Active ingredient and mechanistic analysis of traditional Chinese medicine formulas for the prevention and treatment of COVID-19: Insights from bioinformatics and in vitro experiments

{ 'indexed': {'date-parts': [[2023, 12, 2]], 'date-time': '2023-12-02T05:17:39Z', 'timestamp': 1701494259694}, 'reference-count': 50, 'publisher': 'Ovid Technologies (Wolters Kluwer Health)', 'issue': '48', 'license': [ { 'start': { 'date-parts': [[2023, 12, 1]], 'date-time': '2023-12-01T00:00:00Z', 'timestamp': 1701388800000}, 'content-version': 'unspecified', 'delay-in-days': 0, 'URL': 'http://creativecommons.org/licenses/by/4.0/'}], 'content-domain': {'domain': [], 'crossmark-restriction': False}, 'published-print': {'date-parts': [[2023, 12, 1]]}, 'abstract': '<jats:p>Coronavirus disease 2019 (COVID-19) is an acute infectious disease caused by a novel ' 'coronavirus. Traditional Chinese medicine (TCM) has been proven to have a potential curative ' 'effect on COVID-19. This study preliminarily analyzed the existing TCM prescription’s key ' 'components and action mechanisms for preventing and treating COVID-19 using bioinformatic and ' 'experimental methods. Association and clustering analysis reveals that the “HQ\u2005+\u2005' 'FF\u2005+\u2005BZ” drug combination had a strong correlation and confidence in 93 TCM ' 'prescriptions and may affect the progression of COVID-19 through inflammatory pathways such ' 'as the TNF signaling pathway. Further molecular docking revealed that quercetin has a higher ' 'affinity for IL6 and IL10 in the TNF signaling pathway associated with COVID-19. In vitro ' 'experiments demonstrated that quercetin could effectively reduce the levels of the ' 'inflammatory factor IL-6 and increase the anti-inflammatory factor IL-10, alleviating ' 'inflammation impact on cells. Our results provide a new understanding of the molecular ' 'mechanism of TCM prevention and treatment of COVID-19, which is helpful to the development of ' 'new diagnosis and treatment schemes for COVID-19.</jats:p>', 'DOI': '10.1097/md.0000000000036238', 'type': 'journal-article', 'created': {'date-parts': [[2023, 12, 2]], 'date-time': '2023-12-02T03:06:06Z', 'timestamp': 1701486366000}, 'page': 'e36238', 'source': 'Crossref', 'is-referenced-by-count': 0, 'title': 'Active ingredient and mechanistic analysis of traditional Chinese medicine formulas for the ' 'prevention and treatment of COVID-19: Insights from bioinformatics and in vitro experiments', 'prefix': '10.1097', 'volume': '102', 'author': [ { 'ORCID': 'http://orcid.org/0009-0002-0477-4698', 'authenticated-orcid': False, 'given': 'Jiakai', 'family': 'Yang', 'sequence': 'first', 'affiliation': [ { 'name': 'Department of Biological Engineering, Qilu University of ' 'Technology, Jinan, China.'}]}, { 'given': 'Qianqian', 'family': 'Zhuang', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Biological Engineering, Qilu University of ' 'Technology, Jinan, China.'}]}, { 'given': 'Chi', 'family': 'Zhang', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Biological Engineering, Qilu University of ' 'Technology, Jinan, China.'}]}, { 'given': 'Xinli', 'family': 'Liu', 'sequence': 'additional', 'affiliation': [ { 'name': 'Department of Biological Engineering, Qilu University of ' 'Technology, Jinan, China.'