional Chinese medicine from a holistic perspective.

scholarly journals A Multi-Scale Bioinformatics Study on Novel Mechanism of Xintong Granule for Treating Coronary Heart Disease by Network Pharmacology and Molecular Docking Verification

2020 ◽  
Author(s):  
Zhihong Huang ◽  
Siyu Guo ◽  
Changgeng Fu ◽  
Wei Zhou ◽  
Jingyuan Zhang ◽  
...  
Keyword(s):  
Coronary Heart Disease ◽  
Heart Disease ◽  
Molecular Docking ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Signaling Pathway ◽  
Chinese Herbs ◽  
Network Pharmacology ◽  
Pharmacological Mechanism ◽  
Vascular Regulation

Abstract Background: Xintong Granule (XTG) is a Chinese patent medicine composed of 13 Chinese herbs, which is widely used in the treatment of coronary heart disease (CHD). However, there are few studies on it, and its potential pharmacological mechanism needs to be further elucidated.Methods: In this study, network pharmacology was employed to construct the drug-compounds-targets-pathways molecular regulatory network of the treatment of CHD to explore the effective compounds of XTG and its underlying pharmacological mechanism. First, we established the related ingredients and potential targets of these ingredients databases by Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) and A Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine (BATMAN-TCM). Next, the CHD targets were obtained in DigSee, OMIM, DisGeNET, TTD, GeneCards and GenCLiP3 database. Then, protein-protein interaction (PPI) analysis, GO and KEGG pathway enrichment analysis were carried out and the core targets were filtered by topology. Moreover, molecular docking was performed to assess the binding potential of hub targets and key compounds.Results: The result reflected that 178 components of XTG and 669 putative therapeutic targets were screened out. After a systematic and comprehensive analysis, we identified 9 hub targets (TNF, MAPK1, STAT3, IL6, AKT1, INS, EGFR, EGF, TP53) primarily participated in the comprehensive therapeutic effect related to blood circulation, vascular regulation, cell membrane region, compound binding, receptor activity, signal transduction, AGE-RAGE signaling pathway in diabetic complications, JAK-STAT signaling pathway, PI3K-AKT signaling pathway and MAPK signaling pathway.Conclusion: The results of this study tentatively clarified the potential targets and signaling pathways of XTG against CHD, which may benefit to the development of clinical experimental research and application.

A Study on the Mechanism of Lavender in the Treatment of Insomnia Based on Network Pharmacology

2020 ◽  
Vol 23 (5) ◽  
pp. 419-432
Author(s):  
Yao Wang ◽  
Junbo Zou ◽  
Yanzhuo Jia ◽  
Yulin Liang ◽  
Xiaofei Zhang ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Target Protein ◽  
Ammonium Ion ◽  
Network Pharmacology ◽  
Common Disease ◽  
Active Components ◽  
Target Proteins ◽  
Analysis Platform

Aim and Objective: The common disease of insomnia has complex and diverse clinical manifestations. Lavender represents an effective treatment of insomnia, but the molecular mechanism underlying the effectiveness of this treatment is not clear. The purpose of this study is to investigate the active components, target proteins and molecular pathways of lavender in the treatment of insomnia, thus explaining its possible mechanism. Materials and Methods: Firstly, 54 active components of lavender were identified by gas chromatography-mass spectrometry (GC-MS). The target protein of lavender was predicted by the Traditional Chinese Medicine System Pharmacological Database and Analysis Platform and the SwissTargetPredicating tool, and the target protein of insomnia was predicted by the DisGeNET and DrugBank databases. Then, the "component-target-disease" network diagram was constructed using the Cytoscape 3.7.1 software. KEGG and GO enrichments were analyzed using the R statistical language. Finally, the key target proteins were verified by collecting and verifying the target protein GEO data using the Discovery Studio 3.5 molecular docking verification software. Results: 906 target proteins of lavender were predicted by the Traditional Chinese Medicine System Pharmacological Database and Analysis Platform and the SwissTargetPredicating tool, and 182 insomnia target proteins were predicted by the DisGeNET and DrugBank databases. The results of GO enrichment analysis showed that it included the reaction process of ammonium ion, the regulation of the membrane potential and the secretion of catecholamine, while the results of KEGG enrichment included the calcium signaling pathway, serotonin synapse, morphine addiction and many more. Finally, using the Discovery Studio3.5 molecular docking verification software, it was verified that the key target proteins are ADRB1 and HLA-DRB1. Conclusion: The components in the lavender essential oil include the Ethyl 2-(5-methyl-5-vinyltetrahydrofuran- 2-yl)propan-2-ylcarbonate (0.774); 5-Oxatricyclo[8.2.0.04,6]dodecane, 4,12,12-trimethyl- 9-methylene-, (1R,4R,6R,10S)-(0.147); P-Cymen-7-ol (0.063); .alpha-Humulenem (0.317); Acetic acid, hexyl ester (1.374); etc. The role lavender plays in the treatment of insomnia might be accomplished through the regulation of the key targets ADRB1 and HLA-DRB1.

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