Skip to main content
SpringerLink
Log in

Immunoinformatics as a Tool for New Antifungal Vaccines

  • Protocol
  • First Online:
Vaccines for Invasive Fungal Infections

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1625))

Abstract

Immunoinformatics aids in screening for vaccine candidates, which can be experimentally tested for their efficacy. This chapter describes methods to use immunoinformatics to screen fungal vaccines candidates. Surface-localized molecules called adhesins could elicit immune response and serve as efficient vaccine candidates. The screening process is patterned on two steps, namely, a First Layer screen mostly used for value addition and prioritization based on characteristics of known antigens and a Second Layer highly focussed on core immunoinformatics analysis involving the binding and interactions of the molecules of the immune system. Together they offer a comprehensive objective evaluation of vaccine candidates selection in silico for fungal pathogens.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 179.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Pfaller MA, Diekema DJ (2007) Epidemiology of invasive candidiasis: a persistent public health problem. Clin Microbiol Rev 20:133–163

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Dagenais TR, Keller NP (2009) Pathogenesis of aspergillus fumigatus in invasive aspergillosis. Clin Microbiol Rev 22:447–465

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Latgé JP (1999) Aspergillus fumigatus and aspergillosis. Clin Microbiol Rev 12:310–350

    PubMed  PubMed Central  Google Scholar 

  4. Saubolle MA, McKellar PP, Sussland D (2007) Epidemiologic, clinical, and diagnostic aspects of coccidioidomycosis. J Clin Microbiol 45:26–30

    Article  CAS  PubMed  Google Scholar 

  5. Kauffman CA (2009) Histoplasmosis. Clin Chest Med 30:217–225

    Article  PubMed  Google Scholar 

  6. JA MK, Pappas PG (2009) Blastomycosis: new insights into diagnosis, prevention, and treatment. Clin Chest Med 30:227–239

    Article  Google Scholar 

  7. Cutler JE, Deepe GS, Klein BS (2007) Advances in combating fungal diseases: vaccines on the threshold. Nat Rev Microbiol 5:13–28

    Article  CAS  PubMed  Google Scholar 

  8. Cassone A (2008) Fungal vaccines: real progress from real challenges. Lancet Infect Dis 8:114–124

    Article  CAS  PubMed  Google Scholar 

  9. Chaudhuri R, Ansari FA, Raghunandanan MV, Ramachandran S (2011) FungalRV: adhesin prediction and immunoinformatics portal for human fungal pathogens. BMC Genomics 12:192

    Article  PubMed  PubMed Central  Google Scholar 

  10. Mora M, Veggi D, Santini L, Pizza M, Rappuoli R (2003) Reverse vaccinology. Drug Discov Today 8(10):459–464

    Article  CAS  PubMed  Google Scholar 

  11. Sette A, Rappuoli R (2010) Reverse vaccinology: developing vaccines in the era of genomics. Immunity 33(4):530–541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Vivona S, Gardy JL, Ramachandran S, Brinkman FS, Raghava GP, Flower DR, Filippini F (2008) Computer-aided biotechnology: from immuno-informatics to reverse vaccinology. Trends Biotechnol 26(4):190–200

    Article  CAS  PubMed  Google Scholar 

  13. Spellberg BJ, Ibrahim AS, Avenissian V, Filler SG, Myers CL, Fu Y, Edwards JE (2005) The anti-Candida albicans vaccine composed of the recombinant N terminus of Als1p reduces fungal burden and improves survival in both immunocompetent and immunocompromised mice. Infect Immun 73:6191–6193

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Ibrahim AS, Spellberg BJ, Avanesian V, Fu Y, Edwards JE (2006) The anti-Candida vaccine based on the recombinant N-terminal domain of Als1p is broadly active against disseminated candidiasis. Infect Immun 74:3039–3041

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Wüthrich M, Chang WL, Klein BS (1998) Immunogenicity and protective efficacy of the WI-1 adhesin of Blastomyces dermatitidis. Infect Immun 66:5443–5449

    PubMed  PubMed Central  Google Scholar 

  16. Wüthrich M, Filutowicz HI, Warner T, Klein BS (2002) Requisite elements in vaccine immunity to Blastomyces dermatitidis: plasticity uncovers vaccine potential in immune-deficient hosts. J Immunol 169:6969–6976

    Article  PubMed  Google Scholar 

  17. Braga CJ, Rittner GM, Muñoz Henao JE, Teixeira AF, Massis LM, Sbrogio-Almeida ME, Taborda CP, Travassos LR, Ferreira LC (2009) Paracoccidioides brasiliensis vaccine formulations based on the gp43-derived P10 sequence and the salmonella enterica FliC flagellin. Infect Immun 77:1700–1707

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Pinto AR, Puccia R, Diniz SN, Franco MF, Travassos LR (2000) DNA-based vaccination against murine paracoccidioidomycosis using the gp43 gene from Paracoccidioides brasiliensis. Vaccine 18:3050–3058

