Abstract
In this chapter, the steps of designing candidate vaccine molecules for allergen-specific immunotherapy (AIT) using immunoinformatics are described. The most modern approach of AIT deals with carrier-bound B cell epitope and multi-epitope vaccine molecules. The strategy for designing these molecules and the bioinformatics tools and servers used for that are discussed in detail here.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Sledge RF (1938) Treatment of hay fever with alum-precipitated pollen extract. J Allergy 9:424
Lee WY, Sehon AH (1977) Abrogation of reaginic antibodies with modified allergens. Nature 267(5612):618–619. https://doi.org/10.1038/267618a0
Dorofeeva Y, Shilovskiy I, Tulaeva I, Focke-Tejkl M, Flicker S, Kudlay D, Khaitov M, Karsonova A, Riabova K, Karaulov A, Khanferyan R (2021) Past, present, and future of allergen immunotherapy vaccines. Allergy 76(1):131–149. https://doi.org/10.1111/all.14300
Zieglmayer P, Focke-Tejkl M, Schmutz R, Lemell P, Zieglmayer R, Weber M, Kiss R, Blatt K, Valent P, Stolz F, Huber H (2016) Mechanisms, safety, and efficacy of a B cell epitope-based vaccine for immunotherapy of grass pollen allergy. EBioMedicine 11:43–57. https://doi.org/10.1016/j.ebiom.2016.08.022
Eckl-Dorna J, Weber M, Stanek V, Linhart B, Ristl R, Waltl EE, Villazala-Merino S, Hummel A, Focke-Tejkl M, Froeschel R, Neubauer A (2019) Two years of treatment with the recombinant grass pollen allergy vaccine BM32 induces a continuously increasing allergen-specific IgG4 response. EBioMedicine 50:421–432. https://doi.org/10.1016/j.ebiom.2019.11.006
Focke-Tejkl M, Weber M, Niespodziana K, Neubauer A, Huber H, Henning R, Stegfellner G, Maderegger B, Hauer M, Stolz F, Niederberger V (2015) Development and characterization of a recombinant, hypoallergenic, peptide-based vaccine for grass pollen allergy. J Allergy Clin Immunol 135(5):1207–1217. https://doi.org/10.1016/j.jaci.2014.09.012
Focke M, Mahler V, Ball T, Sperr WR, Majlesi Y, Valent P, Kraft D, Valenta R (2001) Nonanaphylactic synthetic peptides derived from B cell epitopes of the major grass pollen allergen, Phl p 1, for allergy vaccination. FASEB J 15(11):2042–2044. https://doi.org/10.1096/fj.01-0016fje
Sircar G, Jana K, Dasgupta A, Saha S, Bhattacharya SG (2016) Epitope mapping of Rhi o 1 and generation of a hypoallergenic variant: a candidate molecule for fungal allergy vaccines. J Biol Chem 291(34):18016–18029. https://doi.org/10.1074/jbc.M116.732032
Sircar G, Ghosh N, Saha S (2022) Designing next-generation vaccines against common pan-allergens using in silico approaches. Monoclon Antib Immunodiagn Immunother 41(5):231–242. https://doi.org/10.1089/mab.2021.0033
Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In: The proteomics protocols handbook, pp 571–607. https://doi.org/10.1385/1-59259-890-0:571
McGuffin LJ, Bryson K, Jones DT (2000) The PSIPRED protein structure prediction server. Bioinformatics 16(4):404–405. https://doi.org/10.1093/bioinformatics/16.4.404
Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y (2015) The I-TASSER suite: protein structure and function prediction. Nat Methods 12(1):7–8. https://doi.org/10.1038/nmeth.3213
Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK - a program to check the stereochemical quality of protein structures. J App Cryst 26(2):283–291. https://doi.org/10.1107/S0021889892009944
Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB (2003) Protein disorder prediction: implications for structural proteomics. Structure 11(11):1453–1459. https://doi.org/10.1016/j.str.2003.10.002
Grote A, Hiller K, Scheer M, Münch R, Nörtemann B, Hempel DC, Jahn D (2005) JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res 33 (suppl_2):W526-31. https://doi.org/10.1093/nar/gki376
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31(13):3406–3415. https://doi.org/10.1093/nar/gkg595
Nagpal G, Usmani SS, Dhanda SK, Kaur H, Singh S, Sharma M, Raghava GP (2017) Computer-aided designing of immunosuppressive peptides based on IL-10 inducing potential. Sci Rep 7(1):1–10. https://doi.org/10.1038/srep42851
Rapin N, Lund O, Bernaschi M, Castiglione F (2010) Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system. PLoS One 5(4):e9862. https://doi.org/10.1371/journal.pone.0009862
Acknowledgments
NG acknowledges the Vice Chancellor of Vidyasagar University and DST SERB, Government of India funded project (Sanction no. CRG/2019/003276). GS acknowledges DBT/Wellcome Trust India Alliance for providing an Early Career Fellowship Grant (IA/E/17/1/503696). SS acknowledges the BIC COE project funded by the Department of Biotechnology, Government of India (sanction no. BT/PR40174/BTIS/137/45/2022).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Ghosh, N., Sircar, G., Saha, S. (2023). Computational Vaccine Design for Common Allergens. 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_33
Download citation
DOI: https://doi.org/10.1007/978-1-0716-3239-0_33
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-3238-3
Online ISBN: 978-1-0716-3239-0
eBook Packages: Springer Protocols