A Note on Vaccine Design Using Bioinformatics Methods and Applications

Year : 2023 | Volume : 01 | Issue : 01 | Page : 1-9

    K.S. Ravi Teja

  1. Rinku Polachirakkal Varghese

  2. G. Sai Lakshmi

  3. R. Jahnavi

  4. V.Harshavardhani

  5. A. Ranganadha Reddy

  1. Associate Clinical Data Coordinator-IQVIA Bengaluru Karnataka, IQVIA Bengaluru, Karnataka, India.
  2. ICMR-SRF, Vellore Institute of Technology, Tamil Nadu, India
  3. Project Associate-1, CSIR-CCMB,, Whole Genome Sequencing Lab, Siddhartha Medical College, Vijayawada, Andhra Pradesh, India
  4. Production Analyst, Technoarete Research & Development Association, Tamil Nadu, India.
  5. Production Analyst Technoarete, Research & Development Association Chennai Tamil Nadu India. 5Msc Student Bioinformatics Manipal University, Karnataka, India
  6. Associate Professor, Department of Biotechnology, Vignan’s University Vadlamudi Guntur (dt), Andhra Pradesh, India


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: DNA vaccines, RNA vaccines, structural vaccinology, Reverse Vaccinology

[This article belongs to International Journal of Bioinformatics and Computational Biology(ijbcb)]

How to cite this article: K.S. Ravi Teja, Rinku Polachirakkal Varghese, G. Sai Lakshmi, R. Jahnavi, V.Harshavardhani, A. Ranganadha Reddy A Note on Vaccine Design Using Bioinformatics Methods and Applications ijbcb 2023; 01:1-9
How to cite this URL: K.S. Ravi Teja, Rinku Polachirakkal Varghese, G. Sai Lakshmi, R. Jahnavi, V.Harshavardhani, A. Ranganadha Reddy A Note on Vaccine Design Using Bioinformatics Methods and Applications ijbcb 2023 {cited 2023 Mar 06};01:1-9. Available from: https://journals.stmjournals.com/ijbcb/article=2023/view=100205

