Xi Zheng, Xin Ke, Jie Gao, Zhaohui Zheng, Ping Zhu
{"title":"通过网络药理学和分子对接研究全反式维甲酸结合类风湿关节炎相关靶基因的分子基础。","authors":"Xi Zheng, Xin Ke, Jie Gao, Zhaohui Zheng, Ping Zhu","doi":"10.1007/s10067-025-07482-0","DOIUrl":null,"url":null,"abstract":"<p><strong>Objective: </strong>All-trans retinoic acid (ATRA), a natural derivative of Vitamin A, plays a crucial role in cellular proliferation, differentiation, and metabolic functions. It has been reported to possess significant antioxidant and anti-inflammatory properties. However, a comprehensive investigation into its potential mechanisms within the framework of rheumatoid arthritis (RA) has yet to be adequately addressed.</p><p><strong>Methods: </strong>This study aimed to identify potential targets of ATRA by employing databases such as DrugBank and SwissTargetPrediction. Furthermore, disease-associated genes relevant to rheumatoid arthritis were sourced from DisGeNET and GeneCards. Analyses of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were conducted. Drug-target-pathway networks were developed, and significant hub genes were identified. In addition, molecular docking studies were performed to assess the binding affinity of ATRA.</p><p><strong>Results: </strong>The results indicated that ATRA engages with 127 identified target genes, of which 85 are linked to rheumatoid arthritis (RA). Analyses employing Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and network approaches suggested that these targets participate in inflammatory pathways and metabolic processes pertinent to RA. Additionally, molecular docking studies revealed a significant binding affinity between ATRA and the proteins CYP1A1 and CYP2B6.</p><p><strong>Conclusion: </strong>ATRA is anticipated to engage with various proteins and pathways associated with rheumatoid arthritis, suggesting its potential utility in the clinical management of this disorder. Key Points • All-trans retinoic acid (ATRA) has been shown to interact with 85 specific genes in patients with RA, among which 10 key hub genes have been identified. • Molecular docking studies indicate that ATRA exhibits the lowest binding affinity with the genes CYP1 A1 and CYP2B6.</p>","PeriodicalId":10482,"journal":{"name":"Clinical Rheumatology","volume":" ","pages":""},"PeriodicalIF":2.9000,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"The molecular basis of all-trans retinoic acid binding to the target genes involved in rheumatoid arthritis through network pharmacology and molecular docking.\",\"authors\":\"Xi Zheng, Xin Ke, Jie Gao, Zhaohui Zheng, Ping Zhu\",\"doi\":\"10.1007/s10067-025-07482-0\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Objective: </strong>All-trans retinoic acid (ATRA), a natural derivative of Vitamin A, plays a crucial role in cellular proliferation, differentiation, and metabolic functions. It has been reported to possess significant antioxidant and anti-inflammatory properties. However, a comprehensive investigation into its potential mechanisms within the framework of rheumatoid arthritis (RA) has yet to be adequately addressed.</p><p><strong>Methods: </strong>This study aimed to identify potential targets of ATRA by employing databases such as DrugBank and SwissTargetPrediction. Furthermore, disease-associated genes relevant to rheumatoid arthritis were sourced from DisGeNET and GeneCards. Analyses of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were conducted. Drug-target-pathway networks were developed, and significant hub genes were identified. In addition, molecular docking studies were performed to assess the binding affinity of ATRA.</p><p><strong>Results: </strong>The results indicated that ATRA engages with 127 identified target genes, of which 85 are linked to rheumatoid arthritis (RA). Analyses employing Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and network approaches suggested that these targets participate in inflammatory pathways and metabolic processes pertinent to RA. Additionally, molecular docking studies revealed a significant binding affinity between ATRA and the proteins CYP1A1 and CYP2B6.</p><p><strong>Conclusion: </strong>ATRA is anticipated to engage with various proteins and pathways associated with rheumatoid arthritis, suggesting its potential utility in the clinical management of this disorder. Key Points • All-trans retinoic acid (ATRA) has been shown to interact with 85 specific genes in patients with RA, among which 10 key hub genes have been identified. • Molecular docking studies indicate that ATRA exhibits the lowest binding affinity with the genes CYP1 A1 and CYP2B6.</p>\",\"PeriodicalId\":10482,\"journal\":{\"name\":\"Clinical Rheumatology\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":2.9000,\"publicationDate\":\"2025-05-17\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Clinical Rheumatology\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.1007/s10067-025-07482-0\",\"RegionNum\":3,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"RHEUMATOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Clinical Rheumatology","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1007/s10067-025-07482-0","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"RHEUMATOLOGY","Score":null,"Total":0}
The molecular basis of all-trans retinoic acid binding to the target genes involved in rheumatoid arthritis through network pharmacology and molecular docking.
Objective: All-trans retinoic acid (ATRA), a natural derivative of Vitamin A, plays a crucial role in cellular proliferation, differentiation, and metabolic functions. It has been reported to possess significant antioxidant and anti-inflammatory properties. However, a comprehensive investigation into its potential mechanisms within the framework of rheumatoid arthritis (RA) has yet to be adequately addressed.
Methods: This study aimed to identify potential targets of ATRA by employing databases such as DrugBank and SwissTargetPrediction. Furthermore, disease-associated genes relevant to rheumatoid arthritis were sourced from DisGeNET and GeneCards. Analyses of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were conducted. Drug-target-pathway networks were developed, and significant hub genes were identified. In addition, molecular docking studies were performed to assess the binding affinity of ATRA.
Results: The results indicated that ATRA engages with 127 identified target genes, of which 85 are linked to rheumatoid arthritis (RA). Analyses employing Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and network approaches suggested that these targets participate in inflammatory pathways and metabolic processes pertinent to RA. Additionally, molecular docking studies revealed a significant binding affinity between ATRA and the proteins CYP1A1 and CYP2B6.
Conclusion: ATRA is anticipated to engage with various proteins and pathways associated with rheumatoid arthritis, suggesting its potential utility in the clinical management of this disorder. Key Points • All-trans retinoic acid (ATRA) has been shown to interact with 85 specific genes in patients with RA, among which 10 key hub genes have been identified. • Molecular docking studies indicate that ATRA exhibits the lowest binding affinity with the genes CYP1 A1 and CYP2B6.
期刊介绍：
Clinical Rheumatology is an international English-language journal devoted to publishing original clinical investigation and research in the general field of rheumatology with accent on clinical aspects at postgraduate level.
The journal succeeds Acta Rheumatologica Belgica, originally founded in 1945 as the official journal of the Belgian Rheumatology Society. Clinical Rheumatology aims to cover all modern trends in clinical and experimental research as well as the management and evaluation of diagnostic and treatment procedures connected with the inflammatory, immunologic, metabolic, genetic and degenerative soft and hard connective tissue diseases.
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