HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine

Fang, Shuangsang; Li, Dong; Liu, Liu; Guo, Jincheng; Zhao, Lianhe; Zhang, Jia-yuan; Bu, Dechao; Liu, Xinkui; Huo, Peipei; Cao, Wanchen; Dong, Qiongye; Wu, Jiarui; Zeng, Xiaoxi; Wu, Yang; Zhao, Yi

doi:10.1093/nar/gkaa1063

Cited by 370 publications

(242 citation statements)

References 55 publications

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“…HERB database ( https://herb.ac.cn/ ) is a high-throughput experiment and reference-guided database of TCM. This database provides 6164 gene expression profiles from 1037 high-throughput experiments evaluating TCM herbs and ingredients [ 23 ]. In the herb database, we search related gene targets of each drug of HJD and collect them.…”

Section: Methodsmentioning

confidence: 99%

The Research on the Treatment of Metastatic Skin Cutaneous Melanoma by Huanglian Jiedu Decoction Based on the Analysis of Immune Infiltration Analysis

et al. 2021

Evidence-Based Complementary and Alternative Medicine

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Objective. To explore the potential mechanism of Huanglian Jiedu Decoction (HJD) treatment and prevention of metastatic Cutaneous Melanoma (CM) occurrence and metastasis based on network pharmacological methods and immune infiltration analysis. Methods. The GEO database was used to obtain metastatic CM disease targets, the TCMSP database and the HERB database were used to obtain HJD action targets, core genes were screened by protein interaction network, and the potential mechanism of HJD in the treatment of metastatic CM was explored by enrichment analysis, prognostic analysis and immune infiltration analysis. Results. HJD treatment of metastatic CM involved 60 targets, enrichment analysis showed that HJD treatment of metastatic CM involved Chemokine signaling pathway, NF-kappa B signaling pathway, and Fluid shear stress and atherosclerosis, etc. Prognostic analysis revealed that HJD had a certain ability to improve the prognosis of metastatic CM patients. Immune infiltration analysis showed that HJD could inhibit the immune cell infiltration of metastatic CM patients by acting on related targets. Conclusions. Our study identified the potential mechanism of HJD in the treatment of metastatic CM through network pharmacology, and revealed the mechanism of HJD in the prevention of Skin Cutaneous Melanoma metastasis through immune infiltration analysis and prognostic analysis.

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Section: Methodsmentioning

confidence: 99%

The Research on the Treatment of Metastatic Skin Cutaneous Melanoma by Huanglian Jiedu Decoction Based on the Analysis of Immune Infiltration Analysis

et al. 2021

Evidence-Based Complementary and Alternative Medicine

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“…39 HERB (http://herb.ac.cn/) and TargetNet (http://targetnet.scbdd.com). 40,41 Epileptic targets were predicted and gathered using the GeneCards database (http://www.genecards.org). 42 DrukBand platform (https://www.drugbank.ca/).…”

Section: Predicting Functional Targets Of Ba and Mining Known Epilepsy-related Genesmentioning

confidence: 99%

Baicalin Rescues Cognitive Dysfunction, Mitigates Neurodegeneration, and Exerts Anti-Epileptic Effects Through Activating TLR4/MYD88/Caspase-3 Pathway in Rats

