Molecular Docking of Nigella Sativa Phytocompound as Inhibitors of Transcription Factors NF-KB Implicated in Rheumatoid Arthritis

Year : 2024 | Volume : 02 | Issue : 02 | Page : 42 55
    By

    Amaani .,

  1. Student, Department of Bioinformatics, BioNome, Hennur Gardens, Bengaluru, India

Abstract

Objectives: Nigella sativa, a plant considered around the world as the most treasured nutrient-rich herb for centuries together in different civilizations, is exceptionally known for its high levels of antioxidant properties. Free radical intensification due to oxidative stress plays a key role in the pathogenesis of rheumatoid arthritis by activating the NF-KB protein that regulates the expression of the genes involved in inflammation. Methods: This study involves in-silico approach to validate the antioxidant properties of the phytocompounds obtained from Nigella sativa in inhibiting the protein activity of NF-KB by contemplating the binding affinity of the phytochemicals with the target macromolecule virtually by Molecular Docking (PyRx). Results: Phytochemical compounds that surpassed the ADME test were screened based on the binding affinity against the protein. Ligands showing values less than -6 kcal/mol were further visualized, and the computation results manifested phytocompound Nigellone (Dithymoquinone) had the strongest binding affinity against the protein NF-KB, recommending the compound for future therapeutic interventions in the treatment of RA

Keywords: Nigella sativa, Nigellone, NF-KB, free radicals, oxidative stress, rheumatoid arthritis

[This article belongs to International Journal of Molecular Biotechnological Research ]

How to cite this article:
Amaani .. Molecular Docking of Nigella Sativa Phytocompound as Inhibitors of Transcription Factors NF-KB Implicated in Rheumatoid Arthritis. International Journal of Molecular Biotechnological Research. 2024; 02(02):42-55.
How to cite this URL:
Amaani .. Molecular Docking of Nigella Sativa Phytocompound as Inhibitors of Transcription Factors NF-KB Implicated in Rheumatoid Arthritis. International Journal of Molecular Biotechnological Research. 2024; 02(02):42-55. Available from: https://journals.stmjournals.com/ijmbr/article=2024/view=183831


