Araştırma Makalesi


DOI :10.26650/IstanbulJPharm.2022.1058189   IUP :10.26650/IstanbulJPharm.2022.1058189    Tam Metin (PDF)

Comparative assessment of different nanobodies that inhibit the interaction of B7-1/2 with CD28 as a potential therapeutic target for immune-related diseases by molecular modeling

Halil İbrahim BulutNail BeşliGüven Yenmiş

Background and Aims: Active T cells are central players in the self-defense system as well as in immune-related diseases. Being crucial for T cell activation, the interaction of B7-1/2 with CD28 is associated with T cell activation-related diseases such as alloreactivity in transplantation and autoreactivity in autoimmune disorders. Nanobodies are the recombinant variable and single-domain smallest antigen-binding fragments. The focus of this study is to investigate the interactions between B7-1/2 and eight antibodies at the molecular level utilizing computational methods, and to guide the best nanobody for in-vitro and in-vivo studies about immunosuppressive Methods: After receiving the 3D models of agents via Robetta, molecular docking techniques were used to compare the binding modes and affinities of six nanobodies and two FDA-approved fusion protein models against B7-1/2(CD80/CD86). Results: According to our in silico outputs, we selected the top of model clusters from HADDOCK 2.4 (Z-Score of CD80/CD86:- 2.7 to -1.3/-2.1 to -2.1) and distinguished that 1A1 and 1B2 have higher affinities than Belatacept and Abatacept for the percentage of a calculation scale. Conclusion: Our findings suggest that selected nanobodies show higher affinity by interacting with the CD80/86 epitope regions and provide helpful insights into the design and improvement of further computational investigations of nanobody modeling.