Yang

Jia

Xiao

et al. 2021

DDDT

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This study aims to evaluate the beneficial effects of anti-epileptic mechanisms of baicalin (BA) on cognitive dysfunction and neurodegeneration in pentylenetetrazol (PTZ)induced epileptic rats. Methods: First, PTZ-induced epileptic rats were administered intraperitoneally a subconvulsive dose of PTZ (40 mg/kg) daily, and the seizure susceptibility (the degree of seizures and latency) was evaluated using Racine's criterion. Then, classical behavioral experiments were performed to test whether BA ameliorated cognitive dysfunction. Neurodegeneration was assessed using Fluoro Jade-B (FJB), and NeuN staining was used to determine whether BA offered a neuroprotective role. After BA had been proven to possess anti-epileptic effects, its possible mechanisms were analyzed through network pharmacology. Finally, the key targets for predictive mechanisms were experimentally verified.Results: The epileptic model was successfully established, and BA had anti-epileptic effects. Epileptic rats displayed significant cognitive dysfunction, and BA markedly ameliorated cognitive dysfunction. Further, we also discovered that BA treatment mitigated neurodegeneration of the hippocampus CA3 regions, thereby ameliorated cognitive dysfunction of epileptic rats. Subsequent network pharmacology analysis was implemented to reveal a possible mechanism of BA in the anti-epileptic process and the TLR4/MYD88/Caspase-3 pathway was predicted. Finally, experimental studies showed that BA exerted an antiepileptic effect by activating the TLR4/MYD88/Caspase-3 pathway in PTZ-induced epileptic rats. Conclusion:In conclusion, BA had a protective effect against PTZ-induced seizures. BA improved cognitive dysfunction and exerted a neuroprotective action. The anti-epileptic effects of BA may be potentially through activation of the TLR4/MYD88/Caspase-3 pathway.

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“…The compounds of MGMD were extracted from the HERB database 1 (Fang et al, 2020) and the encyclopedia of traditional Chinese medicine (ETCM) 2 (Xu et al, 2019). HERB contains a comprehensive list of 7263 TCM herbs and 49258 ingredients by integrating multiple TCM databases included SymMap (Wu et al, 2019), TCMID 2.0 (Huang et al, 2018), TCMSP 2.3 (Ru et al, 2014), and TCM-ID (Chen et al, 2006).…”

Section: Active Compounds Collectionmentioning

confidence: 99%

Pharmacological Mechanisms Underlying the Anti-asthmatic Effects of Modified Guomin Decoction Determined by Network Pharmacology and Molecular Docking

Wang

Zhou

Wang

et al. 2021

Front. Mol. Biosci.

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BackgroundAsthma is a chronic inflammatory disease characterized by Th2-predominant inflammation and airway remodeling. Modified Guo Min decoction (MGMD) has been an extensive practical strategy for allergic disorders in China. Although its potential anti-asthmatic activity has been reported, the exact mechanism of action of MGMD in asthma remains unexplored.MethodsNetwork pharmacology approach was employed to predict the active components, potential targets, and molecular mechanism of MGMD for asthma treatment, including drug-likeness evaluation, oral bioavailability prediction, protein–protein interaction (PPI) network construction and analysis, Gene Ontology (GO) terms, and Reactome pathway annotation. Molecular docking was carried out to investigate interactions between active compounds and potential targets.ResultsA total of 92 active compounds and 72 anti-asthma targets of MGMD were selected for analysis. The GO enrichment analysis results indicated that the anti-asthmatic targets of MGMD mainly participate in inflammatory and in airway remolding processes. The Reactome pathway analysis showed that MGMD prevents asthma mainly through regulation of the IL-4 and IL-13 signaling and the specialized pro-resolving mediators (SPMs) biosynthesis. Molecular docking results suggest that each bioactive compounds (quercetin, wogonin, luteolin, naringenin, and kaempferol) is capable to bind with STAT3, PTGS2, JUN, VEGFA, EGFR, and ALOX5.ConclusionThis study revealed the active ingredients and potential molecular mechanism by which MGMD treatment is effective against airway inflammation and remodeling in asthma through regulating IL-4 and IL-13 signaling and SPMs biosynthesis.

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HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine

Cited by 370 publications

References 55 publications

The Research on the Treatment of Metastatic Skin Cutaneous Melanoma by Huanglian Jiedu Decoction Based on the Analysis of Immune Infiltration Analysis

The Research on the Treatment of Metastatic Skin Cutaneous Melanoma by Huanglian Jiedu Decoction Based on the Analysis of Immune Infiltration Analysis

Baicalin Rescues Cognitive Dysfunction, Mitigates Neurodegeneration, and Exerts Anti-Epileptic Effects Through Activating TLR4/MYD88/Caspase-3 Pathway in Rats

Pharmacological Mechanisms Underlying the Anti-asthmatic Effects of Modified Guomin Decoction Determined by Network Pharmacology and Molecular Docking

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