Identification and validation of targets of swertiamarin on idiopathic pulmonary fibrosis through bioinformatics and molecular docking-based approach.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37798725", "kind": "science-record", "revision": 4, "content_hash": "sha256:cb4a4003e9758d86d6b101ed3110848fcf774d18c50296b013ae8e9ea1f2f7e2", "created_at": "2026-11-01T19:02:39Z", "updated_at": "2026-11-01T22:10:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of targets of swertiamarin on idiopathic pulmonary fibrosis through bioinformatics and molecular docking-based approach.", "doi": "10.1186/s12906-023-04171-w", "pmid": "37798725", "authors": ["Jun Chang", "Shaoqing Zou", "Yiwen Xiao", "Du Zhu"], "journal": "BMC complementary medicine and therapies", "year": 2023, "abstract": "BACKGROUND: Swertiamarin is the main hepatoprotective component of Swertiapatens and has anti-inflammatory and antioxidation effects. Our previous study showed that it was a potent inhibitor of idiopathic pulmonary fibrosis (IPF) and can regulate the expressions of α-smooth muscle actin (α-SMA) and epithelial cadherin (E-cadherin), two markers of the TGF-β/Smad (transforming growth factor beta/suppressor of mothers against decapentaplegic family) signaling pathway. But its targets still need to be investigated. The main purpose of this study is to identify the targets of swertiamarin.\nMETHODS: GEO2R was used to analyze the differentially expressed genes (DEGs) of GSE10667, GSE110147, and GSE71351 datasets from the Gene Expression Omnibus (GEO) database. The DEGs were then enriched with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis for their biological functions and annotated terms. The protein-protein interaction (PPI) network was constructed to identify hub genes. The identified hub genes were predicted for their bindings to swertiamarin by molecular docking (MD) and validated by experiments.\nRESULTS: 76 upregulated and 27 downregulated DEGs were screened out. The DEGs were enriched in the biological function of cellular component (CC) and 7 cancer-related signaling pathways. Three hub genes, i.e., LOX (lysyl oxidase), COL5A2 (collagen type V alpha 2 chain), and CTGF (connective tissue growth factor) were selected, virtually tested for the interactions with swertiamarin by MD, and validated by in vitro experiments.\nCONCLUSION: LOX, COL5A2, and CTGF were identified as the targets of swertiamarin on IPF.", "claims": [{"id": "claim-method", "statement": "To avoid the batch effect, GSE10667, GSE110147, and GSE71351 datasets were separately analyzed for DEGs with GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r) between control and IPF groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37798725", "locator": "sections[4] \"Identification of differentially expressed genes\" paragraph 2", "quote": "To avoid the batch effect, GSE10667, GSE110147, and GSE71351 datasets were separately analyzed for DEGs with GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r) between control and IPF groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE10667, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10667.GSE110147, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110147.GSE71351, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71351.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37798725", "locator": "sections[25] \"notes\" paragraph 1", "quote": "GSE10667, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10667.GSE110147, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110147.GSE71351, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71351."}], "state": "complete"}, {"id": "claim-target-result", "statement": "LOX, COL5A2, and CTGF were identified as the targets of swertiamarin on IPF.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37798725", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "LOX, COL5A2, and CTGF were identified as the targets of swertiamarin on IPF."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "LOX, COL5A2, and CTGF were identified as the targets of swertiamarin on IPF.", "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:37798725"], "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:GSE10667"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "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:GSE10667"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37798725", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12906-023-04171-w", "sha256": 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