ETCM: an encyclopaedia of traditional Chinese medicine

Xu, Haiyu; Zhang, Yanqiong; Liu, Zhenming; Chen, Tong; Lv, Chuan-Yu; Tang, Shi-Huan; Zhang, Xiaobo; Zhang, Wei; Li, Zhiyong; Zhou, Rongrong; Yang, Hongjun; Wang, Xiu‐Jie; Huang, Luqi

doi:10.1093/nar/gky987

Cited by 530 publications

(359 citation statements)

References 23 publications

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“…CTD provides core information on chemical-gene interactions that are manually curated from scientific literature [35,36]. While TCMIP predicts the potential targets for herbal chemical compounds using MedChem Studio (version 3.0), an efficient drug similarity search tool to identify herbal chemical compounds with high structural similarity (Tanimoto score > 0.8) to known drugs [37]. Basically, the target information in these three databases is complementary, a combination of which could provide relatively comprehensive compound-target interactions.…”

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

112

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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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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

112

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“…In the present study, the chemical compound data of A. oxyphylla were collected from SymMap (http://symmap/org/) [61], which is an integrative database covering information from the Traditional Chinese Medicine System Pharmacology (TCMSP) database and analysis platform, http://ibts.hkbu. edu.hk/LSP/tcmsp.php) [62], the Traditional Chinese Medicine Integrated Database (TCMID) [63] the Traditional Chinese Medicine Information Database (TCM-ID) [64], and the Encyclopedia of Traditional Chinese Medicine (ETCM; http://www.nrc.ac.cn:9090/ETCM/) database [65]. The comprehensive drug-likeness grading and pharmacokinetic properties of A. oxyphylla were evaluated and filtered for the candidate compounds using the absorptions, distribution, metabolism, excretion, and toxicity (ADMET) criterion as oral bioavailability (OB ≥ 30%), drug-likeness (DL ≥ 0.18) evaluation, and blood-brain barrier (BBB ≥ −0.3), respectively.…”

Section: Compound Database Buildingmentioning

confidence: 99%

Pharmacological Mechanisms Underlying the Neuroprotective Effects of Alpinia oxyphylla Miq. on Alzheimer’s Disease

Wang

Guo

et al. 2020

IJMS

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Alpinia oxyphylla Miq. (i.e., A. oxyphylla), a traditional Chinese medicine, can exert neuroprotective effects in ameliorating mild cognitive impairment and improving the pathological hallmarks of Alzheimer's disease (AD). Here, 50 active compounds and 164 putative targets were collected and identified with 251 clinically tested AD-associated target proteins using network pharmacology approaches. Based on the Gene Ontology/Kyoto Encyclopedia of Genes and Genomes pathway enrichments, the compound-target-pathway-disease/protein-protein interaction network constructions, and the network topological analysis, we concluded that A. oxyphylla may have neuroprotective effects by regulating neurotransmitter function, as well as brain plasticity in neuronal networks. Moreover, closely-related AD proteins, including the amyloid-beta precursor protein, the estrogen receptor 1, acetylcholinesterase, and nitric oxide synthase 2, were selected as the bottleneck nodes of network for further verification by molecular docking. Our analytical results demonstrated that terpene, as the main compound of A. oxyphylla extract, exerts neuroprotective effects, providing new insights into the development of a natural therapy for the prevention and treatment of AD.

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“…In addition to this, there are several other, smaller, databases for NPs TCM that can be cited, such as the Chinese Ethnic Minority Traditional Drug Database (CEMTDD) [96], that is maintained, but not updated and contains 4000 NPs, the Chinese Traditional Medicinal Herbs Database (CHDD) [97], not maintained anymore, but according to the publication contained over 30,000 entries, now not accessible and probably lost for the scientific community. Some other databases containing phytochemicals and other active compounds used in TCM can be cited, such as the Comprehensive Herbal Medicine Information System for Cancer (CHMIS-C) [98] that is not maintained anymore, the Encyclopaedia of Traditional Chinese Medicine (ETCM) [99], that is maintained but the chemical structures it contains are not easily retrievable, the database of medicinal materials and chemical compounds in Northeast Asian TM (TM-MC) [100], which is maintained, updated, but no structures but contains precise plant species for all compounds, the Traditional Chinese Medicine Integrative Database (TCMID) [101], maintained, but not updated anymore, The Traditional Chinese Medicine Systems Pharmacology database and analysis platform (TCMSP) [102], that is also not maintained anymore but used to contain over 29,000 NPs. One can quickly realize that there is a lot of databases that focus on chemical compounds used in TCM, and creators of the latter recognize it: there is even a database called "Yet Another Traditional Chinese Medicine Database" (YaTCM) [103] that was published in 2018.…”

Section: Natural Products By Usementioning

confidence: 99%

Review on natural products databases: where to find data in 2020

2020

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Natural products (NPs) have been the centre of attention of the scientific community in the last decencies and the interest around them continues to grow incessantly. As a consequence, in the last 20 years, there was a rapid multiplication of various databases and collections as generalistic or thematic resources for NP information. In this review, we establish a complete overview of these resources, and the numbers are overwhelming: over 120 different NP databases and collections were published and re-used since 2000. 98 of them are still somehow accessible and only 50 are open access. The latter include not only databases but also big collections of NPs published as supplementary material in scientific publications and collections that were backed up in the ZINC database for commercially-available compounds. Some databases, even published relatively recently are already not accessible anymore, which leads to a dramatic loss of data on NPs. The data sources are presented in this manuscript, together with the comparison of the content of open ones. With this review, we also compiled the open-access natural compounds in one single dataset a COlleCtion of Open NatUral producTs (COCONUT), which is available on Zenodo and contains structures and sparse annotations for over 400,000 non-redundant NPs, which makes it the biggest open collection of NPs available to this date.

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ETCM: an encyclopaedia of traditional Chinese medicine

Cited by 530 publications

References 23 publications

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 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

Pharmacological Mechanisms Underlying the Neuroprotective Effects of Alpinia oxyphylla Miq. on Alzheimer’s Disease

Review on natural products databases: where to find data in 2020

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