PDF Görünüm

Referanslar

  • Abbas, A. K., Lichtman, A. H., & Pillai, S. (2019). Basic immunology e-book: Functions and disorders of the immune system. Amsterdam, Netherlands: Elsevier Health Sciences. google scholar
  • Ansari, A. W., Khan, M. A., Schmidt, R. E., & Broering, D. C. (2017). Harnessing the immunotherapeutic potential of T-lymphocyte co-signaling molecules in transplantation. Immunology Letters, 183, 8-16. google scholar
  • Crepeau, R. L., & Ford, M. L. (2017). Challenges and opportunities in targeting the CD28/CTLA-4 pathway in transplantation and autoimmunity. Expert Opinion on Biological Therapy, 17(8), 1001-1012. google scholar
  • Goronzy, J. J., & Weyand, C. M. (2008). T-cell co-stimulatory pathways in autoimmunity. Arthritis Research & Therapy, 10(1), 1-10. google scholar
  • Green, J. M., Noel, P. J., Sperling, A. I., Walunas, T. L., Gray, G. S., Bluestone, J. A., & Thompson, C. B. (1994). Absence of B7-dependent responses in CD28-deficient mice. Immunity, 1(6), 501-508. google scholar
  • Janeway, C. A. J., Travers, P., Walport, M., & Shlomchik, M. J. (2001). Immunopiology: the immune system in health and disease. 5” ed. New York. google scholar
  • Jovcevska, I., & Muyldermans, S. (2020). The therapeutic potential of nanobodies. BioDrugs, 34(1), 11-26. google scholar
  • Khan, U., & Ghazanfar, H. (2018). T lymphocytes and autoimmunity. International Review of Cell and Molecular Biology, 341, 125-168. google scholar
  • Krupa Pawetand Spodzieja, M., & Sieradzan, A. K. (2021). Prediction of CD28-CD86 protein complex structure using different level of resolution approach. Journal of Molecular Graphics and Modelling, 103, 107802. google scholar
  • Larsen, C. P., Pearson, T. C., Adams, A. B., Tso, P., Shirasugi, N., Strob-ert, M. E., ... Peach, R. J. (2005). Rational development of LEA29Y (belatacept), a high-affinity variant of CTLA4-Ig with potent immunosuppressive properties. American Journal of Transplantation, 5(3), 443-453. google scholar
  • Leem, J., Dunbar, J., Georges, G., Shi, J., & Deane, C. M. (2016). A google scholar
  • Body Builder: Automated antibody structure prediction with data-driven accuracy estimation. MAbs, 8(7), 1259-1268. google scholar
  • Mifsud, N. A., Illing, P. T., Lai, J. W., Fettke, H., Hensen, L., Huang, Z., ... & Purcell, A. W. (2021). Carbamazepine induces focused T cell responses in resolved Stevens-Johnson syndrome and toxic epidermal necrolysis cases but does not perturb the immunopepti-dome for T cell recognition. Frontiers in Immunology, 12, 653710. google scholar
  • Noble, J., Jouve, T., Janbon, B., Rostaing, L., & Malvezzi, P. (2019). Belatacept in kidney transplantation and its limitations. Expert Review of Clinical Immunology, 15(4), 359-367. google scholar
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605-1612. google scholar
  • Ramagopal, U. A., Liu, W., Garrett-Thomson, S. C., Bonanno, J. B., Yan, Q., Srinivasan, M., ... Almo, S. C. (2017). Structural basis for cancer immunotherapy by the first-in-class checkpoint inhibitor ipili-mumab. Proceedings of the National Academy of Sciences, 114(21), E4223-E4232. google scholar
  • Raman, S., Vernon, R., Thompson, J., Tyka, M., Sadreyev, R., Pei, J. & Baker, D. (2009). Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins: Structure, Function, and Bioinformatics, 77(S9), 89-99. google scholar
  • Schrodinger, LLC. (2015). The {PyMOL} Molecular Graphics System, Version~1.8. google scholar
  • Siontorou, C. G. (2013). Nanobodies as novel agents for disease diagnosis and therapy. International Journal of Nanomedicine, 8, 4215. google scholar
  • Song, Y., DiMaio, F., Wang, R. Y.-R., Kim, D., Miles, C., Brunette, T. J., Thompson, J., & Baker, D. (2013). High-resolution comparative modeling with Rosetta CM. Structure, 21(10), 1735-1742. google scholar
  • Sun, S., Ding, Z., Yang, X., Zhao, X., Zhao, M., Gao, L., ... Lu, X. (2021). Nanobody: a small antibody with big implications for tumor therapeutic strategy. International Journal of Nanomedicine, 16, 2337. google scholar
  • Van Balen, P., Kester, M. G., de Klerk, W., Crivello, P., Arrieta-Bolanos, E., de Ru, A. H., ... Falkenburg, J. F. (2020). Immunopeptidome analysis of HLA-DPB1 allelic variants reveals new functional hierarchies. The Journal of Immunology, 204(12), 3273-3282. google scholar
  • Vita, R., Zarebski, L., Greenbaum, J. A., Emami, H., & Hoof, I. (2012). Immune Epitope Database and Analysis Resource. google scholar
  • Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M., & Barton, G. J. (2009). Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics, 25(9), 1189-1191. google scholar
  • Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., ... Schwede, T. (2018). SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic acids research, 46(W1), W296-W303. google scholar
  • Weitzner, B. D., Jeliazkov, J. R., Lyskov, S., Marze, N., Kuroda, D., Frick, R., ... Gray, J. J. (2017). Modeling and docking of antibody structures with Rosetta. Nature protocols, 12(2), 401-416. google scholar

Atıflar

Biçimlendirilmiş bir atıfı kopyalayıp yapıştırın veya seçtiğiniz biçimde dışa aktarmak için seçeneklerden birini kullanın


DIŞA AKTAR



APA

Bulut, H.İ., Beşli, N., & Yenmiş, G. (2022). Comparative assessment of different nanobodies that inhibit the interaction of B7-1/2 with CD28 as a potential therapeutic target for immune-related diseases by molecular modeling. İstanbul Journal of Pharmacy, 52(3), 289-296. https://doi.org/10.26650/IstanbulJPharm.2022.1058189


AMA

Bulut H İ, Beşli N, Yenmiş G. Comparative assessment of different nanobodies that inhibit the interaction of B7-1/2 with CD28 as a potential therapeutic target for immune-related diseases by molecular modeling. İstanbul Journal of Pharmacy. 2022;52(3):289-296. https://doi.org/10.26650/IstanbulJPharm.2022.1058189


ABNT

Bulut, H.İ.; Beşli, N.; Yenmiş, G. Comparative assessment of different nanobodies that inhibit the interaction of B7-1/2 with CD28 as a potential therapeutic target for immune-related diseases by molecular modeling. İstanbul Journal of Pharmacy, [Publisher Location], v. 52, n. 3, p. 289-296, 2022.


