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International Journal of Bioinformatics and Computational Biology Review Article

A Note on Vaccine Design Using Bioinformatics Methods and Applications

  1. K.S. Ravi Teja IQVIA Bengaluru
  2. Rinku Polachirakkal Varghese Vellore Institute of Technology
  3. G. Sai Lakshmi Whole Genome Sequencing Lab, Siddhartha Medical College, Vijayawada
  4. R. Jahnavi Technoarete Research & Development Association
  5. V.Harshavardhani Research & Development Association Chennai Tamil Nadu India. 5Msc Student Bioinformatics Manipal University
  6. A. Ranganadha Reddy Department of Biotechnology, Vignan’s University Vadlamudi Guntur (dt)

Abstract

Vaccines prevent infectious diseases caused by viruses and bacteria saving millions of lives.It consists of certain agents that resemble disease causative agentsand stimulates our immune system to recognize and fight foreign antigens. Immune function or an immune response is the fundamental basis of the vaccine's mechanism. Vaccines are pharmaceutical derivatives that provide an affordable way to prevent diseases.Various bioinformatics approaches can be incorporated into vaccine design studies and development. Reverse Vaccinology, Immunoinformatics, DNA vaccines, RNA vaccines, RDT vaccine (Recombinant DNA Technology), and structural vaccinology are different types of approaches for vaccine design. Vaccines are a combination of different antigens. Several vaccines are being developed for various diseases caused by bacteria, viruses, parasites, etc using bioinformatics tools.

Keywords

References (38)