Browse Figures

References

  1. Ferreira HB, Melo T, Paiva A, Domingues MDR. Insights in the role of lipids, oxidative stress and inflammation in rheumatoid arthritis unveiled by new trends in lipidomic investigations. Antioxidants. 2021;10(1):45. doi:10.3390/antiox10010045.
  2. Black RJ, Cross M, Haile LM, Culbreth GT, Steinmetz JD, Hagins H, et al. Global, regional, and national burden of rheumatoid arthritis, 1990–2020, and projections to 2050: a systematic analysis of the Global Burden of Disease Study 2021. Lancet Rheumatol. 2023;5(10):e594–e610. doi:10.1016/S2665-9913(23)00211-4.
  3. Jahid M, Khan KU, Rehan-Ul-Haq, Ahmed RS. Overview of rheumatoid arthritis and scientific understanding of the disease. Mediterr J Rheumatol. 2024;34(3):284.
  4. Cross M, Smith E, Hoy D, Carmona L, Wolfe F, Vos T, et al. The global burden of rheumatoid arthritis: estimates from the global burden of disease 2010 study. Ann Rheum Dis. 2014;73(7):1316–1322. doi:10.1136/annrheumdis-2013-204627.
  5. Hunter TM, Boytsov NN, Zhang X, Schroeder K, Michaud K, Araujo AB. Prevalence of rheumatoid arthritis in the United States adult population in healthcare claims databases, 2004–2014. Rheumatol Int. 2017;37(9):1551–1557. doi:10.1007/s00296-017-3726-1.
  6. Tanner S, Dufault B, Smolik I, Meng X, Anaparti V, Hitchon C, et al. A prospective study of the development of inflammatory arthritis in the family members of Indigenous North American people with rheumatoid arthritis. Arthritis Rheumatol. 2019;71(9):1494–1503. doi:10.1002/art. 40880.
  7. du Montcel ST, Michou L, Petit-Teixeira E, Osorio J, Lemaire I, Lasbleiz S, et al. New classification of HLA–DRB1 alleles supports the shared epitope hypothesis of rheumatoid arthritis susceptibility. Arthritis Rheumatol. 2005;52(4):1063–1068. doi:10. 1002/art. 20989.
  8. El-Gabalawy HS, Maisha JA, O’Neil LJ. Modifiable risk factors linked to the development of rheumatoid arthritis: evidence, immunological mechanisms and prevention. Front Immunol. 2023;14. doi:10.3389/fimmu.2023.1221125.
  9. Wang X, Fan D, Cao X, Ye Q, Wang Q, Zhang M, et al. The role of reactive oxygen species in the rheumatoid arthritis-associated synovial microenvironment. Antioxidants. 2022;11(6):1153. doi:10.3390/antiox11061153.
  10. Fonseca LJS da, Nunes-Souza V, Goulart MOF, Rabelo LA. Oxidative stress in rheumatoid arthritis: What the future might hold regarding novel biomarkers and add-on therapies. Oxid Med Cell Longev. 2019;2019(1). doi:10.1155/2019/7536805.
  11. Sehnert B, Burkhardt H, Dübel S, Voll RE. Cell-type targeted NF-kappaB inhibition for the treatment of inflammatory diseases. Cells. 2020;9(7):1627. doi:10.3390/cells9071627.
  12. Jimi E, Huang F, Nakatomi C. NF-κB signaling regulates physiological and pathological chondrogenesis. Int J Mol Sci. 2019;20(24):6275. doi:10. 3390/ijms20246275.
  13. Zielińska M, Dereń K, Polak-Szczybyło E, Stępień AE. The role of bioactive compounds of Nigella sativa in rheumatoid arthritis therapy—current reports. Nutrients. 2021;13(10):3369. doi:10.3390/nu13103369.
  14. Tekeoglu I, Dogan A, Demiralp L. Retracted: Effects of thymoquinone (volatile oil of black cumin) on rheumatoid arthritis in rat models. Phytother Res. 2007;21(9):895–897. doi:10.1002/ptr.2143.
  15. Hadi V, Naseh P, Mahsa M, Elyas NE, Gholizadeh NJ, Saeid H. Nigella sativa in controlling type 2 diabetes, cardiovascular, and rheumatoid arthritis diseases molecular aspects. J Res Med Sci. 2021;26(1):20. doi:4103/jrms.JRMS_236_20.
  16. Radu AF, Bungau SG. Management of rheumatoid arthritis: An overview. Cells. 2021;10(11):2587. doi:10.3390/cells10112857.
  17. Long Z, Xiang W, He Q, Xiao W, Wei H, Li H, et al. Efficacy and safety of dietary polyphenols in rheumatoid arthritis: A systematic review and meta-analysis of 47 randomized controlled trials. Front Immunol. 2023;14. doi:10.3389/fimmu.2023.1024120.
  18. Salehi B, Quispe C, Imran M, Iahtisham-Ul- Haq, Zivkovic J, Abu-Reidah IM, et al. Nigella plants– traditional uses, bioactive phytoconstituents, preclinical and clinical studies. Front Pharmacol. 2021;12. doi:10.3389/fphar.2021.625386.
  19. Dalli M, Bekkouch O, Azizi SE, Azghar A, Gseyra N, Kim B. Nigella sativa L. phytochemistry and pharmacological activities: a review (2019–2021). Biomol. 2022;12(1):20. doi:10.3390/biom12010020.
  20. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhard K, at al. The Protein Data Bank. Nucleic Acids Res. 2000;28:235–242. doi:10.1107/S0907444902003451.
  21. Kemmish H, Fasnacht M, Yan L. Fully automated antibody structure prediction using BIOVIA tools: Validation study. PLoS One. 2017;12(5):e0177923. doi:10.1371/journal.pone.0177923.
  22. Mohanraj K, Karthikeyan BS, Vivek-Ananth RP, Chand RPB, Aparna SR, Mangalapandi P, et al. IMPPAT: A curated database of Indian medicinal plants, phytochemistry and therapeutics. Sci Rep. 2018;8(1):4329. doi:10.1038/s41598-018-22631-z.
  23. Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S, et al. PubChem substance and compound databases. Nucleic Acids Res. 2016;44(D1):D1202–D1213. doi:10.1093/nar/gkv951.
  24. Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017;7:42717. doi:10.1038/srep42717.
