Molecular Docking Studies of Nyctanthes arbor-tristis Phytochemicals for Targeting TNF Receptor in Arthritis

Year : 2025 | Volume : 03 | Issue : 02 | Page : 11 21
    By

    Shradha Nagawade,

  1. Student, Department of Biotechnology, Fergusson College, Pune, Maharashtra, India

Abstract

Rheumatoid Arthritis is an autoimmune disorder which results in inflammation. Tumor necrosis factor-alpha (TNF-α) is responsible for the progression of inflammatory arthritis by promoting immune cell activation and cytokine release. The present study explores the potential of bioactive compounds derived from Nyctanthes arbor-tristis (Parijat) in modulating TNF receptor activity through molecular docking. Computational methods were employed to evaluate the binding affinity of selected phytocompounds from N. arbor-tristis against the extracellular domain of the TNF receptor. Molecular docking was performed using PyRx, and the pharmacokinetic properties of the ligands were analyzed using ADMET filters to assess their drug-like potential. Molecular docking analysis revealed that the ligands Decan-1-ol, 1,3-Distearin, and 2,3,4,6-Tetramethyl-D-Glucose demonstrated the highest binding affinity toward the 1ext protein, indicating their strong potential for receptor interaction. Further in vitro study is needed to confirm their effectiveness.

Keywords: Nyctanthes arbor-tristis, arthritis, tumor necrosis factor receptor, molecular docking, phytochemicals, computational screening, ADMET analysis

[This article belongs to International Journal of Cell Biology and Cellular Functions ]

How to cite this article:
Shradha Nagawade. Molecular Docking Studies of Nyctanthes arbor-tristis Phytochemicals for Targeting TNF Receptor in Arthritis. International Journal of Cell Biology and Cellular Functions. 2025; 03(02):11-21.
How to cite this URL:
Shradha Nagawade. Molecular Docking Studies of Nyctanthes arbor-tristis Phytochemicals for Targeting TNF Receptor in Arthritis. International Journal of Cell Biology and Cellular Functions. 2025; 03(02):11-21. Available from: https://journals.stmjournals.com/ijcbcf/article=2025/view=229188


