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Immunoinformatics Approaches in Designing Vaccines Against COVID-19

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Computational Vaccine Design

Abstract

Since the onset of the COVID-19 pandemic, a number of approaches have been adopted by the scientific communities for developing efficient vaccine candidate against SARS-CoV-2. Conventional approaches of developing a vaccine require a long time and a series of trials and errors which indeed limit the feasibility of such approaches for developing a dependable vaccine in an emergency situation like the COVID-19 pandemic. Hitherto, most of the available vaccines have been developed against a particular antigen of SARS-CoV, spike protein in most of the cases, and intriguingly, these vaccines are not effective against all the pathogenic coronaviruses. In this context, immunoinformatics-based reverse vaccinology approaches enable a robust design of efficacious peptide-based vaccines against all the infectious strains of coronaviruses within a short frame of time. In this chapter, we enumerate the methodological trajectory of developing a universal anti-SARS-CoV-2 vaccine, namely, “AbhiSCoVac,” through advanced computational biology-based immunoinformatics approach and its in-silico validation using molecular dynamics simulations.

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References

  1. Das NC, Chakraborty P, Bayry J, Mukherjee S (2021) In silico analyses on the comparative potential of therapeutic human monoclonal antibodies against newly emerged SARS-COV-2 variants bearing mutant spike protein. Front Immunol 12:782506. https://doi.org/10.3389/fimmu.2021.782506

    Article  CAS  PubMed  Google Scholar 

  2. Han X, Xu P, Ye Q (2021) Analysis of Covid-19 vaccines: types, thoughts, and application. J Clin Lab Anal 35(9):e23937. https://doi.org/10.1002/jcla.23937

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Ndwandwe D, Wiysonge CS (2021) Covid-19 vaccines. Curr Opin Immunol 71:111–116. https://doi.org/10.1016/j.coi.2021.07.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Choudhury A, Sen Gupta PS, Panda SK, Rana MK, Mukherjee S (2022) Designing AbhiSCoVac — a single potential vaccine for all ‘Corona culprits’: immunoinformatics and immune simulation approaches. J Mol Liq 351:118633. https://doi.org/10.1016/j.molliq.2022.118633

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Ghorbani A, Zare F, Sazegari S, Afsharifar A, Eskandari MH, Pormohammad A (2020) Development of a novel platform of virus-like particle (VLP)-based vaccine against COVID-19 by exposing epitopes: an immunoinformatics approach. New Microbes New Infect 38:100786. https://doi.org/10.1016/j.nmni.2020.100786

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Kumar N, Sood D, Chandra R (2020) Design and optimization of a subunit vaccine targeting COVID-19 molecular shreds using an immunoinformatics framework. RSC Adv 10(59):35856–35872. https://doi.org/10.1039/d0ra06849g

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Behmard E, Soleymani B, Najafi A, Barzegari E (2020) Immunoinformatic design of a COVID-19 subunit vaccine using entire structural immunogenic epitopes of SARS-COV-2. Sci Rep 10(1):20864. https://doi.org/10.1038/s41598-020-77547-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Dong R, Chu Z, Yu F, Zha Y (2020) Contriving multi-epitope subunit of vaccine for COVID-19: immunoinformatics approaches. Front Immunol 11:1784. https://doi.org/10.3389/fimmu.2020.01784

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Naz A, Shahid F, Butt TT, Awan FM, Ali A, Malik A (2020) Designing multi-epitope vaccines to combat emerging coronavirus disease 2019 (COVID-19) by employing immuno-informatics approach. Front Immunol 11:1663. https://doi.org/10.3389/fimmu.2020.01663

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Abdelmageed MI, Abdelmoneim AH, Mustafa MI, Elfadol NM, Murshed NS, Shantier SW, Makhawi AM (2020) Design of a multi epitope-based peptide vaccine against the E protein of human COVID-19: an immunoinformatics approach. Biomed Res Int 2020. https://doi.org/10.1155/2020/2683286

  11. Choudhury A, Das NC, Patra R, Bhattacharya M, Ghosh P, Patra BC, Mukherjee S (2021) Exploring the binding efficacy of ivermectin against the key proteins of SARS-CoV-2 pathogenesis: an in silico approach. Future Virol 16(4):277–291. https://doi.org/10.2217/fvl-2020-0342

    Article  CAS  Google Scholar 

  12. Yuan S, Chan HCS, Hu Z (2017) Using PyMol as a platform for computational drug design. WIREs Comput Mol Sci 7(2):1298. https://doi.org/10.1002/wcms.1298

    Article  CAS  Google Scholar 

  13. Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda S (2017) The ClusPro web server for protein–protein docking. Nat Protoc 12(2):255–278. https://doi.org/10.1038/nprot.2016.169

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5(4):725–738. https://doi.org/10.1038/nprot.2010.5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Vita R, Mahajan S, Overton JA, Dhanda SK, Martini S, Cantrell JR, Wheele DK, Sette A, Peters B (2019) The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res 47(D1):D339–D343. https://doi.org/10.1093/nar/gky1006