}]}], 'member': '276', 'reference': [ { 'key': 'R1-20231202', 'doi-asserted-by': 'crossref', 'first-page': '1545', 'DOI': '10.1007/s11606-020-05762-w', 'article-title': 'Review of the clinical characteristics of coronavirus disease 2019 ' '(COVID-19).', 'volume': '35', 'author': 'Jiang', 'year': '2020', 'journal-title': 'J Gen Intern Med'}, { 'key': 'R2-20231202', 'doi-asserted-by': 'crossref', 'first-page': '470', 'DOI': '10.1016/S0140-6736(20)30185-9', 'article-title': 'A novel coronavirus outbreak of global health concern.', 'volume': '395', 'author': 'Wang', 'year': '2020', 'journal-title': 'Lancet'}, { 'key': 'R4-20231202', 'first-page': '86', 'article-title': 'Latest understanding of the epidemiological characteristics of ' 'COVID-19.', 'volume': '10', 'year': '2020', 'journal-title': 'Chin J Viral Dis'}, { 'key': 'R5-20231202', 'doi-asserted-by': 'crossref', 'first-page': '271', 'DOI': '10.1016/j.cell.2020.02.052', 'article-title': 'SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a ' 'clinically proven protease inhibitor.', 'volume': '181', 'author': 'Hoffmann', 'year': '2020', 'journal-title': 'Cell'}, { 'key': 'R6-20231202', 'doi-asserted-by': 'crossref', 'first-page': '77', 'DOI': '10.1038/s41368-020-0074-x', 'article-title': 'High expression of ACE2 receptor of 2019-nCoV on the epithelial cells ' 'of the oral mucosa.', 'volume': '12', 'author': 'Xu', 'year': '2020', 'journal-title': 'Int J Oral Sci'}, { 'key': 'R7-20231202', 'doi-asserted-by': 'crossref', 'DOI': '10.1038/s41586-020-2012-7', 'article-title': 'A pneumonia outbreak associated with a new coronavirus of probable bat ' 'origin.', 'volume': '579', 'author': 'Zhou', 'year': '2020', 'journal-title': 'Nature'}, { 'key': 'R8-20231202', 'article-title': 'Severity of omicron (B11529) and DELTA (B16172) SARS-CoV-2 infection ' 'among hospitalized adults: a prospective cohort study in Bristol, ' 'United Kingdom.', 'volume': '25', 'author': 'Catherine', 'year': '2023', 'journal-title': 'Lancet Reg Health Eur'}, { 'key': 'R10-20231202', 'first-page': '125', 'article-title': 'Global development and prospects of antiviral drug research.', 'volume': '42', 'author': 'Wu', 'year': '2022', 'journal-title': 'Chin J Biotechnol'}, { 'key': 'R11-20231202', 'first-page': '1', 'article-title': 'Latest research and development progress of drugs for COVID-19.', 'volume': '04', 'author': 'Yu', 'year': '2022', 'journal-title': 'China Pharm Ind J'}, { 'key': 'R12-20231202', 'first-page': '3743', 'article-title': 'Pharmaceutical evaluation of Lianhua Qingwen granules combined with ' 'other drugs on clinical efficacy of COVID-19 caused by Omicron variant.', 'volume': '44', 'author': 'Li', 'year': '2022', 'journal-title': 'Tradit Chin Med'}, { 'key': 'R13-20231202', 'first-page': '3667', 'article-title': 'Clinical observation of Xuanfei Baidu decoction in the treatment of ' 'severe COVID-19 cases.', 'volume': '47', 'author': 'Li', 'year': '2022', 'journal-title': 'Chin J Tradit Chin Med'}, { 'key': 'R14-20231202', 'first-page': '1788', 'article-title': 'A retrospective study on the clinical efficacy of Qingfei Paidu ' 'decoction combined with conventional Western medicine in treating 157 ' 'elderly patients with COVID-19.', 'volume': '62', 'author': 'Wang', 'year': '2021', 'journal-title': 'Chin J Tradit Chin Med'}, { 'key': 'R15-20231202', 'first-page': '1021', 'article-title': 'Retrospection and reflection on the prevention and treatment of ' 'COVID-19 with traditional Chinese medicine based on the theory of ' '“preventing disease before it occurs”.', 'volume': '44', 'author': 'Li', 'year': '2021', 'journal-title': 'Chin J Med Mater'}, { 'key': 'R16-20231202', 'first-page': '1', 'article-title': 'Investigation of the mechanism of Hunan COVID-19 formula 2 in ' 'preventing influenza virus in immunosuppressed mice based on network ' 'pharmacology and experimental verification.', 'volume': '10', 'author': 'Ma', 'year': '2022', 'journal-title': 'Chin J Immunol'}, { 'key': 'R17-20231202', 'doi-asserted-by': 'crossref', 'first-page': '13', 'DOI': '10.1186/1758-2946-6-13', 'article-title': 'TCMSP: a database of systems pharmacology for drug discovery from ' 'herbal medicines.', 'volume': '6', 'author': 'Ru', 'year': '2014', 'journal-title': 'J Cheminf'}, { 'key': 'R18-20231202', 'doi-asserted-by': 