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Gayathri K, Abhinand P, Gayathri V, Prasanna Lakshmi V, Chamundeeswari D, Jiang L, Tian Z, Malathi N. Computational analysis of phytocompounds in Centella asiatica for its antifibrotic and drug-likeness properties - Herb to drug study. Heliyon 2024; 10:e33762. [PMID: 39027607 PMCID: PMC11255509 DOI: 10.1016/j.heliyon.2024.e33762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/20/2024] Open
Abstract
Oral submucous fibrosis (OSMF) is a potentially malignant disorder with no permanent cure that affects the quality of life due to trismus. Computational pharmacology has accelerated the discovery of drug candidates for the treatment of incurable diseases. The present study aimed to screen the compounds of the miracle herb Centella asiatica with drug-likeness properties based on the absorption, distribution, metabolism, and excretion (ADME) properties. The pharmacological actions of these screened compounds against OSMF were identified by network pharmacology, gene ontology, pathway enrichment analysis, molecular docking, and simulation. Fifteen drug-like ligands were identified after virtual screening viz; asiatic acid, kaempferol, quercetin, luteolin, apigenin, bayogenin, gallic acid, isothankunic acid, madecassic acid, madasiatic acid, arjunolic acid, terminolic acid, catechin, epicatechin, and nobiletin. 850 potential targets were predicted for the ligands, which were analyzed against 354 proteins associated with OSMF. Compound pathway analysis and disease pathway analysis identified 53 common proteins. The GO enrichment analysis identified 472 biological process terms, 76 molecular function terms, and 44 cellular component terms. Pathway enrichment analysis predicted 142 KEGG pathways, 35 Biocarta pathways, and 236 Reactome pathways for the target proteins. The analysis revealed that the herb targets crucial events of fibrosis such as inflammation, oxidative stress, apoptosis, collagen deposition, and epithelial-mesenchymal transition. The common 53 proteins were used for protein-protein interaction (PPI) network analysis, which revealed 4 key proteins interacting with the phytocompounds viz; transforming growth factor-β1 (TGF-β1), mothers against decapentaplegic-3 (SMAD-3), mitogen-activated protein kinase-1 (MAPK-1) and proto-oncogene tyrosine-protein kinase (SRC). Molecular docking revealed that all ligands had a good binding affinity to the target proteins. Bayogenin had the highest binding affinity towards MAPK-1 (-9.7 kcal/mol), followed by isothankunic acid towards SRC protein (-9.3 kcal/mol). Madasiatic acid had the highest binding affinity to SMAD-3 (-7.6 kcal/mol) and TGF-β1 (-7.1 kcal/mol). Molecular dynamics simulation demonstrated stable ligand protein interactions of bayogenin and MAPK complex, isothankunic acid and SRC complex. This in silico study is the first to identify potential phytochemicals present in Centella asiatica and their target molecules, which might be responsible for reversing OSMF.
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Affiliation(s)
- K. Gayathri
- Faculty of Biomedical Sciences, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, 600116, India
- Department of Oral Pathology and Microbiology, Sri Ramachandra Dental College, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, 600116, India
| | - P.A. Abhinand
- Department of Bioinformatics, Faculty of Engineering and Technology, Sri Ramachandra Institute of Higher Education & Research, Porur, Chennai, 600116, India
| | - V. Gayathri
- Centre for Toxicology and Developmental Research, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, 600116, India
| | - V. Prasanna Lakshmi
- Department of Bioinformatics, Faculty of Engineering and Technology, Sri Ramachandra Institute of Higher Education & Research, Porur, Chennai, 600116, India
| | - D. Chamundeeswari
- Faculty of Pharmacy, Meenakshi Academy of Higher Education and Research, Chennai, India
| | - Li Jiang
- Department of Oral Pathology, The Ninth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhen Tian
- Department of Oral Pathology, The Ninth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - N. Malathi
- Department of Oral Pathology and Microbiology, Sri Ramachandra Dental College, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, 600116, India
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Smetanina MA, Korolenya VA, Kel AE, Sevostyanova KS, Gavrilov KA, Shevela AI, Filipenko ML. Epigenome-Wide Changes in the Cell Layers of the Vein Wall When Exposing the Venous Endothelium to Oscillatory Shear Stress. EPIGENOMES 2023; 7:epigenomes7010008. [PMID: 36975604 PMCID: PMC10048778 DOI: 10.3390/epigenomes7010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Epigenomic changes in the venous cells exerted by oscillatory shear stress towards the endothelium may result in consolidation of gene expression alterations upon vein wall remodeling during varicose transformation. We aimed to reveal such epigenome-wide methylation changes. Primary culture cells were obtained from non-varicose vein segments left after surgery of 3 patients by growing the cells in selective media after magnetic immunosorting. Endothelial cells were either exposed to oscillatory shear stress or left at the static condition. Then, other cell types were treated with preconditioned media from the adjacent layer's cells. DNA isolated from the harvested cells was subjected to epigenome-wide study using Illumina microarrays followed by data analysis with GenomeStudio (Illumina), Excel (Microsoft), and Genome Enhancer (geneXplain) software packages. Differential (hypo-/hyper-) methylation was revealed for each cell layer's DNA. The most targetable master regulators controlling the activity of certain transcription factors regulating the genes near the differentially methylated sites appeared to be the following: (1) HGS, PDGFB, and AR for endothelial cells; (2) HGS, CDH2, SPRY2, SMAD2, ZFYVE9, and P2RY1 for smooth muscle cells; and (3) WWOX, F8, IGF2R, NFKB1, RELA, SOCS1, and FXN for fibroblasts. Some of the identified master regulators may serve as promising druggable targets for treating varicose veins in the future.