    Article  CAS  PubMed  Google Scholar 

  16. Mesel-Lemoine M, Millet J, Vidalain PO, Law H, Vabret A, Lorin V, Escriou N, Albert ML, Nal B, Tangy F (2012) A human coronavirus responsible for the common cold massively kills dendritic cells but not monocytes. J Virol 86(14):7577–7587. https://doi.org/10.1128/JVI.00269-12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A (2016) Prodigy: a web server for predicting the binding affinity of protein–protein complexes. Bioinformatics 32(23):3676–3678. https://doi.org/10.1093/bioinformatics/btw514

    Article  CAS  PubMed  Google Scholar 

  18. Patronov A, Doytchinova I (2013) T-cell epitope vaccine design by immunoinformatics. Open Biol 3(1):120139. https://doi.org/10.1098/rsob.120139

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Galanis KA, Nastou KC, Papandreou NC, Petichakis GN, Pigis DG, Iconomidou VA (2021) Linear B-cell epitope prediction for in silico vaccine design: a performance review of methods available via command-line interface. Int J Mol Sci 22(6):3210. https://doi.org/10.3390/ijms22063210

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Vashi Y, Jagrit V, Kumar S (2020) Understanding the B and T cell epitopes of spike protein of severe acute respiratory syndrome coronavirus-2: a computational way to predict the immunogens. Infect Genet Evol 84:104382. https://doi.org/10.1016/j.meegid.2020.104382

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Gorai S, Das NC, Gupta PS, Panda SK, Rana MK, Mukherjee S (2022) Designing efficient multi-epitope peptide-based vaccine by targeting the antioxidant thioredoxin of bancroftian filarial parasite. Infect Genet Evol 98:105237. https://doi.org/10.1016/j.meegid.2022.105237

    Article  CAS  PubMed  Google Scholar 

  22. Dalsass M, Brozzi A, Medini D, Rappuoli R (2019) Comparison of open-source reverse vaccinology programs for bacterial vaccine antigen discovery. Front Immunol 10:113. https://doi.org/10.3389/fimmu.2019.00113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Hou J, Liu Y, Hsi J, Wang H, Tao R, Shao Y (2014) Cholera toxin B subunit acts as a potent systemic adjuvant for HIV-1 DNA vaccination intramuscularly in mice. Hum Vaccin Immunother 10(5):1274–1283. https://doi.org/10.4161/hv.28371

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Clem AS (2011) Fundamentals of vaccine immunology. J Glob Infect Dis 3(1):73–78. https://doi.org/10.4103/0974-777X.77299

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Das NC, Sen Gupta PS, Biswal S, Patra R, Rana MK, Mukherjee S (2022) In-silico evidences on filarial cystatin as a putative ligand of human TLR4. J Biomol Struct Dyn 40(19):8808–8824. https://doi.org/10.1080/07391102.2021.1918252

  26. López-Blanco JR, Aliaga JI, Quintana-Ortí ES, Chacón P (2014) IMODS: internal coordinates normal mode analysis server. Nucleic Acids Res 42(Web Server issue):W271–W276. https://doi.org/10.1093/nar/gku339

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Wang J, Morin P, Wang W, Kollman PA (2001) Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT OF TIBO derivatives and predicting the binding mode to HIV-1 RT of Efavirenz by docking and MM-PBSA. J Am Chem Soc 123(22):5221–5230. https://doi.org/10.1021/ja003834q

    Article  CAS  PubMed  Google Scholar 

  28. Weng G, Wang E, Wang Z, Liu H, Zhu F, Li D, Hou T (2019) Hawkdock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA. Nucleic Acids Res 47(W1):W322–W330. https://doi.org/10.1093/nar/gkz397

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Ylilauri M, Pentikäinen OT (2013) MMGBSA as a tool to understand the binding affinities of filamin–peptide interactions. J Chem Inf Model 53(10):2626–2633. https://doi.org/10.1021/ci4002475

    Article  CAS  PubMed  Google Scholar 

  30. Kar T, Narsaria U, Basak S, Deb D, Castiglione F, Mueller DM, Srivastava AP (2020) A candidate multi-epitope vaccine against SARS-COV-2. Sci Rep 10(1):10895. https://doi.org/10.1038/s41598-020-67749-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

JB and SM acknowledge Department of Science & Technology (DST)-Science & Engineering Research Board (SERB), Govt. of India (Sanction no. CRG/2021/002605), for providing core research grant to them. All the uncited articles which have not been cited due to space limitations are respectfully acknowledged. We acknowledge the use of BioRender.com for making of the illustrations.

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Correspondence to Jagadeesh Bayry or Suprabhat Mukherjee .

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Chakraborty, A., Bayry, J., Mukherjee, S. (2023). Immunoinformatics Approaches in Designing Vaccines Against COVID-19. In: Reche, P.A. (eds) Computational Vaccine Design. Methods in Molecular Biology, vol 2673. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3239-0_29

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  • DOI: https://doi.org/10.1007/978-1-0716-3239-0_29

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  • Publisher Name: Humana, New York, NY

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