  25. Dallakyan S, Olson AJ. Small-Molecule Library Screening by Docking with PyRx. In: Hempel J, Williams C, Hong C, editors. Chemical Biology. Methods in Molecular Biology. New York, NY: Humana Press; 2015. 243–250. doi:10.1007/978-1-4939-2269-7_19.
  26. Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, PDBsum JT. Structural summaries of PDB entries. 2018;27. doi:10.1002/pro.;3289:129-34.
  27. http://cib. cf. ocha. ac. jp/bitool/EMBOSS-6. 0. 1/doc/programs/master/emboss/apps/pepstats. html.
  28. Larson CJ, Verdine GL, Müller CW. Structure of the human NF-kappaB p52 homodimer-DNA complex at 2.1 A resolution. EMBO J. 1997;16:7078–7090. doi:10.1093/emboj/16.23.7078.
  29. Jendele L, Krivak R, Skoda P, Novotny M, Hoksza D. PrankWeb: a web server for ligand binding site prediction and visualization. Nucleic Acids Res. 2019;47(W1):W345–349. doi:10. 1093/nar/gkz424.
  30. Tian W, Chen C, Lei X, Zhao J, CAST JL. 3.0: Computed atlas of surface topography of proteins. 2018;46:W363–W367. doi:10.1093/nar/gky473.
  31. Venables P, Maini RN. Diagnosis and differential diagnosis of rheumatoid arthritis. UpToDate2012. 2014.
  32. Rossetti M, Spreafico R, Consolaro A, Leong JY, Chua C, Massa M, et al. TCR repertoire sequencing identifies synovial treg cell clonotypes in the bloodstream during active inflammation in human arthritis. Ann Rheum Dis. 2017;76(2):435–441. doi:10.1136/annrheumdis-2015-208992.
  33. Long H, Yin H, Wang L, Gershwin ME, Lu Q. The critical role of epigenetics in systemic lupus erythematosus and autoimmunity. J Autoimmun. 2016;74:118–138. doi:10.1016/j.jaut.2016.06. 020.
  34. Khan MF, Wang G. Environmental agents, oxidative stress and autoimmunity. Curr Opin Toxicol. 2018;7:22–27. doi:10.1016/j.cotox.2017.10.012.
  35. Smallwood MJ, Nissim A, Knight AR, Whiteman M, Haigh R, Winyard PG. Oxidative stress in autoimmune rheumatic diseases. Free Radic Biol Med. 2018;125:3–14. doi:10.1016/j.freeradbiomed.2018.05.086
  36. Dröge W. Free radicals in the physiological control of cell function. Physiol Rev. 2002;82(1):47–95. doi:10.1152/physrev. 00018.2001.
  37. Schreck R, Rieber P, Baeuerle PA. Reactive oxygen intermediates as apparently widely used messengers in the activation of the NF-kappa B transcription factor and HIV-1. EMBO J. 1991;10(8):2247–2258. doi:10.1002/j.1460-2075.1991.tb07761.x.
  38. Rhee SG. Redox signaling: hydrogen peroxide as intracellular messenger. Exp Mol Med. 1999;31(2):53–59. doi:10.1038/emm.1999.9.
  39. Kondo N, Kanai T, Okada M. Rheumatoid arthritis and reactive oxygen species: a review. Curr Issues Mol Biol. 2023;45(4):3000–3015. doi:10.3390/cimb45040197.
  40. Makarov SS. NF-kappaB in rheumatoid arthritis: a pivotal regulator of inflammation, hyperplasia, and tissue destruction. Arthritis Res Ther. 2001;3:200. doi:10.1186/ar300.
  41. Mitchell S, Vargas J, Hoffmann A. Signaling via the NFκB system: signaling via the NFκB system. Wiley Interdiscip Rev Syst Biol Med. 2016;8(3):227–241. doi:10.1002/wsbm.1331.
  42. Hayden MS, Ghosh S. Shared principles in NF-kappaB signaling. Cell. 2008;132(3):344–362. doi:10.1016/j.cell.2008.01.020.
  43. Lingappan K. NF-κB in oxidative stress. Curr Opin Toxicol. 2018;7:81–86. doi:10.1016/j.cotox.2017.11.002.
  44. Seymour M, Pétavy F, Chiesa F, Perry H, Lukey PT, Binks M, et al. Ultrasonographic measures of synovitis in an early phase clinical trial: a double-blind, randomised, placebo and comparator controlled phase IIa trial of GW274150 (a selective inducible nitric oxide synthase inhibitor) in rheumatoid arthritis. Clin Exp Rheumatol. 2012;30(2):254–261.
  45. Dey S, Bishayi B. Effect of iNOS inhibitor LNMMA along with antibiotics chloramphenicol or ofloxacin in murine peritoneal macrophages regulates S. aureus infection as well as inflammation: An in vitro study. Microb Pathog. 2017;105:307–320. doi:10.1016/j.micpath.2017.02.031.
  46. Bullock J, Rizvi SAA, Saleh AM, Ahmed SS, Ansari RA, Ahmed J, Rheumatoid arthritis: a brief overview of the treatment. Med Princ Pract. 2019;27(6):501–507. doi:10.1159/000493390.
  47. Nasim N, Sandeep IS, Mohanty S. Plant-derived natural products for drug discovery: current approaches and prospects. 2022;65:399–411. doi:10.1007/s13237-022-00405-3.
  48. Ahmad A, Husain A, Mujeeb M, Khan SA, Najmi AK, Siddique NA, Damanhouri ZA, Anwar F. A review on therapeutic potential of Nigella sativa: A miracle herb. Asian Pac J Trop Biomed. 2013;3(5):337–352. doi:10.1016/S2221-1691(13)60075-1.
  49. Arjumand S, Shahzad M, Shabbir A, Yousaf MZ. Thymoquinone attenuates rheumatoid arthritis by downregulating TLR2, TLR4, TNF-α, IL-1, and NFκB expression levels. Biomed Pharmacother. 2019;111:958–963. doi:10.1016/j.biopha.2019.01.006.
  50. Hadi V, Kheirouri S, Alizadeh M, Khabbazi A, Hosseini H. Effects of Nigella sativa oil extract on inflammatory cytokine response and oxidative stress status in patients with rheumatoid arthritis: A randomized; double-blind; placebo-controlled clinical trial. Avicenna J Phytomed. 2016;6(1):34–43.

Regular Issue Subscription Original Research
Volume 02
Issue 02
Received 30/08/2024
Accepted 28/10/2024
Published 18/11/2024
Publication Time 80 Days


Login


My IP

PlumX Metrics