Potential molecular targets and drugs for basement membranes-related intervertebral disk degeneration through bioinformatics analysis and molecular docking.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37784117", "kind": "science-record", "revision": 4, "content_hash": "sha256:ffffa61f5374f16b9c21f7ee09d4633b7fd4fb57efd2b31ed9b6fa7ad87e0758", "created_at": "2026-11-01T19:02:38Z", "updated_at": "2026-11-01T22:52:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Potential molecular targets and drugs for basement membranes-related intervertebral disk degeneration through bioinformatics analysis and molecular docking.", "doi": "10.1186/s12891-023-06891-z", "pmid": "37784117", "authors": ["Zelin Zhou", "Weicheng Qin", "Peng Zhang", "Jiahui He", "Zhaojun Cheng", "Yan Gong", "Guangye Zhu", "De Liang", "Hui Ren", "Xiaobing Jiang", "Yuping Sun"], "journal": "BMC musculoskeletal disorders", "year": 2023, "abstract": "BACKGROUND: Through bioinformatics analysis to identify the hub genes of Intervertebral disc degeneration (IVDD) associated with basement membranes (BMs) and find out the potential molecular targets and drugs for BMs-related annulus fibrosus (AF) degeneration based on bioinformatic analysis and molecular approach.\nMETHODS: Intervertebral disc degeneration (IVDD) related targets were obtained from GeneCards, DisGenet and OMIM databases. BMs related genes were obtained from Basement membraneBASE database. The intersection targets were identified and subjected to protein-to-protein interaction (PPI) construction via STRING. Hub genes were identified and conducted Gene ontology (GO) and pathway enrichment analysis through MCODE and Clue GO in Cytospace respectively. DSigDB database was retrieved to predict therapeutic drugs and molecular docking was performed through PyMOL, AutoDock 1.5.6 to verify the binding energy between the drug and the different expressed hub genes. Finally, GSE70362 from GEO database was obtained to verify the different expression and correlation of each hub gene for AF degeneration.\nRESULTS: We identified 41 intersection genes between 3 disease targets databases and Basement membraneBASE database. PPI network revealed 25 hub genes and they were mainly enriched in GO terms relating to glycosaminoglycan catabolic process, the TGF-β signaling pathway. 4 core targets were found to be significant via comparison of microarray samples and they showed strong correlation. The molecular docking results showed that the core targets have strong binding energy with predicting drugs including chitosamine and retinoic acid.\nCONCLUSIONS: In this study, we identified hub genes, pathways, potential targets, and drugs for treatment in BMs-related AF degeneration and IVDD.", "claims": [{"id": "claim-method", "statement": "The comparison between the expression of hub genes from the dataset was conducted with the student t-test. After that, the correlation of the significant genes was analyzed by Spearman correlation analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37784117", "locator": "sections[7] \"Hub genes verification and correlation analysis\" paragraph 2", "quote": "The comparison between the expression of hub genes from the dataset was conducted with the student t-test. After that, the correlation of the significant genes was analyzed by Spearman correlation analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE70362 dataset used in this study can be found in the Gene Expression Omnibus (http://www.nicb.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37784117", "locator": "sections[21] \"Data Availability\" paragraph 2", "quote": "The GSE70362 dataset used in this study can be found in the Gene Expression Omnibus (http://www.nicb.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "4 core targets were found to be significant via comparison of microarray samples and they showed strong correlation.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37784117", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "4 core targets were found to be significant via comparison of microarray samples and they showed strong correlation."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "4 core targets were found to be significant via comparison of microarray samples and they showed strong correlation.", "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:37784117"], "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:GSE70362"], "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:GSE70362"], "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:37784117", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12891-023-06891-z", "sha256": "sha256:ef65a24ea5b1d2df0fc5b99c8a6ff702a64dbd681e2d199b5457bfbe2ea18029", "bytes": 39334, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12891-023-06891-z", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10544312", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE70362", "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=GSE70362", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70362", "version": null, "note": "The GSE70362 dataset used in this study can be found in the Gene Expression Omnibus (http://www.nicb.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The GSE70362 dataset used in this study can be found in the Gene Expression Omnibus (http://www.nicb.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1725780", "GSM1725781", "GSM1725782", "GSM1725783", "GSM1725784", "GSM1725785", "GSM1725786", "GSM1725787", "GSM1725788", "GSM1725789", "GSM1725790", "GSM1725791", "GSM1725792", "GSM1725793", "GSM1725794", "GSM1725795", "GSM1725796", "GSM1725797", "GSM1725798", "GSM1725799", "GSM1725800", "GSM1725801", "GSM1725802", "GSM1725803", "GSM1725804", "GSM1725805", "GSM1725806", "GSM1725807", "GSM1725808", "GSM1725809", "GSM1725810", "GSM1725811", "GSM1725812", "GSM1725813", "GSM1725814", "GSM1725815", "GSM1725816", "GSM1725817", "GSM1725818", "GSM1725819", "GSM1725820", "GSM1725821", "GSM1725822", "GSM1725823", "GSM1725824", "GSM1725825", "GSM1725826", "GSM1725827"], "sample_count": 48, "group_sizes": null, "group_sizes_basis": null, "platform": "17810", "taxon": "Homo sapiens", "title": "Gene Expression Profiling Identifies Interferon Signalling Molecules and IGFBP3 in Human Degenerative Annulus Fibrosus", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE70362 not downloaded", "asset:data:geo:GSE70362 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The comparison between the expression of hub genes from the dataset was conducted with the student t-test. 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