    Article  CAS  PubMed  Google Scholar 

  19. Hung CY, Ampel NM, Christian L, Seshan KR, Cole GT (2000) A major cell surface antigen of Coccidioides immitis which elicits both humoral and cellular immune responses. Infect Immun 68:584–593

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Koonin EV (2005) Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 39:309–338

    Article  CAS  PubMed  Google Scholar 

  21. Hung CY, JJ Y, Seshan KR, Reichard U, Cole GT (2002) A parasitic phase-specific adhesin of Coccidioides immitis contributes to the virulence of this respiratory fungal pathogen. Infect Immun 70:3443–3456

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D, Bryant SH (2005) CDD: a conserved domain database for protein classification. Nucleic Acids Res 33(Database issue):D192–D196

    Article  CAS  PubMed  Google Scholar 

  23. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410

    Article  CAS  PubMed  Google Scholar 

  24. Bradley P, Cowen L, Menke M, King J, Berger B (2001) BETAWRAP: successful prediction of parallel beta -helices from primary sequence reveals an association with many microbial pathogens. Proc Natl Acad Sci U S A 98(26):14819–14824

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305(3):567–580

    Article  CAS  PubMed  Google Scholar 

  26. Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FS (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26(13):1608–1615

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Kolaskar AS, Tongaonkar PC (1990) A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett 276(1–2):172–174

    Article  CAS  PubMed  Google Scholar 

  28. Saha S, Raghava GP (2007) Prediction methods for B-cell epitopes. Methods Mol Biol 409:387–394

    Article  CAS  PubMed  Google Scholar 

  29. Haste Andersen P, Nielsen M, Lund O (2006) Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci 15(11):2558–2567

    Article  PubMed  PubMed Central  Google Scholar 

  30. Sweredoski MJ, Baldi P (2008) PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinformatics 24(12):1459–1460

    Article  CAS  PubMed  Google Scholar 

  31. Parker KC, Bednarek MA, Coligan JE (1994) Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J Immunol 152(1):163–175

    CAS  PubMed  Google Scholar 

  32. Singh H, Raghava GP (2003) ProPred1: prediction of promiscuous MHC class-I binding sites. Bioinformatics 19(8):1009–1014

    Article  CAS  PubMed  Google Scholar 

  33. Bui HH, Sidney J, Peters B, Sathiamurthy M, Sinichi A, Purton KA, Mothé BR, Chisari FV, Watkins DI, Sette A (2005) Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics 57(5):304–314

    Article  CAS  PubMed  Google Scholar 

  34. Moutaftsi M, Peters B, Pasquetto V, Tscharke DC, Sidney J, Bui HH, Grey H, Sette A (2006) A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus. Nat Biotechnol 24(7):817–819

    Article  CAS  PubMed  Google Scholar 

  35. Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, Nielsen M (2008) NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11. Nucleic Acids Res 36(Web Server):W509–W512

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B (2008) Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res 36(Web Server issue):W513–W518

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Wang P, Sidney J, Kim Y, Sette A, Lund O, Nielsen M, Peters B (2010) Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics 11:568

    Article  PubMed  PubMed Central  Google Scholar 

  38. Saha S, Raghava GP (2006) AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. Nucleic Acids Res 34(Web Server issue):W202–W209

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Björklund AK, Soeria-Atmadja D, Zorzet A, Hammerling U, Gustafsson MG (2005) Supervised identification of allergen-representative peptides for in silico detection of potentially allergenic proteins. Bioinformatics 21(1):39–50

    Article  PubMed  Google Scholar 

  40. Fiers MW, Kleter GA, Nijland H, Peijnenburg AA, Nap JP, van Ham RC (2004) Allermatch, a webtool for the prediction of potential allergenicity according to current FAO/WHO codex alimentarius guidelines. BMC Bioinformatics 5:133

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. IBM India Private Limited, Bangalore, India

    Rupanjali Chaudhuri

  2. CSIR-Institute of Genomics and Integrative Biology, Room 130, Mathura Road, Near Sukhdev Vihar DTC Bus Depot, New Delhi, 110 025, India

    Srinivasan Ramachandran

Authors
  1. Rupanjali Chaudhuri
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Srinivasan Ramachandran
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Srinivasan Ramachandran .

Editor information

Editors and Affiliations

  1. Department of Molecular Immunology, Beckman Research Institute of City of Hope, Duarte, California, USA

    Markus Kalkum

  2. Department of Molecular Immunology, Beckman Research Institute of City of Hope, Duarte, California, USA

    Margarita Semis

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Chaudhuri, R., Ramachandran, S. (2017). Immunoinformatics as a Tool for New Antifungal Vaccines. In: Kalkum, M., Semis, M. (eds) Vaccines for Invasive Fungal Infections. Methods in Molecular Biology, vol 1625. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7104-6_3

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7104-6_3

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7103-9

  • Online ISBN: 978-1-4939-7104-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation