Brief literature review and comprehensive bioinformatics analytics unravel the potential mechanism of curcumin in the treatment of periodontitis

Xufeng Huang; Ying Liu; Qi Wang; Hafiz Muzzammel Rehman; Dorottya Horváth; Shujing Zhou; Rao Fu; Ling Zhang; Attila Gábor Szöllősi; Zhengrui Li

doi:10.1186/s12903-023-03181-x

Brief literature review and comprehensive bioinformatics analytics unravel the potential mechanism of curcumin in the treatment of periodontitis

BMC Oral Health. 2023 Jul 8;23(1):469. doi: 10.1186/s12903-023-03181-x.

Authors

Xufeng Huang^#^{1

2}, Ying Liu^#³, Qi Wang^#⁴, Hafiz Muzzammel Rehman^{5

6}, Dorottya Horváth², Shujing Zhou², Rao Fu^{7

8

9}, Ling Zhang^{10

11

12}, Attila Gábor Szöllősi¹³, Zhengrui Li^{14

15

16}

Affiliations

¹ Faculty of Dentistry, University of Debrecen, Debrecen, Hungary.
² Department of Immunology, University of Debrecen, Debrecen, Hungary.
³ Department of Cardiology, Sixth Medical Center, PLA General Hospital, Beijing, China.
⁴ Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China.
⁵ School of Biochemistry and Biotechnology, University of the Punjab, LahorePunjab, 54590, Pakistan.
⁶ Alnoorians Group of Institutes, 55-Elahi Bukhsh Park, Amir Road, Shad Bagh, Lahore, 54000, Pakistan.
⁷ Department 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 University, Shanghai, China.
⁸ National Center for Stomatology and National Clinical Research Center for Oral Diseases, Shanghai, China.
⁹ Shanghai Key Laboratory of Stomatology, Shanghai, China.
¹⁰ Department 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 University, Shanghai, China. topgun1128@163.com.
¹¹ National Center for Stomatology and National Clinical Research Center for Oral Diseases, Shanghai, China. topgun1128@163.com.
¹² Shanghai Key Laboratory of Stomatology, Shanghai, China. topgun1128@163.com.
¹³ Department of Immunology, University of Debrecen, Debrecen, Hungary. szollosi.attila@med.unideb.hu.
¹⁴ Department 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 University, Shanghai, China. lzr_0108@sjtu.edu.cn.
¹⁵ National Center for Stomatology and National Clinical Research Center for Oral Diseases, Shanghai, China. lzr_0108@sjtu.edu.cn.
¹⁶ Shanghai Key Laboratory of Stomatology, Shanghai, China. lzr_0108@sjtu.edu.cn.

^# Contributed equally.

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.

Keywords: Bioinformatics; Curcumin; Molecular docking; Molecular dynamic simulation; Periodontitis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods
Curcumin* / pharmacology
Curcumin* / therapeutic use
Gene Expression Profiling / methods
Humans
Molecular Docking Simulation
Periodontitis* / drug therapy
Periodontitis* / genetics
Protein Interaction Maps / genetics

Substances

Curcumin