'crossref', 'first-page': '976', 'DOI': '10.1093/nar/gky987', 'article-title': 'ETCM: an encyclopedia of traditional Chinese medicine.', 'volume': '47', 'author': 'Hai-Yu', 'year': '2019', 'journal-title': 'Nucleic Acids Res'}, { 'key': 'R19-20231202', 'doi-asserted-by': 'crossref', 'first-page': '21146', 'DOI': '10.1038/srep21146', 'article-title': 'BATMAN-TCM: a bioinformatics analysis tool for molecular mechANism of ' 'traditional Chinese medicine.', 'volume': '6', 'author': 'Zhongyang', 'year': '2016', 'journal-title': 'Sci Rep'}, { 'key': 'R20-20231202', 'doi-asserted-by': 'crossref', 'first-page': '668', 'DOI': '10.1093/nar/gkj067', 'article-title': 'DrugBank: a comprehensive resource for in silico drug discovery and ' 'exploration.', 'volume': '34', 'author': 'Wishart', 'year': '2006', 'journal-title': 'Nucleic Acids Res'}, { 'key': 'R21-20231202', 'first-page': '1.30.1', 'article-title': 'The GeneCards suite: from gene data mining to disease genome sequence ' 'analyses.', 'volume': '54', 'author': 'Gil', 'year': '2016', 'journal-title': 'Curr Protoc Bioinform'}, { 'key': 'R22-20231202', 'first-page': '1398', 'article-title': 'Therapeutic target database update 2022: facilitating drug discovery ' 'with enriched comparative data of targeted agents.', 'volume': '50', 'author': 'Ying', 'year': '2021', 'journal-title': 'Nucleic Acids Res'}, { 'key': 'R23-20231202', 'first-page': '845', 'article-title': 'The DisGeNET knowledge platform for disease genomics: 2019 update.', 'volume': '48', 'author': 'Janet', 'year': '2020', 'journal-title': 'Nucleic Acids Res'}, { 'key': 'R24-20231202', 'first-page': '523', 'article-title': 'UniProt: the Universal Protein Knowledgebase in 2023.', 'year': '2022', 'journal-title': 'Nucleic Acids Res'}, { 'key': 'R25-20231202', 'doi-asserted-by': 'crossref', 'first-page': '2498', 'DOI': '10.1101/gr.1239303', 'article-title': 'Cytoscape: a software environment for integrated models of biomolecular ' 'interaction networks.', 'volume': '13', 'author': 'Paul', 'year': '2003', 'journal-title': 'Genome Res'}, { 'key': 'R26-20231202', 'doi-asserted-by': 'crossref', 'first-page': '207', 'DOI': '10.1093/nar/30.1.207', 'article-title': 'Gene expression omnibus: NCBI gene expression and hybridization array ' 'data repository.', 'volume': '30', 'author': 'Edgar', 'year': '2002', 'journal-title': 'Nucleic Acids Res'}, { 'key': 'R27-20231202', 'doi-asserted-by': 'crossref', 'first-page': 'W216', 'DOI': '10.1093/nar/gkac194', 'article-title': 'DAVID: a web server for functional enrichment analysis and functional ' 'annotation of gene lists (2021 update).', 'volume': '50', 'author': 'Sherman', 'year': '2022', 'journal-title': 'Nucleic Acids Res'}, { 'key': 'R28-20231202', 'doi-asserted-by': 'crossref', 'first-page': '44', 'DOI': '10.1038/nprot.2008.211', 'article-title': 'Systematic and integrative analysis of large gene lists using DAVID ' 'bioinformatics resources.', 'volume': '4', 'author': 'Huang da', 'year': '2009', 'journal-title': 'Nat Protocols'}, { 'key': 'R29-20231202', 'doi-asserted-by': 'crossref', 'first-page': 'D437', 'DOI': '10.1093/nar/gkaa1038', 'article-title': 'RCSB protein data bank: powerful new tools for exploring 3D structures ' 'of biological macromolecules for basic and applied research and ' 'education in fundamental biology, biomedicine, biotechnology, ' 'bioengineering and energy sciences.', 'volume': '49', 'author': 'Burley', 'year': '2020', 'journal-title': 'Nucleic Acids Res'}, { 'key': 'R30-20231202', 'doi-asserted-by': 'crossref', 'first-page': 'W530', 'DOI': '10.1093/nar/gkab294', 'article-title': 'PLIP 2021: expanding the scope of the protein-ligand interaction ' 'profiler to DNA and RNA.', 'volume': '49', 'author': 'Adasme', 'year': '2021', 'journal-title': 'Nucleic Acids Res'}, { 