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Affiliation(s)
- Mariya A Smetanina
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Department of Fundamental Medicine, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University (NSU), Novosibirsk 630090, Russia
| | - Valeria A Korolenya
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University (NSU), Novosibirsk 630090, Russia
| | - Alexander E Kel
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Department of Research & Development, GeneXplain GmbH, D-38302 Wolfenbüttel, Germany
| | - Ksenia S Sevostyanova
- Center of New Medical Technologies, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Laboratory of Invasive Medical Technologies, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Department of Surgical Diseases, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University (NSU), Novosibirsk 630090, Russia
| | - Konstantin A Gavrilov
- Center of New Medical Technologies, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Department of Surgical Diseases, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University (NSU), Novosibirsk 630090, Russia
| | - Andrey I Shevela
- Center of New Medical Technologies, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Laboratory of Invasive Medical Technologies, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Department of Surgical Diseases, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University (NSU), Novosibirsk 630090, Russia
| | - Maxim L Filipenko
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
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James A, Jayan L, Ramadoss R, Arunachalam P. Leaving no stone unturned: Role of profibrotic genes in oral submucous fibrosis - A systematic review. J Oral Maxillofac Pathol 2022; 26:228-235. [PMID: 35968163 PMCID: PMC9364652 DOI: 10.4103/jomfp.jomfp_102_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/05/2021] [Indexed: 11/11/2022] Open
Abstract
Introduction Understanding the molecular pathogenesis of an entity helps in devising the mode of progression as well as mode of therapy. Even with years of research to claim the understanding of the molecular pathogenesis of oral submucous fibrosis (OSMF) is limited. More deeper knowledge of the genes responsible for this will help in understanding and managing this disease better. Materials and Methods The articles published during a time period of 1990-2020 were chosen in accordance with the inclusion and exclusion criteria according to the PRISMA guidelines. Results From a total of 80 articles obtained from both electronic search of PUBMED, EMBASE, MEDLINE and Cochrane registry as well as the manual search only 21 articles were selected and analyzed. Conclusion Careful analysis of the samples revealed that transforming growth factor-beta may be a potential biomarker or a candidate for targeted therapy in OSMF.
