In silico analysis of the potential mechanism of a preventive Chinese medicine formula on coronavirus disease 2019.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33831468", "kind": "science-record", "revision": 8, "content_hash": "sha256:d64ca9298d0cd8a8d832f0c98212d3ecbb6068e5ec1021b5ff1eef7dd8cdceb4", "created_at": "2026-11-01T15:41:31Z", "updated_at": "2026-11-01T22:03:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "In silico analysis of the potential mechanism of a preventive Chinese medicine formula on coronavirus disease 2019.", "doi": "10.1016/j.jep.2021.114098", "pmid": "33831468", "authors": ["Huaying Wu", "Ke Gong", "You Qin", "Zhiying Yuan", "Shuaishuai Xia", "Shiying Zhang", "Jingjing Yang", "Ping Yang", "Liang Li", "Mengzhou Xie"], "journal": "Journal of ethnopharmacology", "year": 2021, "abstract": "ETHNOPHARMACOLOGICAL RELEVANCE: With the spread of Coronavirus Disease (2019) (COVID-19), combination with traditional Chinese medicine (TCM) has been widely used as a prevention and therapy strategy in China. Xin guan No.1 (XG-1) prescription is a preventive formula recommended by the Hunan Provincial Administration of TCM to prevent the pandemic of COVID-19.\nAIM OF THE STUDY: To explore the potential preventive mechanisms of XG-1 against COVID-19 in the combination of network pharmacology approach, single-cell RNA expression profiling analysis, molecular docking and retrospective study.\nMATERIALS AND METHODS: Encyclopedia of Traditional Chinese Medicine (ETCM) database was used to determine the meridian tropism, active components and target genes of XG-1. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis were conducted by R Cluster Profiler package (3.14.3). Single cell RNA sequencing (scRNA-seq) data of human lung (GSE122960) was downloaded from Gene Expression Omnibus (GEO) database and analyzed by R Seurat package (3.1.2). Cytoscape (3.7.2) was used to construct the interaction network. The main ingredients in XG-1 were identified by HPLC- Q-TOF- MS and used for molecular docking with COVID-19 3CL hydrolytic enzyme and angiotensin converting enzyme II (ACE2). A retrospective study of 47 close contact participants from Dongtang Community of Hunan Province was conducted to evaluated the preventive effect of XG-1.\nRESULTS: According to the network pharmacology analysis, XG-1 formula was closely related to lung-, spleen- and stomach-meridians and include a total of 206 active components and 853 target genes. GO and KEGG pathway enrichment revealed that XG-1 mainly regulated cellular amino acid metabolism process and neuroactive ligand-receptors interaction. The scRNA-seq profiling showed that angiotensin converting enzyme 2 (ACE2) was principally expressed in alveolar type 2 epithelial cells (AT2). 153 genes were up-regulated in AT2 cells expressing ACE2 and 12 genes were obtained by intersecting with XG-1 target genes, of which 3 were related to immunity. Five main chemical ingredients were detected in XG-1 sample by HPLC-Q-TOF-MS. The molecular docking showed that Rutin, Liquiritin and Astragaloside Ⅳ had a good affinity with COVID-19 3CL hydrolytic enzyme and ACE2. Compared with participants who didn't take XG-1, preventive treatment with XG-1gradules resulted in a significant lower rate of testing positive for SARS-CoV-2 nucleic acid (P < 0.0001).\nCONCLUSION: The present study showed that XG-1 exerts a preventive effect in close contacts against COVID-19. The underlying mechanism may be related to modulate immunity response through multiple components, pathways, and several target genes co-expressed with ACE2. These findings provide preliminary evidences and methodological reference for the potential preventive mechanism of XG-1 against COVID-19.", "claims": [{"id": "claim-data-access", "statement": "The human lung tissue single cell transcriptome sequencing data (GSE122960) was downloaded from the GEO database, and the Seurat software package in R (3.6.2) ((http://satijalab.org/seurat/, version: 3.1.2) was used to perform cell clustering.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33831468", "locator": "sections[5] \"Single-cell RNA expression profiling cluster analysis\" paragraph 2", "quote": "The human lung tissue single cell transcriptome sequencing data (GSE122960) was downloaded from the GEO database, and the Seurat software package in R (3.6.2) ((http://satijalab.org/seurat/, version: 3.1.2) was used to perform cell clustering."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:33831468"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE122960"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE122960"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33831468", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.jep.2021.114098", "sha256": "sha256:4ab3e0a56f47a54f6ad596b33732720b1b0e02b40dc25790c3620b6c43d28a6e", "bytes": 58673, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.jep.2021.114098", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8020622", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE122960", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122960", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE122960", "version": null, "note": "The human lung tissue single cell transcriptome sequencing data (GSE122960) was downloaded from the GEO database, and the Seurat software package in R (3.6.2) ((http://satijalab.org/seurat/, version: 3.1.2) was used to perform cell clustering.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The human lung tissue single cell transcriptome sequencing data (GSE122960) was downloaded from the GEO database, and the Seurat software package in R (3.6.2) ((http://satijalab.org/seurat/, version: 3.1.2) was used to perform cell clustering.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM3489182", "GSM3489183", "GSM3489184", "GSM3489185", "GSM3489186", "GSM3489187", "GSM3489188", "GSM3489189", "GSM3489190", "GSM3489191", "GSM3489192", "GSM3489193", "GSM3489194", "GSM3489195", "GSM3489196", "GSM3489197", "GSM3489198"], "sample_count": 17, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis II", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33831468:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5f4a5d982a875c39237762d47dd178be806166edc3037aa6db96f1bf48f6b363", "bytes": 821, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tbl1", "version": null, "note": "Number of compounds contained in herbs of XG-1 and corresponding putative targets.", "structure": {"pmcid": "PMC8020622", "section_index": 3, "section_title": "Information collection of XG-1", "row_count": 9, "column_count": 4}, "table": {"label": "Table 1", "caption": "Number of compounds contained in herbs of XG-1 and corresponding putative targets.", "rows": [["Chinese name", "Scientific name", "Number of active ingredients", "Number of targets"], ["HUANG QI", "Astragalus mongholicus Bunge", "27", "461"], ["BAI ZHU", "Atractylodes macrocephala Koidz.", "20", "368"], ["LIAN QIAO", "Forsythia suspensa (Thunb.) 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