'key': 'R31-20231202', 'first-page': '3036', 'article-title': 'Biotechnology - Bioinformatics; New Bioinformatics Study Results ' 'Reported from the University of Pompeu Fabra (DeepSite: Protein binding ' 'site predictor using 3D-convolutional neural networks).', 'volume': '33', 'author': 'Jiménez', 'year': '2017', 'journal-title': 'Network Weekly News'}, { 'key': 'R32-20231202', 'doi-asserted-by': 'crossref', 'first-page': '2778', 'DOI': '10.1021/ci200227u', 'article-title': 'LigPlot+: multiple ligand-protein interaction diagrams for drug ' 'discovery.', 'volume': '51', 'author': 'Laskowski', 'year': '2011', 'journal-title': 'J Chem Inf Model'}, { 'key': 'R33-20231202', 'doi-asserted-by': 'crossref', 'first-page': '293', 'DOI': '10.1186/1471-2105-15-293', 'article-title': 'jvenn: an interactive Venn diagram viewer.', 'volume': '15', 'author': 'Philippe', 'year': '2014', 'journal-title': 'BMC Bioinf'}, { 'key': 'R34-20231202', 'first-page': '523', 'article-title': 'Protection against dextran sulfate sodium-induced ulcerative colitis in ' 'mice by neferine, a natural product from Nelumbo nucifera Gaertn.', 'volume': '22', 'author': 'Xiangjing', 'year': '2021', 'journal-title': 'Cell J'}, { 'key': 'R35-20231202', 'doi-asserted-by': 'crossref', 'first-page': '139', 'DOI': '10.1016/j.theriogenology.2022.11.017', 'article-title': 'Differential expression of inflammatory cytokines, prostaglandin ' 'synthases and secretory leukocyte protease inhibitor in the endometrium ' 'and circulation in different graded CEH-pyometra in bitch.', 'volume': '197', 'author': 'Sasidharan', 'year': '2023', 'journal-title': 'Theriogenology'}, { 'key': 'R36-20231202', 'doi-asserted-by': 'crossref', 'first-page': '103672', 'DOI': '10.1016/j.isci.2021.103672', 'article-title': 'Integrated miRNA/cytokine/chemokine profiling reveals ' 'severity-associated step changes and principal correlates of fatality ' 'in COVID-19.', 'volume': '25', 'author': 'Wilson', 'year': '2021', 'journal-title': 'iScience'}, { 'key': 'R37-20231202', 'first-page': '531', 'article-title': 'BDNF regulates airway ASMC inflammation via the TrkB-PKC-Ca2+ signaling ' 'pathway.', 'volume': '39', 'author': 'Nie', 'year': '2023', 'journal-title': 'Chin J Immunol'}, { 'key': 'R38-20231202', 'first-page': '2375', 'article-title': 'Quercetin C inhibits TNFα-induced endothelial cell inflammation by ' 'upregulating Krüppel-like factor 2.', 'volume': '58', 'author': 'Lei', 'year': '2023', 'journal-title': 'Acta Pharmaceutica Sinica'}, { 'key': 'R39-20231202', 'doi-asserted-by': 'crossref', 'first-page': '929284', 'DOI': '10.3389/fcvm.2022.929284', 'article-title': 'Serial thrombin generation and exploration of alternative ' 'anticoagulants in critically ill COVID-19 patients: observations from ' 'maastricht intensive care COVID cohort&#13.', 'volume': '9', 'author': 'van de Berg', 'year': '2022', 'journal-title': 'Front Cardiovasc Med'}, { 'key': 'R40-20231202', 'doi-asserted-by': 'crossref', 'first-page': '1658', 'DOI': '10.3390/life12101658', 'article-title': 'Coagulation profile of COVID-19 patients.', 'volume': '12', 'author': 'Georgia', 'year': '2022', 'journal-title': 'Life'}, { 'key': 'R41-20231202', 'first-page': '90', 'article-title': 'Abnormal coagulation function in patients with COVID-19 and its ' 'possible mechanisms and treatment strategies.', 'volume': '36', 'author': 'Wu', 'year': '2022', 'journal-title': 'J Shanghai Univ Tradit Chin Med'}, { 'key': 'R42-20231202', 'first-page': '1116923', 'article-title': 'Data mining and network pharmacology analysis of kidney-tonifying herbs ' 'on the treatment of renal osteodystrophy based on the theory of “Kidney ' 'Governing Bones” in traditional Chinese medicine.', 'volume': '2022', 'author': 'Xue', 'year': '2022', 'journal-title': 'Evid-Based Complement