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Affiliation(s)
- Amritha James
- Department of Oral Pathology and Microbiology, SRM Dental College, Chennai, Tamil Nadu, India,Address for correspondence: Dr. Amritha James, SRM Dental College, Ramapuram, Chennai - 600 089, Tamil Nadu, India. E-mail:
| | - Lekshmy Jayan
- Department of Oral Pathology and Microbiology, SRM Dental College, Chennai, Tamil Nadu, India
| | - Ramya Ramadoss
- Department of Oral Pathology and Microbiology, Saveetha Dental College, Chennai, Tamil Nadu, India
| | - Preethi Arunachalam
- Department of Oral Pathology and Microbiology, SRM Dental College, Chennai, Tamil Nadu, India
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Gene Expression Profiling and Biofunction Analysis of HepG2 Cells Targeted by Crocetin. Mediators Inflamm 2021; 2021:5512166. [PMID: 33867857 PMCID: PMC8035019 DOI: 10.1155/2021/5512166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/03/2021] [Accepted: 03/17/2021] [Indexed: 11/17/2022] Open
Abstract
Crocetin is a carotenoid extracted from Gardenia jasminoides, one of the most popular traditional Chinese medicines, which has been used in the prevention and treatment of various diseases. The present study is aimed at clarifying the effect of crocetin on gene expression profiling of HepG2 cells by RNA-sequence assay and further investigating the molecular mechanism underlying the multiple biofunctions of crocetin based on bioinformatics analysis and molecular evidence. Among a total 23K differential genes identified, crocetin treatment upregulated the signals of 491 genes (2.14% of total gene probes) and downregulated the signals of 283 genes (1.24% of total gene probes) by ≥2-fold. The Gene Ontology analysis enriched these genes mainly on cell proliferation and apoptosis (BRD4 and DAXX); lipid formation (EHMT2); cell response to growth factor stimulation (CYP24A1 and GCNT2); and growth factor binding (ABCB1 and ABCG1), metabolism, and signal transduction processes. The KEGG pathway analysis revealed that crocetin has the potential to regulate transcriptional misregulation, ABC transporters, bile secretion, alcoholism, systemic lupus erythematosus (SLE), and other pathways, of which SLE was the most significantly disturbed pathway. The PPI network was constructed by using the STRING online protein interaction database and Cytoscape software, and 21 core proteins were obtained. RT-qPCR datasets serve as the solid evidence that verified the accuracy of transcriptome sequencing results with the same change trend. This study provides first-hand data for comprehensively understanding crocetin targeting on hepatic metabolism and its multiple biofunctions.
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Genetic Susceptibility and Protein Expression of Extracellular Matrix Turnover-Related Genes in Oral Submucous Fibrosis. Int J Mol Sci 2020; 21:ijms21218104. [PMID: 33143101 PMCID: PMC7663238 DOI: 10.3390/ijms21218104] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/14/2022] Open
Abstract
Betel quid (BQ) chewing increased the risk of oral cancer and oral submucous fibrosis (OSMF), an oral premalignant disorder (OPMD) with malignant transformation potential. BQ components such as areca nut (AN), trauma by coarse AN fiber, catechin, copper, alkaloids, stimulated reactive oxygen species (ROS), inflammation and cytotoxicity are suggested to be the contributing factors. They may induce tissue inflammation, proliferation of fibroblasts and collagen deposition, myofibroblast differentiation and contraction, collagen cross-links and inhibit collagen phagocytosis, finally leading to the development of OSMF and oral cancer. These events are mediated by BQ components-induced changes of extracellular matrix (ECM) turnover via regulation of TGF-β1, plasminogen activator inhibitor-1 (PAI-1), cystatin, lysyl oxidase (LOX) and tissue inhibitors of metalloproteinases (TIMPs) and metalloproteinases (MMPs). Genetic susceptibility is also involved in these disease processes. Further understanding the molecular mechanisms of BQ-induced OSMF and oral cancer can be helpful for future disease prevention and treatment.
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Shetty SS, Sharma M, Fonseca FP, Jayaram P, Tanwar AS, Kabekkodu SP, Kapaettu S, Radhakrishnan R. Signaling pathways promoting epithelial mesenchymal transition in oral submucous fibrosis and oral squamous cell carcinoma. JAPANESE DENTAL SCIENCE REVIEW 2020; 56:97-108. [PMID: 32874377 PMCID: PMC7452314 DOI: 10.1016/j.jdsr.2020.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/02/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a critical process that occurs during the embryonic development, wound healing, organ fibrosis and the onset of malignancy. Emerging evidence suggests that the EMT is involved in the invasion and metastasis of cancers. The inflammatory reaction antecedent to fibrosis in the onset of oral submucous fibrosis (OSF) and the role of EMT in its malignant transformation indicates a hitherto unexplored involvement of EMT. This review focuses on the role of EMT markers which are regulators of the EMT mediated complex network of molecular mechanisms involved in the pathogenesis of OSF and OSCC. Further the gene enrichment analysis and pathway analysis supports the association of the upregulated and downregulated genes in various EMT regulating pathways.
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Affiliation(s)
- Smitha Sammith Shetty
- Department of Oral Pathology, Faculty of Dentistry, Melaka Manipal Medical College, Manipal Academy of Higher Education, Manipal 576104, India
| | - Mohit Sharma
- Department of Oral Pathology, Sudha Rustagi College of Dental Sciences and Research, Faridabad 121004, India
| | - Felipe Paiva Fonseca
- Department of Oral Surgery and Pathology, School of Dentistry, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Pradyumna Jayaram
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Ankit Singh Tanwar
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Satyamoorthy Kapaettu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
- Corresponding author.
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