Browse Figures


  1. Amanat, F., & Krammer, F. (2020). SARS-CoV-2 Vaccines: Status Report. Immunity, 52(4), 583–589. https://doi.org/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, V. W., & Perrie, Y. (2005). The rational design of vaccines. Drug Discovery Today, 10(22), 1527–1534. https://doi.org/10.1016/S1359-6446(05)03600-7
  4. Ahmed, S. F., Quadeer, A. A., & McKay, M. R. (2020). Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies. Viruses, 12(3), 254. https://doi.org/10.3390/v12030254
  5. Chung,J.Y., Thone,M.N., Kwon, Y.J. COVID-19 vaccines: The status and perspectives in delivery points of view,Advanced Drug Delivery Reviews,Volume 170,2021,Pages 1-25,ISSN 0169-409X,https://doi.org/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. (2018). Age and immunity: What is “immunosenescence”? Experimental Gerontology, 105, 4–9. https://doi.org/10.1016/j.exger.2017.10.024
  8. Romano, F.; Perotto, S.; Mohamed, S.E.O.; Bernardi, S.; Giraudi, M.; Caropreso, P.; Mengozzi, G.; Baima, G.; Citterio, F.; Berta, G.N.; Durazzo, M.; Gruden, G.; Aimetti, M. Bidirectional Association between Metabolic Control in Type-2 Diabetes Mellitus and Periodontitis Inflammatory Burden: A Cross-Sectional Study in an Italian Population. Clin. Med. 2021, 10, 1787. https://doi.org/10.3390/jcm10081787
  9. Chuan, Y. P., Wibowo, N., Lua, L. H. L., &Middelberg, A. P. J. (2014). The economics of virus-like particle and capsomere vaccines. Biochemical Engineering Journal, 90, 255–263. https://doi.org/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, S. P., Skountzou, I., Albrecht, R. A., Koutsonanos, D., Hua, T., Nakaya, H. I., Ravindran, R., Stewart, S., Alam, M., Kwissa, M., Villinger, F., Murthy, N., Steel, J., Jacob, J., Hogan, R. J., García-Sastre, A., Compans, R., &Pulendran, B. (2011). Programming the magnitude and persistence of antibody responses with innate immunity. Nature, 470(7335), 543–547. https://doi.org/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, T. A., Jakobs, S., Dyba, M., Egner, A., & Hell, S. W. (2000). Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission. Proceedings of the National Academy of Sciences, 97(15), 8206–8210. https://doi.org/10.1073/pnas.97.15.8206
  15. Nakamura, T., Isoda, N., Sakoda,Y. Hideyoshi Harashima,Strategies for fighting pandemic virus infections: Integration of virology and drug delivery,Journal of Controlled Release,Volume 343,2022,Pages 361-378,ISSN 0168 3659,https://doi.org/10.1016/j.jconrel.2022.01.046.
  16. Rubin, L. G., Levin, M. J., Ljungman, P., Davies, E. G., Avery, R., Tomblyn, M., Bousvaros, A., Dhanireddy, S., Sung, L., Keyserling, H., & Kang, I. (2014). 2013 IDSA Clinical Practice Guideline for Vaccination of the Immunocompromised Host. Clinical Infectious Diseases, 58(3), e44–e100. https://doi.org/10.1093/cid/cit684
  17. Saphire, E. O., Schendel, S. L., Gunn, B. M., Milligan, J. C., & Alter, G. (2018). Antibody-mediated protection against Ebola virus. Nature Immunology, 19(11), 1169–1178. https://doi.org/10.1038/s41590-018-0233-9
  18. Taylor, D. N., Trofa, A. C., Sadoff, J., Chu, C., Bryla, D., Shiloach, J., Cohen, D., Ashkenazi, S., Lerman, Y., & Egan, W. (1993). 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 (Plesiomonasshigelloides) bound to bacterial toxoids. Infection and Immunity, 61(9), 3678–3687. https://doi.org/10.1128/iai.61.9.3678-3687.1993
  19. Sinha, S., Kuo, C.-Y., Ho, J. K., White, P. J., Jazayeri, J. A., &Pouton, C. W. (2017). A suicidal strain of Listeria monocytogenes is effective as a DNA vaccine delivery system for oral administration. Vaccine, 35(38), 5115–5122. https://doi.org/10.1016/j.vaccine.2017.08.014
  20. Voysey, M., Clemens, S. A. C., Madhi, S. A., Weckx, L. Y., Folegatti, P. M., Aley, P. K., Angus, B., Baillie, V. L., Barnabas, S. L., Bhorat, Q. E., Bibi, S., Briner, C., Cicconi, P., Collins, A. M., Colin-Jones, R., Cutland, C. L., Darton, T. C., Dheda, K., Duncan, C. J. A., … Zuidewind, P. (2021). 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, 397(10269), 99–111. https://doi.org/10.1016/S0140-6736(20)32661-1
  21. Bayart, C., Peronin, S., Jean, E., Paladino, J., Talaga, P., & Borgne, M. L. (2017). The combined use of analytical tools for exploring tetanus toxin and tetanus toxoid structures. Journal of Chromatography B, 1054, 80–92. https://doi.org/10.1016/j.jchromb.2017.04.009