  1. Amanat F, Krammer F. SARS-CoV-2 Vaccines: Status Report. Immunity. 2020;52(4):583-589. doi:10.1016/j.immuni.2020.03.007
  2. Ames, H.M.R., Meike Zuske, Jonathan D. King, Peter Steinmann, Xavier Bosch-Capblanch, Chapter Six - Community and Drug Distributor Perceptions and Experiences of Mass Drug Administration for the Elimination of Lymphatic Filariasis: A Rapid Review of Qualitative Research, Editor(s): Jennifer Keiser,Advances in Parasitology,Academic Press,Volume 103,2019, Pages 117-149,ISSN 0065-308X,ISBN 9780081027509,https://doi.org/10.1016/bs.apar.2018. 003.
  3. Bramwell VW, Perrie Y. The rational design of vaccines. Drug Discovery Today. 2005;10(22):1527-1534. doi:10.1016/s1359-6446(05)03600-7
  4. Ahmed SF, Quadeer AA, McKay MR. Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies. Viruses. 2020;12(3):254. doi:10.3390/v12030254
  5. Chung JY, Thone MN, Kwon YJ. COVID-19 vaccines: The status and perspectives in delivery points of view. Advanced Drug Delivery Reviews. 2021;170:1-25. doi:10.1016/j.addr.2020.12.011
  6. Peele,K.A., Chandrasai. P, T.Srihansa, Krupanidhi, A.Vijayasai, D.Johnbabu, M.Indira, A.RanganadhaReddy, T.C. Venkateswarulu, (2020) Molecular docking and dynamic simulations for antiviral compounds against SARS-CoV-2: A computational study. Informatics in Medicine Unlocked. 19(100345): pp 01-06.
  7. Pawelec G. Age and immunity: What is “immunosenescence”? Experimental Gerontology. 2018;105:4-9. doi:10.1016/j.exger.2017.10.024
  8. Romano F, Perotto S, Mohamed SEO, Bernardi S, Giraudi M, Caropreso P, et al. Bidirectional Association between Metabolic Control in Type-2 Diabetes Mellitus and Periodontitis Inflammatory Burden: A Cross-Sectional Study in an Italian Population. Journal of Clinical Medicine. 2021;10(8):1787. doi:10.3390/jcm10081787
  9. Chuan YP, Wibowo N, Lua LHL, Middelberg APJ. The economics of virus-like particle and capsomere vaccines. Biochemical Engineering Journal. 2014;90:255-263. doi:10.1016/j.bej.2014.06.005
  10. Abraham Peele Karlapudi, Chinna Venkateswarulu Thirupati, Krupanidhi Srirrama, Divyashree Coimbatore Nageswaran, Indira Mikkili,, Vijayasai Sai Ayyagari, Ranganadha Reddy Aluri, Yasha Nazir Butt, Aishwarya Gangadhar. (2020). Design of CRISPR-Based Targets for the Development of a Diagnostic Method for SARS-CoV-2: An in Silico Approach. Eurasian journal of medicine and oncology. 4(4): 304 - 308.
  11. Furuya, Y., Regner, M., Lobigs, M., & Koskinen, A. (n.d.). Effect of inactivation method on the cross- protective immunity induced by whole ‘killed’ influenza A viruses and commercial vaccine preparations. Journal of General Virology, 11.
  12. Kasturi SP, Skountzou I, Albrecht RA, Koutsonanos D, Hua T, Nakaya HI, et al. Programming the magnitude and persistence of antibody responses with innate immunity. Nature. 2011;470(7335):543-547. doi:10.1038/nature09737
  13. Rodrigues, C. M. C., & Plotkin, S. A. (2020). Impact of Vaccines; Health, Economic and Social Perspectives. Frontiers in Microbiology, 11. https://www.frontiersin.org/articles/10.3389/fmicb. 01526
  14. Klar TA, Jakobs S, Dyba M, Egner A, Hell SW. Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission. Proceedings of the National Academy of Sciences. 2000;97(15):8206-8210. doi:10.1073/pnas.97.15.8206
  15. Nakamura T, Isoda N, Sakoda Y, Harashima H. Strategies for fighting pandemic virus infections: Integration of virology and drug delivery. Journal of Controlled Release. 2022;343:361-378. doi:10.1016/j.jconrel.2022.01.046
  16. Rubin LG, Levin MJ, Ljungman P, Davies EG, Avery R, Tomblyn M, et al. 2013 IDSA Clinical Practice Guideline for Vaccination of the Immunocompromised Host. Clinical Infectious Diseases. 2013;58(3):e44-e100. doi:10.1093/cid/cit684
  17. Saphire EO, Schendel SL, Gunn BM, Milligan JC, Alter G. Antibody-mediated protection against Ebola virus. Nature Immunology. 2018;19(11):1169-1178. doi:10.1038/s41590-018-0233-9
  18. Taylor DN, Trofa AC, Sadoff J, Chu C, Bryla D, Shiloach J, et al. Synthesis, characterization, and clinical evaluation of conjugate vaccines composed of the O-specific polysaccharides of Shigella dysenteriae type 1, Shigella flexneri type 2a, and Shigella sonnei (Plesiomonas shigelloides) bound to bacterial toxoids. Infection and Immunity. 1993;61(9):3678-3687. doi:10.1128/iai.61.9.3678-3687.1993
