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Articles

Utilising capsid proteins of poliovirus to design a multi-epitope based subunit vaccine by immunoinformatics approach

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Pages 419-428 | Received 21 Sep 2019, Accepted 12 Jan 2020, Published online: 03 Feb 2020

References

  • Trevelyan B, Smallman-Raynor M, Cliff AD. The spatial dynamics of poliomyelitis in the United States: from epidemic emergence to vaccine-induced retreat, 1910–1971. Ann Assoc AM Geogr. 2005;95(2):269–293.
  • Atkinson W, Hamborsky J, McIntyre L, et al. 2017. Epidemiology and prevention of vaccine-preventable diseases. 13th ed. Public Health Foundation (US).
  • Ohri LK, Marquess JG. Polio: will we soon vanquish an old enemy. Drug Benefit Trends. 1999;11(6):41–54.
  • Kew OM, Sutter RW, de Gourville EM, et al. Vaccine-derived polioviruses and the endgame strategy for global polio eradication. Annu Rev Microbiol. 2005;59:587–635.
  • Chander S, Pandey RK, Penta A, et al. Molecular docking and molecular dynamics simulation based approach to explore the dual inhibitor against HIV-1 reverse transcriptase and integrase. Comb Chem High Throughput Screen. 2017;20(8):734–746.
  • Khatoon N, Pandey RK, Prajapati VK. Exploring Leishmania secretory proteins to design B and T cell multi-epitope subunit vaccine using immunoinformatics approach. Sci Rep. 2017;7(1):8285.
  • Moyle PM, Toth I. Modern subunit vaccines: development, components, and research opportunities. ChemMedChem. 2013;8(3):360–376.
  • Vakili B, Eslami M, Hatam GR, et al. Immunoinformatics-aided design of a potential multi-epitope peptide vaccine against Leishmania infantum. Int J Biol Macromol. 2018;120:1127–1139.
  • Consortium U. Uniprot: a worldwide hub of protein knowledge. Nucleic Acids Res. 2018;47(D1):D506–D515.
  • Duvvuri VR, Duvvuri B, Alice C, et al. Preexisting CD4+ T-cell immunity in human population to avian influenza H7N9 virus: whole proteome-wide immunoinformatics analyses. PLoS One. 2014;9(3):e91273.
  • Wang P, Sidney J, Kim Y, et al. Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics. 2010;11(1):568.
  • Nielsen M, Lund O. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics. 2009;10(1):296.
  • Nielsen M, Lundegaard C, Lund O. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics. 2007;8(1):238.
  • Sidney J, Assarsson E, Moore C, et al. Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries. Immunome Res. 2008;4(1):2.
  • Sturniolo T, Bono E, Ding J, et al. Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat Biotechnol. 1999;17(6):555.
  • Vita R, Overton JA, Greenbaum JA, et al. The immune epitope database (IEDB) 3.0. Nucleic Acids Res. 2014;43(D1):D405–D412.
  • Larsen MV, Lundegaard C, Lamberth K, et al. Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics. 2007;8(1):424.
  • Peters B, Bulik S, Tampe R, et al. Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol. 2003;171(4):1741–1749.
  • Lund O, Nielsen M, Kesmir C, et al. Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics. 2004;55(12):797–810.
  • Hajighahramani N, Nezafat N, Eslami M, et al. Immunoinformatics analysis and in silico designing of a novel multi-epitope peptide vaccine against Staphylococcus aureus. Infect Genet Evol. 2017;48:83–94.
  • Mohan T, Sharma C, Bhat AA, et al. Modulation of HIV peptide antigen specific cellular immune response by synthetic α-and β-defensin peptides. Vaccine. 2013;31(13):1707–1716.
  • Gasteiger E, Hoogland C, Gattiker A, et al. Protein identification and analysis tools on the ExPASy server. The proteomicsprotocols handbook. Totowa (NJ): Springer; 2005.
  • Chen J, Liu H, Yang J, et al. Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. Amino Acids. 2007;33(3):423–428.
  • EL-Manzalawy Y, Dobbs D, Honavar V. Predicting linear B-cell epitopes using string kernels. J Mol Recognition Inter. 2008;21(4):243–255.
  • Ponomarenko J, Bui H-H, Li W, et al. Ellipro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics. 2008;9(1):514.
  • Dimitrov I, Bangov I, Flower DR, et al. AllerTOP v. 2—a server for in silico prediction of allergens. J Mol Model. 2014;20(6):2278.
  • Wold S, Jonsson J, Sjörström M, et al. DNA and peptide sequences and chemical processes multivariately modelled by principal component analysis and partial least-squares projections to latent structures. Anal Chim Acta. 1993;277(2):239–253.
  • Magnan CN, Baldi P. SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity. Bioinformatics. 2014;30(18):2592–2597.
  • Doytchinova IA, Flower DR. Vaxijen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics. 2007;8(1):4.
  • Grote A, Hiller K, Scheer M, et al. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res. 2005;33(suppl_2):W526–W531.
  • Carbone A, Zinovyev A, Képes F. Codon adaptation index as a measure of dominating codon bias. Bioinformatics. 2003;19(16):2005–2015.
  • Yang J, Yan R, Roy A, et al. The I-TASSER Suite: protein structure and function prediction. Nat Methods. 2015;12(1):7.
  • Shin W-H, Lee GR, Heo L, et al. Prediction of protein structure and interaction by GALAXY protein modeling programs. Bio Design. 2014;2(1):1–11.
  • Vajda S, Yueh C, Beglov D, et al. New additions to the ClusPro server motivated by CAPRI. Proteins Struct Funct Bioinformatics. 2017;85(3):435–444.
  • Sasidharan S, Saudagar P. Biochemical and structural characterization of tyrosine aminotransferase suggests broad substrate specificity and a two state folding mechanism in Leishmania donovani. FEBS Open Bio. 2019;9(10):1769–1783.
  • Rapin N, Lund O, Bernaschi M, et al. Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system. PLoS One. 2010;5(4):e9862.
  • Urrutia-Baca VH, Gomez-Flores R, De La Garza-Ramos MA, et al. Immunoinformatics approach to design a novel epitope-based oral vaccine against helicobacter pylori. J Comput Biol. 2019;26(10):1177–1190.
  • Ghahremanifard P, Afzali F, Rostami A, et al. Designing a novel multi-epitope T vaccine for “targeting protein for Xklp-2” (TPX2) in hepatocellular carcinoma based on immunoinformatics approach. Int J Pept Res Ther. 2019: 1–10. https://doi.org/10.1007/s10989-019-09915-2.
  • Kalita P, Lyngdoh DL, Padhi AK, et al. Development of multi-epitope driven subunit vaccine against Fasciola gigantica using immunoinformatics approach. Int J Biol Macromol. 2019;138:224–233.
  • Jenssen H, Aspmo SI. Serum stability of peptides. Peptide-based drug design. New York: Springer; 2008. p. 177–186.
  • Guruprasad K, Reddy BB, Pandit MW. Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng Des Sel. 1990;4(2):155–161.

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