Bioinformatic Analysis and Molecular Docking Identify Isorhamnetin Is a Candidate Compound in the Treatment of Pulmonary Artery Hypertension.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39605239", "kind": "science-record", "revision": 4, "content_hash": "sha256:ffbba2f66da7133f9b4bb471c2ed1c351fc544927b6bd09f646d6741a9cacfc8", "created_at": "2026-11-01T20:29:52Z", "updated_at": "2026-11-01T22:55:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatic Analysis and Molecular Docking Identify Isorhamnetin Is a Candidate Compound in the Treatment of Pulmonary Artery Hypertension.", "doi": "10.14744/AnatolJCardiol.2024.4723", "pmid": "39605239", "authors": ["Chen Shao", "Wei Xia", "Yang Liu"], "journal": "Anatolian journal of cardiology", "year": 2025, "abstract": "BACKGROUND: The current study aims to identify the key pathways and potential therapeutic targets for pulmonary arterial hypertension (PAH) and to further evaluate the anti-PAH effects of isorhamnetin.\nMETHODS: The dataset of gene expression profiling for PAH (GSE113439) was downloaded from the gene expression omnibus (GEO) database. Isorhamnetin target genes were extracted from the comparative toxicogenomics database (CTD). Various bioinformatics methods were employed to identify the core pathways associated with PAH and potential intervention targets. Molecular docking was conducted between the interacting target and the candidate compound, isorhamnetin.\nRESULTS: One thousand nine hundred sixty-two upregulated genes and 642 downregulated genes were identified. Molecular complex detection analyses revealed that the significant biological processes associated with upregulated genes included DNA damage response, mitotic cell cycle, and chromosome organization. In contrast, the signifi ant biological processes related to downregulated genes encompassed cellular response to growth factor stimulus, response to growth factor, and blood vessel development. Immune infilt ation analysis indicated that PAH is associated with signifi ant changes in the distribution of immune cells and differential expression of immune checkpoints. Furthermore, 58 isorhamnetin targets were extracted from the CTD, and we identified 1 interacting gene, NFE2L2, among the differentially expressed genes (DEGs), DEGs related to ferroptosis, and isorhamnetin targets. Isorhamnetin demonstrated strong affinities with vascular endothelial growth factor (VEGF) receptors and transcription factors (ATM and ZNF24) associated with VEGFs, as well as the ferroptosis protein NFE2L2.\nCONCLUSIONS: Pulmonary arterial hypertension is characterized by a series of abnormalities in downstream molecular signaling pathways, including DNA damage, immune dysregulation, VEGF signaling deficienc , and the ferroptosis process. These may represent the core pathophysiological mechanisms of PAH. Ferroptosis-related genes, such as NFE2L2 and TF (ATM, ZNF24) associated with VEGFs, are potential therapeutic targets that contribute to the mechanisms mentioned above. Isorhamnetin is a promising candidate compound for the treatment of PAH.", "claims": [{"id": "claim-method", "statement": "The limma package in the R software was employed to analyze the differentially expressed mRNAs (R software is developed by Synopsys in the United States).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39605239", "locator": "sections[5] \"Differentially Expressed Genes\" paragraph 2", "quote": "The limma package in the R software was employed to analyze the differentially expressed mRNAs (R software is developed by Synopsys in the United States)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All original materials can be obtained from the PubMed database (GSE113439) and corresponding study (Mura et al16, Respirology 2019;24(11):1104-1110).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39605239", "locator": "sections[25] \"fn-group\" paragraph 1", "quote": "All original materials can be obtained from the PubMed database (GSE113439) and corresponding study (Mura et al16, Respirology 2019;24(11):1104-1110)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 2604 differentially expressed genes were identified in PAH, comprising 1962 upregulated genes and 642 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39605239", "locator": "sections[15] \"Identification of DEGs in PAH\" paragraph 2", "quote": "We identified a total of 2604 DEGs, comprising 1962 upregulated genes and 642 downregulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 2604 differentially expressed genes were identified in PAH, comprising 1962 upregulated genes and 642 downregulated genes.", "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:39605239"], "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. 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