Systems Pharmacology for Investigation of the Mechanisms of Action of Traditional Chinese Medicine in Drug Discovery

Zhang, Wenjuan; Huai, Ying; Miao, Zhiping; Qian, Airong; Wang, Yonghua

doi:10.3389/fphar.2019.00743

Cited by 151 publications

(108 citation statements)

References 117 publications

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“…Because Chinese herbal medicines contain many ingredients, and multiple absorbable ingredients might exert their effects on the body, the general effects of herbs may be dictated by all of the absorbable ingredients they contain. With this consideration in mind, we extracted the recorded ingredients of each of the plants selected from the Chinese medicine database and screened these ingredients for drug-likeness and oral availability (via ADME filter) [26,32]. The target proteins of all ingredients passing ADME selection were used for network enrichment to predict the general effects of the herbal plants.…”

Section: Discussionmentioning

confidence: 99%

In silico screening of Chinese herbal medicines with the potential to directly inhibit 2019 novel coronavirus

Zhang¹,

Zhang³

et al. 2020

Journal of Integrative Medicine

432

395

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a b s t r a c tObjective: In this study we execute a rational screen to identify Chinese medical herbs that are commonly used in treating viral respiratory infections and also contain compounds that might directly inhibit 2019 novel coronavirus (2019-nCoV), an ongoing novel coronavirus that causes pneumonia. Methods: There were two main steps in the screening process. In the first step we conducted a literature search for natural compounds that had been biologically confirmed as against sever acute respiratory syndrome coronavirus or Middle East respiratory syndrome coronavirus. Resulting compounds were cross-checked for listing in the Traditional Chinese Medicine Systems Pharmacology Database. Compounds meeting both requirements were subjected to absorption, distribution, metabolism and excretion (ADME) evaluation to verify that oral administration would be effective. Next, a docking analysis was used to test whether the compound had the potential for direct 2019-nCoV protein interaction. In the second step we searched Chinese herbal databases to identify plants containing the selected compounds. Plants containing 2 or more of the compounds identified in our screen were then checked against the catalogue for classic herbal usage. Finally, network pharmacology analysis was used to predict the general in vivo effects of each selected herb. Results: Of the natural compounds screened, 13 that exist in traditional Chinese medicines were also found to have potential anti-2019-nCoV activity. Further, 125 Chinese herbs were found to contain 2 or more of these 13 compounds. Of these 125 herbs, 26 are classically catalogued as treating viral respiratory infections. Network pharmacology analysis predicted that the general in vivo roles of these 26 herbal plants were related to regulating viral infection, immune/inflammation reactions and hypoxia response. Conclusion: Chinese herbal treatments classically used for treating viral respiratory infection might contain direct anti-2019-nCoV compounds.

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Section: Discussionmentioning

confidence: 99%

In silico screening of Chinese herbal medicines with the potential to directly inhibit 2019 novel coronavirus

Zhang¹,

Zhang³

et al. 2020

Journal of Integrative Medicine

432

395

View full text Add to dashboard Cite

show abstract

“…Comprehensive determination of potential compound-target interaction profiles is a critical step for the system biology analysis [30]. Currently, multiple databases/platforms, such as DrugBank Database, Comparative Toxicogenomics Database (CTD), Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and Integrative Pharmacology-based Research Platform of Traditional Chinese Medicine (TCMIP), were commonly applied to acquire potential targets of small molecular compounds [31][32][33]. DrugBank contains detailed drug, drug-target, drug action and drug interaction information about FDA-approved drugs as well as experimental drugs [34].…”

Section: Gene Target Acquisition and Screeningmentioning

confidence: 99%

A Novel Combination of Vitamin C, Curcumin and Glycyrrhizic Acid Potentially Regulates Immune and Inflammatory Response Associated with Coronavirus Infections: A Perspective from System Biology Analysis

