Study of the antidiabetic mechanism of berberine compound on FOXO1 transcription factor through molecular docking and molecular dynamics simulations.
Berberine
Diabetes mellitus
FOXO1
In silico
Journal
Journal of molecular modeling
ISSN: 0948-5023
Titre abrégé: J Mol Model
Pays: Germany
ID NLM: 9806569
Informations de publication
Date de publication:
09 Jul 2024
09 Jul 2024
Historique:
received:
11
01
2024
accepted:
02
07
2024
medline:
10
7
2024
pubmed:
10
7
2024
entrez:
9
7
2024
Statut:
epublish
Résumé
Diabetes mellitus (DM) is a metabolic disorder disease that causes hyperglycemia conditions and associated with various chronic complications leading to mortality. Due to high toxicity of conventional diabetic drugs, the exploration of natural compounds as alternative diabetes treatments has been widely carried out. Previous in silico studies have highlighted berberine, a natural compound, as a promising alternative in antidiabetic therapy, potentially acting through various pathways, including the inhibition of the FOXO1 transcription factor in the gluconeogenesis pathway. However, the specific mechanism by which berberine interacts with FOXO1 remains unclear, and research in this area is relatively limited. Therefore, this study aims to determine the stability of berberine structure with FOXO1 based on RMSD, RMSF, binding energy, and trajectory analysis to determine the potential of berberine to inhibit the gluconeogenesis pathway. This research was conducted by in silico method with molecular docking using AutoDock4.2 and molecular dynamics study using Amber20, then visualized by VMD. Docking between ligand and FOXO1 receptor was carried out with Autodock4.2. For molecular dynamics simulations, the force fields of DNA.OL15, protein.ff14SB, gaff2, and tip3p were used.
Identifiants
pubmed: 38981921
doi: 10.1007/s00894-024-06060-6
pii: 10.1007/s00894-024-06060-6
doi:
Substances chimiques
Berberine
0I8Y3P32UF
Hypoglycemic Agents
0
Forkhead Box Protein O1
0
FOXO1 protein, human
0
Ligands
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
260Subventions
Organisme : Universitas Padjadjaran
ID : 1549/UN6.3.1/PT.00/2023
Organisme : Universitas Padjadjaran
ID : 1549/UN6.3.1/PT.00/2023
Organisme : Universitas Padjadjaran
ID : 1549/UN6.3.1/PT.00/2023
Organisme : Universitas Padjadjaran
ID : 1549/UN6.3.1/PT.00/2023
Organisme : Universitas Padjadjaran
ID : 1549/UN6.3.1/PT.00/2023
Organisme : Universitas Padjadjaran
ID : 1549/UN6.3.1/PT.00/2023
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Références
Bare Y, Maulidi A, Sari DRT, Tiring SSND (2019) Studi in Silico Prediksi Potensi 6-Gingerol sebagai inhibitor c-Jun N-terminal kinases (JNK). J Jejaring Mat dan Sains 1(2):59–63. https://doi.org/10.36873/jjms.v1i2.211
doi: 10.36873/jjms.v1i2.211
Yin J, Ye J, Jia W (2012) Effects and mechanisms of berberine in diabetes treatment. Acta Pharm Sin B 2(4):327–334. https://doi.org/10.1016/j.apsb.2012.06.003
doi: 10.1016/j.apsb.2012.06.003
International Diabetes Federation (2021) IDF diabetes atlas, 10th edn. International Diabetes Federation. IDF, Brussels, Belgium. https://diabetesatlas.org/atlas/tenth-edition/
Widowati W (2008) Potensi antioksidan sebagai antidiabetes. Maranatha J Med Heal 7(2):1–11. https://doi.org/10.52574/syiahkualauniversitypress.350
Chang W, Chen L, Hatch GM (2015) Berberine as a therapy for type 2 diabetes and its complications: from mechanism of action to clinical studies1. Biochem Cell Biol 93(5):479–486. https://doi.org/10.1139/bcb-2014-0107
doi: 10.1139/bcb-2014-0107
pubmed: 25607236
Kesuma D, Siswandono S, Purwanto BT, Hardjono S (2018) Uji in silico aktivitas sitotoksik dan toksisitas senyawa Turunan N-(Benzoil)-N’-feniltiourea sebagai calon obat antikanker. J Pharm Sci Clin Res 3(1):1–11. https://doi.org/10.20961/jpscr.v3i1.16266
doi: 10.20961/jpscr.v3i1.16266
Xu L, Li Y, Dai Y, Peng J (2018) Natural products for the treatment of type 2 diabetes mellitus: pharmacology and mechanisms. Pharmacol Res 130:451–465. https://doi.org/10.1016/j.phrs.2018.01.015
doi: 10.1016/j.phrs.2018.01.015
pubmed: 29395440
Di S, Han L, An X, Kong R, Gao Z, Yang Y et al (2021) In silico network pharmacology and in vivo analysis of berberine-related mechanisms against type 2 diabetes mellitus and its complications. J Ethnopharmacol 276:114180. https://doi.org/10.1016/j.jep.2021.114180
doi: 10.1016/j.jep.2021.114180
pubmed: 33957209
Mohanty I, Kumar S, Rajesh S (2017) Dipeptidyl peptidase IV inhibitory activity of berberine and mangiferin: an in silico approach. Int J Clin Endocrinol Metab 3(1):018–022. https://doi.org/10.17352/ijcem.000024
doi: 10.17352/ijcem.000024