References

  1. Bullock J, Rizvi SA, Saleh AM, Ahmed SS, Do DP, Ansari RA, et al. Rheumatoid Arthritis: A Brief Overview of the Treatment. Med Princ Pract. 2019;27(6):501–7. doi:10.1159/000493390.
  2. Idriss HT, Naismith JH. TNF alpha and the TNF receptor superfamily: Structure-function relationship(s). Microsc Res Tech. 2000;50(3):184–95. doi:10.1002/1097-0029(20000801)50:33.0.CO;2-H.
  3. Ding Q, Liu G, Zeng Y, Zhu J, Zhang L, Liu Z, et al. Signaling pathways in rheumatoid arthritis: Implications for targeted therapy. Signal Transduct Target Ther. 2023;8(1):1. doi:10.1038/s41392-023-01331-9.
  4. Gruss HJ, Dower SK. The TNF ligand superfamily and its relevance for human diseases. Cytokines Mol Ther. 1995;1(2):75–105.
  5. Hiremath V, Hiremath BS, Mohapatra S, Das AK. Literary Review of Parijata (Nyctanthus Arbor-Tristis Linn.) An Herbal Medicament with Special Reference to Ayurveda and Botanical Literatures. Biomed Pharmacol J. 2016;9(3):1019–25.
  6. A Review on Nyctanthes arbortristis Linn an important traditional Plant of Herbal Medications | World J Pharm Sci [Internet]. 2025 Feb 6 [cited 2025 Jun 20]. Available from: https://wjpsonline.com/index.php/wjps/article/view/96.
  7. Sen SK, Behera LM. Ethno-medicinal uses of Nyctanthes arbor-tristis L. in Bargarh district, Odisha. Int J Herb Med. 2020;8(2):22–4.
  8. Singh AK, Kumar A. Medicinal value of the leaves of Nyctanthes arbor-tristis: A review. J Med Plants Stud. 2022;10(1):205–7. doi:10.22271/plants.2022.v10.i1c.1381.
  9. Saxena RS, Gupta B, Saxena KK, Singh RC, Prasad DN. Study of anti-inflammatory activity in the leaves of Nyctanthes arbor tristis Linn.–an Indian medicinal plant. J Ethnopharmacol. 1984;11(3):319–30. doi:10.1016/0378-8741(84)90077-1.
  10. Sharma VK, Prateeksha, Singh SP, Rao CV, Singh BN. Nyctanthes arbor-tristis bioactive extract ameliorates LPS-induced inflammation through the inhibition of NF-κB signalling pathway. J Ethnopharmacol. 2024;320:117382. doi:10.1016/j.jep.2023.117382.
  11. OSADHI – An online structural and analytics based database for herbs of India – ScienceDirect [Internet]. [cited 2025 Feb 5]. Available from: https://www.sciencedirect.com/science/article/
    abs/pii/S1476927122001797.
  12. Kim S, Chen J, Cheng T, Gindulyte A, He S, He J, et al. PubChem 2025 update. Nucleic Acids Res. 2025;53(D1):D1516–25. doi:10.1093/nar/gkae1059.
  13. Bittrich S, Rose Y, Duarte JM, Prlić A, Goodsell DS, Burley SK. RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances. J Mol Biol. 2023;435(14):167994. doi:10.1016/j.jmb.2023.167994.
  14. Ayodele PF, John N, Hussaini AA, Chikwendu LI, Ilesanmi AN, Adedotun TA, et al. Illustrated Procedure to Perform Molecular Docking Using PyRx and Biovia Discovery Studio Visualizer: A Case Study of 10kt With Atropine. Prog Drug Discov Biomed Sci. 2023;6(1). doi:10.36877/pddbs.a0000424.
  15. Ramachandran Plot – an overview | ScienceDirect Topics [Internet]. [cited 2025 Feb 5]. Available from: https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/ramachandran-plot.
  16. Hollingsworth SA, Karplus PA. A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins. Biomol Concepts. 2010;1(3–4):271–83. doi:10.1515/BMC.2010.022.
  17. Laskowski RA. PDBsum1: A standalone program for generating PDBsum analyses. Protein Sci. 2022;31(12):e4473. doi:10.1002/pro.4473.
  18. Bakchi B, Chakraborty A, Mandal M. An overview on applications of SwissADME web tool in the design and development of anticancer, antitubercular and antimicrobial agents: A medicinal chemist’s perspective. J Mol Struct. 2022;1259:132712. doi:10.1016/j.molstruc.2022.132712.
  19. SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules | Scientific Reports [Internet]. [cited 2025 Feb 5]. Available from: https://www.nature.com/articles/srep42717.
  20. Roskoski R. Properties of FDA-approved small molecule protein kinase inhibitors. Pharmacol Res. 2019;144:19–50. doi:10.1016/j.phrs.2019.03.006.
  21. Xiong G, Wu Z, Yi J, Fu L, Yang Z, Hsieh C, et al. ADMETlab 2.0: An integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Res. 2021;49(W1):W5–14. doi:10.1093/nar/gkab255.
  22. Evaluation of Free Online ADMET Tools for Academic or Small Biotech Environments [Internet]. 2025 Feb 7 [cited 2025 Jun 20]. Available from: https://www.mdpi.com/1420-3049/28/2/776.
  23. Kannan DC, Radhakrishnan MS, Sambathkumar DR, Dhanaraja MD, Muvendhiran MS, Dharnisha MNJ. A Review on Step into the Future: Python Prescription (PyRx) Transforms Virtual Drug Discovery with AI-Driven Tools. Afr J Biomed Res. 2024;27(3S):790–5. doi:10.53555/AJBR.v27i3S.2119.
  24. Meng XY, Zhang HX, Mezei M, Cui M. Molecular Docking: A powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des. 2011;7(2):146–57.
  25. Heo J, Heo S, Kang JR, Kweon J, Lee Y, Baek JH. Rheumatoid arthritis: A complex tale of autoimmune hypersensitivity. Explor Immunol. 2024;4(3):3. doi:10.37349/ei.2024.00146.
  26. Gorman CL, Cope AP. Immune-mediated pathways in chronic inflammatory arthritis. Best Pract Res Clin Rheumatol. 2008;22(2):221–38. doi:10.1016/j.berh.2008.01.003.
Regular Issue Subscription Original Research
Volume 03
Issue 02
Received 16/05/2025
Accepted 19/06/2025
Published 23/08/2025
Publication Time 99 Days
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