Chen¹,

Hu²,

Hood

et al. 2020

Nutrients

119

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Novel coronaviruses (CoV) have emerged periodically around the world in recent years. The recurrent spreading of CoVs imposes an ongoing threat to global health and the economy. Since no specific therapy for these CoVs is available, any beneficial approach (including nutritional and dietary approach) is worth investigation. Based on recent advances in nutrients and phytonutrients research, a novel combination of vitamin C, curcumin and glycyrrhizic acid (VCG Plus) was developed that has potential against CoV infection. System biology tools were applied to explore the potential of VCG Plus in modulating targets and pathways relevant to immune and inflammation responses. Gene target acquisition, gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment were conducted consecutively along with network analysis. The results show that VCG Plus can act on 88 hub targets which are closely connected and associated with immune and inflammatory responses. Specifically, VCG Plus has the potential to regulate innate immune response by acting on NOD-like and Toll-like signaling pathways to promote interferons production, activate and balance T-cells, and regulate the inflammatory response by inhibiting PI3K/AKT, NF-κB and MAPK signaling pathways. All these biological processes and pathways have been well documented in CoV infections studies. Therefore, our findings suggest that VCG Plus may be helpful in regulating immune response to combat CoV infections and inhibit excessive inflammatory responses to prevent the onset of cytokine storm. However, further in vitro and in vivo experiments are warranted to validate the current findings with system biology tools. Our current approach provides a new strategy in predicting formulation rationale when developing new dietary supplements.

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“…The systematic and comprehensive characteristics of network pharmacology have something in common with the wholism of TCM. Therefore, in recent years, network pharmacology has gradually penetrated into the research eld of Chinese herbal compound [28,29]. Our study is the rst to identify the bioactive ingredients of SED and explore its mechanisms in DKD treatment by using network pharmacology approach.…”

Section: Introductionmentioning

confidence: 99%

A Network Pharmacology-Based Strategy for Predicting Active Ingredients and Potential Targets of Shuilu Erxian Dan in Treating Diabetic Kidney Disease

Yue

2020

Preprint

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Background and objective: Recent years, some Chinese scholars have applied Shuilu Erxian Dan (SED) to the treatment of treating diabetic kidney disease (DKD) and achieved well curative effect. However, these studies are mostly limited to clinical observation. This study aimed to explore the molecular mechanisms of SED in treating DKD. Methods The active components of SED were retrieved in TCMSP database and BATMAN-TCM database, and the herbal targets were obtained by drugbank database and SwissTargetPrediction platform. The gene expression data of DKD patients were downloaded from GEO database and analyzed to obtain DKD-related targets. The ingredient-target network and the PPI network were constructed by Cytoscape software. The clusterProfiler package of R software is used for bioinformatic analysis. Molecular docking was further applied to verify the interaction between compounds and targets by Autodock Vina software. Results 610 differential expressed genes of DKD patients were obtained, and 29 potential targets of SED against DKD were screened out (including PPTGS2, FABP3, HSD17B2, FABP1, HSD11B2, CYP27B1, JUN, UGT2B7, VCAM1, CA2, MAOA, MMP2, CXCR1, SLC22A6, EPHX2, SLC47A1, FOS, EGF, CCL2, COL3A1, GSTA1, GSTA2, HSPA1A, DAO, ALDH2, ALB, GPR18, FPR2, and LPL). All the active ingredients in SED can act on the DKD-related targets, among which quercetin, Ellagic acid, and kaempferol may be the key active compounds. SED may play a therapeutic role in DKD by regulating pathways including “Fluid shear stress and atherosclerosis”, “AGE − RAGE signaling pathway in diabetic complications” and “IL-17 signaling pathway”. Conclusion This study suggests that the mechanism of SED treating DKD is a complex network with multi-target and multi-pathway, which provides a reference for future experimental studies.

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Systems Pharmacology for Investigation of the Mechanisms of Action of Traditional Chinese Medicine in Drug Discovery

Cited by 151 publications

References 117 publications

In silico screening of Chinese herbal medicines with the potential to directly inhibit 2019 novel coronavirus

In silico screening of Chinese herbal medicines with the potential to directly inhibit 2019 novel coronavirus

A Novel Combination of Vitamin C, Curcumin and Glycyrrhizic Acid Potentially Regulates Immune and Inflammatory Response Associated with Coronavirus Infections: A Perspective from System Biology Analysis

A Network Pharmacology-Based Strategy for Predicting Active Ingredients and Potential Targets of Shuilu Erxian Dan in Treating Diabetic Kidney Disease

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