Brief literature review and comprehensive bioinformatics analytics unravel the potential mechanism of curcumin in the treatment of periodontitis
Abstract Objective Periodontitis is a chronic oral disease prevalent worldwide, and natural products are recommended as adjunctive therapy due to their minor side effects. Curcumin, a widely used ancient compound, has been reported to possess therapeutic effects in periodontitis. However, the exact...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-07-01
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| Series: | BMC Oral Health |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12903-023-03181-x |
| _version_ | 1797784374947610624 |
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| author | Xufeng Huang Ying Liu Qi Wang Hafiz Muzzammel Rehman Dorottya Horváth Shujing Zhou Rao Fu Ling Zhang Attila Gábor Szöllősi Zhengrui Li |
| author_facet | Xufeng Huang Ying Liu Qi Wang Hafiz Muzzammel Rehman Dorottya Horváth Shujing Zhou Rao Fu Ling Zhang Attila Gábor Szöllősi Zhengrui Li |
| author_sort | Xufeng Huang |
| collection | DOAJ |
| description | Abstract Objective Periodontitis is a chronic oral disease prevalent worldwide, and natural products are recommended as adjunctive therapy due to their minor side effects. Curcumin, a widely used ancient compound, has been reported to possess therapeutic effects in periodontitis. However, the exact mechanism underlying its activity remains unclear. In this context, the present study aimed to conduct computational simulations to uncover the potential mechanism of action of Curcumin in the treatment of periodontitis. Materials and methods Single-cell analysis was conducted using a dataset (i.e., GSE164241) curated from the Gene Expression Omnibus (GEO) database through an R package "Seurat package." Bulk RNA sequencing data were curated from GSE10334 and GSE16134 and processed by R package "Limma." Then, the marker genes in the single-cell transcriptome and differentially expressed genes (DEGs) in the bulk transcriptome were integrated. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were also carried out to reveal their functionalities. Key targets were mined from their protein–protein interaction (PPI) network topologically. Afterward, molecular docking was performed. The top-ranked pose was subjected to molecular dynamics simulations to investigate the stability of the docking result. Results FOS, CXCL1, CXCL8, and IL1B, were filtered after a series of selected processes. The results of molecular modeling suggested that except for IL1B, the Vena Scores of the rest exceeded -5 kcal/mol. Furthermore, the molecular dynamic simulation indicated that the binding of the CXCL8-Curcumin complex was stable over the entire 100 ns simulation. Conclusion The present study unlocked the binding modes of CXCL1, FOS, and CXCL8 with the Curcumin molecule, which were relatively stable, especially for CXCL8, hindering its promising potential to serve as the critical targets of Curcumin in periodontitis treatment. |
| first_indexed | 2024-03-13T00:38:59Z |
| format | Article |
| id | doaj.art-b4f911ff34904647b633c966a62fcf53 |
| institution | Directory Open Access Journal |
| issn | 1472-6831 |
| language | English |
| last_indexed | 2024-03-13T00:38:59Z |
| publishDate | 2023-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Oral Health |
| spelling | doaj.art-b4f911ff34904647b633c966a62fcf532023-07-09T11:26:50ZengBMCBMC Oral Health1472-68312023-07-0123111310.1186/s12903-023-03181-xBrief literature review and comprehensive bioinformatics analytics unravel the potential mechanism of curcumin in the treatment of periodontitisXufeng Huang0Ying Liu1Qi Wang2Hafiz Muzzammel Rehman3Dorottya Horváth4Shujing Zhou5Rao Fu6Ling Zhang7Attila Gábor Szöllősi8Zhengrui Li9Faculty of Dentistry, University of DebrecenDepartment of Cardiology, Sixth Medical Center, PLA General HospitalDepartment of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu UniversitySchool of Biochemistry and Biotechnology, University of the PunjabDepartment of Immunology, University of DebrecenDepartment of Immunology, University of DebrecenDepartment of Oral and Maxillofacial-Head and Neck Oncology, College of Stomatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong UniversityDepartment of Oral and Maxillofacial-Head and Neck Oncology, College of Stomatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong UniversityDepartment of Immunology, University of DebrecenDepartment of Oral and Maxillofacial-Head and Neck Oncology, College of Stomatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong UniversityAbstract Objective Periodontitis is a chronic oral disease prevalent worldwide, and natural products are recommended as adjunctive therapy due to their minor side effects. Curcumin, a widely used ancient compound, has been reported to possess therapeutic effects in periodontitis. However, the exact mechanism underlying its activity remains unclear. In this context, the present study aimed to conduct computational simulations to uncover the potential mechanism of action of Curcumin in the treatment of periodontitis. Materials and methods Single-cell analysis was conducted using a dataset (i.e., GSE164241) curated from the Gene Expression Omnibus (GEO) database through an R package "Seurat package." Bulk RNA sequencing data were curated from GSE10334 and GSE16134 and processed by R package "Limma." Then, the marker genes in the single-cell transcriptome and differentially expressed genes (DEGs) in the bulk transcriptome were integrated. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were also carried out to reveal their functionalities. Key targets were mined from their protein–protein interaction (PPI) network topologically. Afterward, molecular docking was performed. The top-ranked pose was subjected to molecular dynamics simulations to investigate the stability of the docking result. Results FOS, CXCL1, CXCL8, and IL1B, were filtered after a series of selected processes. The results of molecular modeling suggested that except for IL1B, the Vena Scores of the rest exceeded -5 kcal/mol. Furthermore, the molecular dynamic simulation indicated that the binding of the CXCL8-Curcumin complex was stable over the entire 100 ns simulation. Conclusion The present study unlocked the binding modes of CXCL1, FOS, and CXCL8 with the Curcumin molecule, which were relatively stable, especially for CXCL8, hindering its promising potential to serve as the critical targets of Curcumin in periodontitis treatment.https://doi.org/10.1186/s12903-023-03181-xCurcuminPeriodontitisBioinformaticsMolecular dockingMolecular dynamic simulation |
| spellingShingle | Xufeng Huang Ying Liu Qi Wang Hafiz Muzzammel Rehman Dorottya Horváth Shujing Zhou Rao Fu Ling Zhang Attila Gábor Szöllősi Zhengrui Li Brief literature review and comprehensive bioinformatics analytics unravel the potential mechanism of curcumin in the treatment of periodontitis BMC Oral Health Curcumin Periodontitis Bioinformatics Molecular docking Molecular dynamic simulation |
| title | Brief literature review and comprehensive bioinformatics analytics unravel the potential mechanism of curcumin in the treatment of periodontitis |
| title_full | Brief literature review and comprehensive bioinformatics analytics unravel the potential mechanism of curcumin in the treatment of periodontitis |
| title_fullStr | Brief literature review and comprehensive bioinformatics analytics unravel the potential mechanism of curcumin in the treatment of periodontitis |
| title_full_unstemmed | Brief literature review and comprehensive bioinformatics analytics unravel the potential mechanism of curcumin in the treatment of periodontitis |
| title_short | Brief literature review and comprehensive bioinformatics analytics unravel the potential mechanism of curcumin in the treatment of periodontitis |
| title_sort | brief literature review and comprehensive bioinformatics analytics unravel the potential mechanism of curcumin in the treatment of periodontitis |
| topic | Curcumin Periodontitis Bioinformatics Molecular docking Molecular dynamic simulation |
| url | https://doi.org/10.1186/s12903-023-03181-x |
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