Alternat Med'}, { 'key': 'R43-20231202', 'first-page': '1273', 'article-title': 'Observation on the clinical efficacy of Yupingfeng granules in the ' 'treatment of asthma in children during the remission period.', 'volume': '33', 'author': 'Wei', 'year': '2018', 'journal-title': 'Mod Tradit Chin Med'}, { 'key': 'R44-20231202', 'first-page': '118', 'article-title': 'Clinical application observation of Yupingfeng granules in children ' 'with Mycoplasma pneumoniae pneumonia.', 'volume': '25', 'author': 'Zhang', 'year': '2019', 'journal-title': 'Contemp Med'}, { 'key': 'R45-20231202', 'first-page': '134', 'article-title': 'Clinical observation of modified Xiaochaihu decoction combined with ' 'Yupingfeng powder in the treatment of suspected COVID-19 cases.', 'volume': '23', 'author': 'Zheng', 'year': '2021', 'journal-title': 'J Liaoning Univ Tradit Chin Med'}, { 'key': 'R46-20231202', 'first-page': '68', 'article-title': 'Feasibility of Yupingfeng powder in preventing and treating COVID-19 ' 'infection in children with deficiency syndrome of spontaneous ' 'perspiration aged 1 to 6 years based on “preventing disease before it ' 'occurs” theory.', 'volume': '30', 'author': 'He', 'year': '2022', 'journal-title': 'China Folk Med'}, { 'key': 'R47-20231202', 'first-page': '2412', 'article-title': 'Research progress of antiviral activity of quercetin and its ' 'derivatives.', 'volume': '39', 'author': 'Shi', 'year': '2022', 'journal-title': 'Chin J Mod Appl Pharmacy'}, { 'key': 'R48-20231202', 'doi-asserted-by': 'crossref', 'first-page': '16056', 'DOI': '10.3390/ijms232416056', 'article-title': 'Quercetin ameliorates testicular damage in Zucker diabetic fatty rats ' 'through its antioxidant, anti-inflammatory, and anti-apoptotic ' 'properties.', 'volume': '23', 'author': 'Eva', 'year': '2022', 'journal-title': 'Int J Mol Sci'}, { 'key': 'R51-20231202', 'first-page': '119', 'article-title': 'Overview of K-means clustering algorithm research.', 'volume': '39', 'author': 'Wang', 'year': '2022', 'journal-title': 'J East China Jiaotong Univ'}, { 'key': 'R52-20231202', 'doi-asserted-by': 'crossref', 'first-page': '271', 'DOI': '10.1016/j.cell.2020.02.052', 'article-title': 'SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a ' 'clinically proven protease inhibitor.', 'volume': '181', 'author': 'Hoffmann', 'year': '2020', 'journal-title': 'Cell'}, { 'key': 'R53-20231202', 'doi-asserted-by': 'crossref', 'first-page': '37', 'DOI': '10.1186/s41232-020-00146-3', 'article-title': 'How COVID-19 induces cytokine storm with high mortality.', 'volume': '40', 'author': 'Hojyo', 'year': '2020', 'journal-title': 'Inflamm Regen'}, { 'key': 'R54-20231202', 'doi-asserted-by': 'crossref', 'first-page': '8', 'DOI': '10.1186/s13765-023-00769-3', 'article-title': 'Anti-inflammatory effect of taxifolin in TNF-α/IL-17A/IFN-γ induced ' 'HaCaT human keratinocytes.', 'volume': '66', 'author': 'Eun', 'year': '2023', 'journal-title': 'Appl Biol Chem'}], 'container-title': 'Medicine', 'original-title': [], 'language': 'en', 'link': [ { 'URL': 'https://journals.lww.com/10.1097/MD.0000000000036238', 'content-type': 'unspecified', 'content-version': 'vor', 'intended-application': 'similarity-checking'}], 'deposited': { 'date-parts': [[2023, 12, 2]], 'date-time': '2023-12-02T03:06:42Z', 'timestamp': 1701486402000}, 'score': 1, 'resource': {'primary': {'URL': 'https://journals.lww.com/10.1097/MD.0000000000036238'}}, 'subtitle': [], 'short-title': [], 'issued': {'date-parts': [[2023, 12, 1]]}, 'references-count': 50, 'journal-issue': {'issue': '48', 'published-print': {'date-parts': [[2023]]}}, 'URL': 'http://dx.doi.org/10.1097/MD.0000000000036238', 'relation': {}, 'ISSN': ['0025-7974', '1536-5964'], 'subject': ['General Medicine'], 'published': {'date-parts': [[2023, 12, 1]]}}