  22. Soria-Guerra, R. E., Nieto-Gomez, R., Govea-Alonso, D. O., & Rosales-Mendoza, S. (2015). An overview of bioinformatics tools for epitope prediction: Implications on vaccine development. Journal of Biomedical Informatics, 53, 405–414. https://doi.org/10.1016/j.jbi.2014.11.003
  23. Ulmer, J. B., Donnelly, J. J., Parker, S. E., Rhodes, G. H., Felgner, P. L., Dwarki, V. J., Gromkowski, S. H., Deck, R. R., DeWitt, C. M., Friedman, A., Hawe, L. A., Leander, K. R., Martinez, D., Perry, H. C., Shiver, J. W., Montgomery, D. L., & Liu, M. A. (1993). Heterologous Protection Against Influenza by Injection of DNA Encoding a Viral Protein. Science, 259(5102), 1745–1749. https://doi.org/10.1126/science.8456302
  24. Park, C. L., Pustejovsky, J. E., Trevino, K., Sherman, A. C., Esposito, C., Berendsen, M., &Salsman, J. M. (2019). Effects of psychosocial interventions on meaning and purpose in adults with cancer: A systematic review and meta-analysis. Cancer, 125(14), 2383–2393. https://doi.org/10.1002/cncr.32078
  25. Baxter, A. L., Cohen, L. L., Burton, M., Mohammed, A., & Lawson, M. L. (2017). The number of injected same-day preschool vaccines relates to preadolescent needle fear and HPV uptake. Vaccine, 35(33), 4213–4219. https://doi.org/10.1016/j.vaccine.2017.06.029
  26. Parvizpour, S.,. Pourseif,M.M., Razmara,J., Rafi,M.A. Yadollah Omidi,Epitope-based vaccine design: a comprehensive overview of bioinformatics approaches,Drug Discovery Today,Volume 25, Issue 6,2020,Pages 1034-1042,ISSN 1359-6446,https://doi.org/10.1016/j.drudis.2020.03.006.
  27. Pyclik, M., Górska, S., Brzozowska, E., Dobrut, A., Ciekot, J., Gamian, A., &Brzychczy-Włoch, M. (2018). Epitope Mapping of Streptococcus agalactiae Elongation Factor Tu Protein Recognized by Human Sera. Frontiers in Microbiology, 09. https://doi.org/10.3389/fmicb.2018.00125
  28. Sun, G. G., Lei, J. J., Ren, H. N., Zhang, Y., Guo, K. X., Long, S. R., Liu, R. D., Jiang, P., Wang, Z. Q., & Cui, J. (2019). Intranasal immunization with recombinant Trichinella spiralis serine protease elicits protective immunity in BALB/c mice. Experimental Parasitology, 201, 1–10. https://doi.org/10.1016/j.exppara.2019.04.006
  29. Araújo, C. L., Alves, J., Nogueira, W., Pereira, L. C., Gomide, A. C., Ramos, R., Azevedo, V., Silva, A., &Folador, A. (2019). Prediction of new vaccine targets in the core genome of Corynebacterium pseudotuberculosis through omics approaches and reverse vaccinology. Gene, 702, 36–45. https://doi.org/10.1016/j.gene.2019.03.049
  30. Yadav, D. K., Yadav, N., & Khurana, S. M. P. (2020). Chapter 26 – Vaccines: Present status and applications. In A. S. Verma & A. Singh (Eds.), Animal Biotechnology (Second Edition) (pp. 523–542). Academic Press. https://doi.org/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 Vet Res 18, 59 (2022). https://doi.org/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, 1072. https://doi.org/10.3390/biom11081072
  34. Doeschl-Wilson, P.W. Knap, T. Opriessnig, S.J. More,Review: Livestock disease resilience: from individual to herd level,Animal,Volume 15, Supplement 1,2021,100286,ISSN 1751-7311,https://doi.org/10.1016/j.animal.2021.100286.
  35. Zhou, X., Berglund, P., Rhodes, G., Parker, S. E., Jondal, M., &Liljeström, P. (1994). Self-replicating Semliki Forest virus RNA as recombinant vaccine. Vaccine, 12(16), 1510–1514. https://doi.org/10.1016/0264-410X(94)90074-4
  36. Xiang, R., Lode, H. N., Chao, T.-H., Ruehlmann, J. M., Dolman, C. S., Rodriguez, F., Whitton, J. L., Overwijk, W. W., Restifo, N. P., &Reisfeld, R. A. (2000). An autologous oral DNA vaccine protects against murine melanoma. Proceedings of the National Academy of Sciences, 97(10), 5492–5497. https://doi.org/10.1073/pnas.090097697
  37. Madhusudana, S. N., Shamsundar, R., & Seetharaman, S. (2004). In vitro inactivation of the rabies virus by ascorbic acid. International Journal of Infectious Diseases, 8(1), 21–25. https://doi.org/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.

Regular Issue Subscription Review Article
Volume 01
Issue 01
Received February 20, 2023
Accepted February 22, 2023
Published March 6, 2023