Chicago: Author-Date Style

Bulut, Halil İbrahim, and Nail Beşli and Güven Yenmiş. 2022. “Comparative assessment of different nanobodies that inhibit the interaction of B7-1/2 with CD28 as a potential therapeutic target for immune-related diseases by molecular modeling.” İstanbul Journal of Pharmacy 52, no. 3: 289-296. https://doi.org/10.26650/IstanbulJPharm.2022.1058189


Chicago: Humanities Style

Bulut, Halil İbrahim, and Nail Beşli and Güven Yenmiş. Comparative assessment of different nanobodies that inhibit the interaction of B7-1/2 with CD28 as a potential therapeutic target for immune-related diseases by molecular modeling.” İstanbul Journal of Pharmacy 52, no. 3 (Jun. 2023): 289-296. https://doi.org/10.26650/IstanbulJPharm.2022.1058189


Harvard: Australian Style

Bulut, Hİ & Beşli, N & Yenmiş, G 2022, 'Comparative assessment of different nanobodies that inhibit the interaction of B7-1/2 with CD28 as a potential therapeutic target for immune-related diseases by molecular modeling', İstanbul Journal of Pharmacy, vol. 52, no. 3, pp. 289-296, viewed 7 Jun. 2023, https://doi.org/10.26650/IstanbulJPharm.2022.1058189


Harvard: Author-Date Style

Bulut, H.İ. and Beşli, N. and Yenmiş, G. (2022) ‘Comparative assessment of different nanobodies that inhibit the interaction of B7-1/2 with CD28 as a potential therapeutic target for immune-related diseases by molecular modeling’, İstanbul Journal of Pharmacy, 52(3), pp. 289-296. https://doi.org/10.26650/IstanbulJPharm.2022.1058189 (7 Jun. 2023).


MLA

Bulut, Halil İbrahim, and Nail Beşli and Güven Yenmiş. Comparative assessment of different nanobodies that inhibit the interaction of B7-1/2 with CD28 as a potential therapeutic target for immune-related diseases by molecular modeling.” İstanbul Journal of Pharmacy, vol. 52, no. 3, 2022, pp. 289-296. [Database Container], https://doi.org/10.26650/IstanbulJPharm.2022.1058189


Vancouver

Bulut Hİ, Beşli N, Yenmiş G. Comparative assessment of different nanobodies that inhibit the interaction of B7-1/2 with CD28 as a potential therapeutic target for immune-related diseases by molecular modeling. İstanbul Journal of Pharmacy [Internet]. 7 Jun. 2023 [cited 7 Jun. 2023];52(3):289-296. Available from: https://doi.org/10.26650/IstanbulJPharm.2022.1058189 doi: 10.26650/IstanbulJPharm.2022.1058189


ISNAD

Bulut, Halilİbrahim - Beşli, Nail - Yenmiş, Güven. Comparative assessment of different nanobodies that inhibit the interaction of B7-1/2 with CD28 as a potential therapeutic target for immune-related diseases by molecular modeling”. İstanbul Journal of Pharmacy 52/3 (Jun. 2023): 289-296. https://doi.org/10.26650/IstanbulJPharm.2022.1058189



ZAMAN ÇİZELGESİ


Gönderim15.01.2022
Kabul19.07.2022
Çevrimiçi Yayınlanma30.12.2022

LİSANS


Attribution-NonCommercial (CC BY-NC)

This license lets others remix, tweak, and build upon your work non-commercially, and although their new works must also acknowledge you and be non-commercial, they don’t have to license their derivative works on the same terms.


PAYLAŞ




İstanbul Üniversitesi Yayınları, uluslararası yayıncılık standartları ve etiğine uygun olarak, yüksek kalitede bilimsel dergi ve kitapların yayınlanmasıyla giderek artan bilimsel bilginin yayılmasına katkıda bulunmayı amaçlamaktadır. İstanbul Üniversitesi Yayınları açık erişimli, ticari olmayan, bilimsel yayıncılığı takip etmektedir.