  19. Sinha S, Kuo CY, Ho JK, White PJ, Jazayeri JA, Pouton CW. A suicidal strain of Listeria monocytogenes is effective as a DNA vaccine delivery system for oral administration. Vaccine. 2017;35(38):5115-5122. doi:10.1016/j.vaccine.2017.08.014
  20. Voysey M, Clemens SAC, Madhi SA, Weckx LY, Folegatti PM, Aley PK, et al. Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK. The Lancet. 2021;397(10269):99-111. doi:10.1016/s0140-6736(20)32661-1
  21. Bayart C, Peronin S, Jean E, Paladino J, Talaga P, Borgne ML. The combined use of analytical tools for exploring tetanus toxin and tetanus toxoid structures. Journal of Chromatography B. 2017;1054:80-92. doi:10.1016/j.jchromb.2017.04.009
  22. Soria-Guerra RE, Nieto-Gomez R, Govea-Alonso DO, Rosales-Mendoza S. An overview of bioinformatics tools for epitope prediction: Implications on vaccine development. Journal of Biomedical Informatics. 2015;53:405-414. doi:10.1016/j.jbi.2014.11.003
  23. Ulmer JB, Donnelly JJ, Parker SE, Rhodes GH, Felgner PL, Dwarki VJ, et al. Heterologous Protection Against Influenza by Injection of DNA Encoding a Viral Protein. Science. 1993;259(5102):1745-1749. doi:10.1126/science.8456302
  24. Park CL, Pustejovsky JE, Trevino K, Sherman AC, Esposito C, Berendsen M, et al. Effects of psychosocial interventions on meaning and purpose in adults with cancer: A systematic review and meta‐analysis. Cancer. 2019;125(14):2383-2393. doi:10.1002/cncr.32078
  25. Baxter AL, Cohen LL, Burton M, Mohammed A, Lawson ML. The number of injected same-day preschool vaccines relates to preadolescent needle fear and HPV uptake. Vaccine. 2017;35(33):4213-4219. doi:10.1016/j.vaccine.2017.06.029
  26. Parvizpour S, Pourseif MM, Razmara J, Rafi MA, Omidi Y. Epitope-based vaccine design: a comprehensive overview of bioinformatics approaches. Drug Discovery Today. 2020;25(6):1034-1042. doi:10.1016/j.drudis.2020.03.006
  27. Pyclik M, Górska S, Brzozowska E, Dobrut A, Ciekot J, Gamian A, et al. Epitope Mapping of Streptococcus agalactiae Elongation Factor Tu Protein Recognized by Human Sera. Frontiers in Microbiology. 2018;9. doi:10.3389/fmicb.2018.00125
  28. Sun GG, Lei JJ, Ren HN, Zhang Y, Guo KX, Long SR, et al. Intranasal immunization with recombinant Trichinella spiralis serine protease elicits protective immunity in BALB/c mice. Experimental Parasitology. 2019;201:1-10. doi:10.1016/j.exppara.2019.04.006
  29. Araújo CL, Alves J, Nogueira W, Pereira LC, Gomide AC, Ramos R, et al. Prediction of new vaccine targets in the core genome of Corynebacterium pseudotuberculosis through omics approaches and reverse vaccinology. Gene. 2019;702:36-45. doi:10.1016/j.gene.2019.03.049
  30. Yadav DK, Yadav N, Khurana SMP. Vaccines: present status and applications. Animal Biotechnology. 2020:523-542. doi:10.1016/b978-0-12-811710-1.00024-0
  31. Khan, K. H. (2013). Gene Expression in Mammalian Cells and its Applications. Advanced Pharmaceutical Bulletin, 3(2), 257–263. https://doi.org/10.5681/apb.2013.042
  32. Viidu DA, Mõtus K. Implementation of a pre-calving vaccination programme against rotavirus, coronavirus and enterotoxigenic Escherichia coli (F5) and association with dairy calf survival. BMC Veterinary Research. 2022;18(1). doi:10.1186/s12917-022-03154-2
  33. Cid R, Bolívar J. Platforms for Production of Protein-Based Vaccines: From Classical to Next-Generation Strategies. Biomolecules. 2021;11(8):1072. doi:10.3390/biom11081072
  34. Doeschl-Wilson A, Knap PW, Opriessnig T, More SJ. Review: Livestock disease resilience: from individual to herd level. Animal. 2021;15:100286. doi:10.1016/j.animal.2021.100286
  35. Zhou X, Berglund P, Rhodes G, Parker SE, Jondal M, Liljeström P. Self-replicating Semliki Forest virus RNA as recombinant vaccine. Vaccine. 1994;12(16):1510-1514. doi:10.1016/0264-410x(94)90074-4
  36. Xiang R, Lode HN, Chao TH, Ruehlmann JM, Dolman CS, Rodriguez F, et al. An autologous oral DNA vaccine protects against murine melanoma. Proceedings of the National Academy of Sciences. 2000;97(10):5492-5497. doi:10.1073/pnas.090097697
  37. Madhusudana SN, Shamsundar R, Seetharaman S. In vitro inactivation of the rabies virus by ascorbic acid. International Journal of Infectious Diseases. 2004;8(1):21-25. doi:10.1016/j.ijid.2003.09.002
  38. Rappuoli, R. (2019). Comparison of Open-Source Reverse Vaccinology Programs for Bacterial Vaccine Antigen Discovery. Frontiers in Immunology, 10, 12.