Mandar BK, Khanal P, Patil BM, Dey YN, Pasha I (2021) In silico analysis of phytoconstituents from tinospora cordifolia with targets related to diabetes and obesity. Silico Pharmacol 9(1):1–9. https://doi.org/10.1007/s40203-020-00063-w
Damián-Medina K, Salinas-Moreno Y, Milenkovic D, Figueroa-Yáñez L, Marino-Marmolejo E, Higuera-Ciapara I et al (2020) In silico analysis of antidiabetic potential of phenolic compounds from blue corn (Zea mays L.) and black bean (Phaseolus vulgaris L.). Heliyon 6(3):1–13. https://doi.org/10.1016/j.heliyon.2020.e03632
Zabidi NA, Ishak NA, Hamid M, Ashari SE, Mohammad Latif MA (2021) Inhibitory evaluation of Curculigo latifolia on α-glucosidase, DPP (IV) and in vitro studies in antidiabetic with molecular docking relevance to type 2 diabetes mellitus. J Enzyme Inhib Med Chem 36(1):109–121. https://doi.org/10.1080/14756366.2020.1844680
doi: 10.1080/14756366.2020.1844680
pubmed: 33249946
Femi-Olabisi FJ, Ishola AA, Faokunla O, Agboola AO, Babalola BA (2021) Evaluation of the inhibitory potentials of selected compounds from Costus spicatus (Jacq.) rhizome towards enzymes associated with insulin resistance in polycystic ovarian syndrome: an in silico study. J Genet Eng Biotechnol 19(1):176. https://doi.org/10.1186/s43141-021-00276-2
Jhong CH, Riyaphan J, Lin SH, Chia YC, Weng CF (2015) Screening alpha-glucosidase and alpha-amylase inhibitors from natural compounds by molecular docking in silico. BioFactors 41(4):242–251
doi: 10.1002/biof.1219
pubmed: 26154585
Yin J, Xing H, Ye J (2008) Efficacy of berberine in patients with type 2 diabetes. Metabolism 57(5):712–717
doi: 10.1016/j.metabol.2008.01.013
pubmed: 18442638
pmcid: 2410097
Zhang H, Wei J, Xue R, Wu JD, Zhao W, Wang ZZ et al (2010) Berberine lowers blood glucose in type 2 diabetes mellitus patients through increasing insulin receptor expression. Metabolism 59(2):285–292. https://doi.org/10.1016/j.metabol.2009.07.029
doi: 10.1016/j.metabol.2009.07.029
pubmed: 19800084
Utami AR, Maksum IP, Deawati Y (2023) Berberine and its study as an antidiabetic compound. Biology (Basel) 12(7). https://doi.org/10.3390/biology12070973
Purwaningsih I, Maksum IP, Sumiarsa D, Sriwidodo S (2023) A review of Fibraurea tinctoria and its component, berberine, as an antidiabetic and antioxidant. Molecules 28(3):1–38. https://doi.org/10.3390/molecules28031294
doi: 10.3390/molecules28031294
Ávila-Flores A, Arranz-Nicolás J, Mérida I (2019) Transcriptional activity of FOXO transcription factors measured by luciferase assays. Methods Mol Biol 1890:91–102. https://doi.org/10.1007/978-1-4939-8900-3_8
doi: 10.1007/978-1-4939-8900-3_8
pubmed: 30414147
Katarina P, Kohoutova K, Obsilova V, Ausserlechner MJ, Veverka V, Obsil T (2019) Forkhead Domains of FOXO transcription factors differ in both overall conformation and dynamics. Cells 8(9):1–14. https://doi.org/10.3390/cells8090966
doi: 10.3390/cells8090966
Peng S, Li W, Hou N, Huang N (2020) A Review of FoxO1-regulated metabolic diseases and related drug discoveries. Cells 9(1):1–10. https://doi.org/10.3390/cells9010184
doi: 10.3390/cells9010184
Xia X, Yan J, Shen Y, Tang K, Yin J, Zhang Y et al (2011) Berberine improves glucose metabolism in diabetic rats by inhibition of hepatic gluconeogenesis. PLoS ONE 6(2):1–10. https://doi.org/10.1371/journal.pone.0016556
doi: 10.1371/journal.pone.0016556
Sui M, Chen G, Mao X, Wei X, Chen Y, Liu C et al (2019) Gegen Qinlian decoction ameliorates hepatic insulin resistance by silent Information Regulator1 (SIRT1)-dependent deacetylation of forkhead box O1 (FOXO1). Med Sci Monit 25:8544–8553. https://doi.org/10.12659/MSM.919498
doi: 10.12659/MSM.919498
pubmed: 31719515
pmcid: 6873633
Sui M, Jiang X, Sun H, Liu C, Fan Y (2021) Berberine ameliorates hepatic insulin resistance by regulating microrna-146b/sirt1 pathway. Diabetes Metab Syndr Obes 14:2525–2537. https://doi.org/10.2147/DMSO.S313068
doi: 10.2147/DMSO.S313068
pubmed: 34113144
pmcid: 8187038
Rasul HO, Aziz BK, Ghafour DD, Kivrak A (2023) Screening the possible anti-cancer constituents of Hibiscus rosa-sinensis flower to address mammalian target of rapamycin: an in silico molecular docking, HYDE scoring, dynamic studies, and pharmacokinetic prediction. Mol Divers 27(5):2273–2296. https://doi.org/10.1007/s11030-022-10556-9
doi: 10.1007/s11030-022-10556-9
pubmed: 36318405
Fariz A, Iman M, Maksum P, Sriwidodo S, Rukayadi Y (2024) Proposed molecular mechanism of non ‑ competitive inhibition using molecular dynamics simulations between α ‑ glucosidase enzyme and mangostin compound as antidiabetic. J Mol Model 30(5):1–12. https://doi.org/10.1007/s00894-024-05934-z