Design of an epitope-based peptide vaccine against spike protein of human coronavirus: an in silico approach

References

• González JM Gomez-Puertas P Cavanagh D Gorbalenya AE Enjuanes L A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae Arch Virol 2003 148 11 2207 2235 14579179
   PubMed Web of Science ®Google Scholar
• Siddell SG The Coronaviridae New York, NY Plenum Press 1995
   Google Scholar
• Drexler JF Gloza-Rausch F Glende J Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences J Virol 2010 84 21 11336 11349 20686038
   PubMed Web of Science ®Google Scholar
• Cavanagh D Mawditt K Welchman Dde B Britton P Gough RE Coronaviruses from pheasants (Phasianus colchicus) are genetically closely related to coronaviruses of domestic fowl (infectious bronchitis virus) and turkeys Avian Pathol 2002 31 1 81 93 12425795
   PubMed Web of Science ®Google Scholar
• Parry J WHO investigates China’s fall in SARS cases BMJ 2003 326 7402 1285
   Web of Science ®Google Scholar
• Yoo D Deregt D A single amino acid change within antigenic domain II of the spike protein of bovine coronavirus confers resistance to virus neutralization Clin Diagn Lab Immunol 2001 8 2 297 302 11238212
   PubMedGoogle Scholar
• Poland GA Ovsyannikova IG Jacobson RM Application of pharmacogenomics to vaccines Pharmacogenomics 2009 10 5 837 852 19450131
   PubMed Web of Science ®Google Scholar
• Flower DR Bioinformatics for Vaccinology Chichester John Wiley & Sons, Ltd 2008
   Google Scholar
• Bourdette DN Edmonds E Smith C A highly immunogenic trivalent T cell receptor peptide vaccine for multiple sclerosis Mult Scler 2005 11 5 552 561 16193893
   PubMed Web of Science ®Google Scholar
• López JA Weilenman C Audran R A synthetic malaria vaccine elicits a potent CD8(+) and CD4(+) T lymphocyte immune response in humans. Implications for vaccination strategies Eur J Immunol 2001 31 7 1989 1998 11449351
   PubMed Web of Science ®Google Scholar
• Knutson KL Schiffman K Disis ML Immunization with a HER-2/neu helper peptide vaccine generates HER-2/neu CD8 T-cell immunity in cancer patients J Clin Invest 2001 107 4 477 484 11181647
   PubMed Web of Science ®Google Scholar
• Petrovsky N Brusic V Computational immunology: The coming of age Immunol Cell Biol 2002 80 3 248 254 12067412
   PubMed Web of Science ®Google Scholar
• Brusic V Bajic VB Petrovsky N Computational methods for prediction of T-cell epitopes – a framework for modelling, testing, and applications Methods 2004 34 4 436 443 15542369
   PubMed Web of Science ®Google Scholar
• Peters B Bulik S Tampe R Van Endert PM Holzhütter HG Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors J Immunol 2003 171 4 1741 1749 12902473
   PubMed Web of Science ®Google Scholar
• Bhasin M Raghava GP Analysis and prediction of affinity of TAP binding peptides using cascade SVM Protein Sci 2004 13 3 596 607 14978300
   PubMed Web of Science ®Google Scholar
• Nielsen M Lundegaard C Lund O Keşmir C The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage Immunogenetics 2005 57 1–2 33 41 15744535
   PubMed Web of Science ®Google Scholar
• Apweiler R Bairoch A Wu CH UniProt: the universal protein knowledgebase Nucleic Acids Res 2004 32 Suppl 1 D115 D119 14681372
   PubMed Web of Science ®Google Scholar
• Larkin MA Blackshields G Brown NP Clustal W and Clustal X version 2.0 Bioinformatics 2007 23 21 2947 2948 17846036
   PubMed Web of Science ®Google Scholar
• Doytchinova IA Flower DR VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines BMC Bioinformatics 2007 8 4 17207271
   PubMed Web of Science ®Google Scholar
• Larsen MV Lundegaard C Lamberth K Buus S Lund O Nielsen M Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction BMC Bioinformatics 2007 8 424 17973982
   PubMed Web of Science ®Google Scholar
• Buus S Lauemøller SL Worning P Sensitive quantitative predictions of peptide-MHC binding by a ‘Query by Committee’ artificial neural network approach Tissue Antigens 2003 62 5 378 384 14617044
   PubMedGoogle Scholar
• Peters B Sette A Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method BMC Bioinformatics 2005 6 132 15927070
   PubMed Web of Science ®Google Scholar
• Tenzer S Peters B Bulik S Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding Cell Mol Life Sci 2005 62 1025 1037 15868101
   PubMed Web of Science ®Google Scholar
• Bui HH Sidney J Li W Fusseder N Sette A Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines BMC Bioinformatics 2007 8 1 361 17897458
   PubMed Web of Science ®Google Scholar
• Muh HC Tong JC Tammi MT AllerHunter: a SVM-pairwise system for assessment of allergenicity and allergic cross-reactivity in proteins PLoS One 2009 4 6 e5861 19516900
   PubMed Web of Science ®Google Scholar
• Liao L Noble WS Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships J Comput Biol 2003 10 6 857 868 14980014
   PubMed Web of Science ®Google Scholar
• Chen YPP Wong L A Better Gap Penalty for Pairwise-SVM: Proceedings of the 3rd Asia-Pacific Bioinformatics, Singapore, January 17–21, 2005 Singapore Scientific Publishing Co 2005
   Google Scholar
• Thévenet P Shen Y Maupetit J Guyon F Derreumaux P Tufféry P PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides Nucleic Acids Res 2012 40 Web Server issue W288 W293 22581768
   PubMed Web of Science ®Google Scholar
• Thomsen R Christensen MH MolDock: a new technique for high-accuracy molecular docking J Med Chem 2006 49 11 3315 3321 16722650
   PubMed Web of Science ®Google Scholar
• Berman HM Westbrook J Feng Z The protein data bank Nucleic Acids Res 2000 28 1 235 242 10592235
   PubMed Web of Science ®Google Scholar
• Nair DT Singh K Siddiqui Z Nayak BP Rao KV Salunke DM Epitope recognition by diverse antibodies suggests conformational convergence in an antibody response J Immunol 2002 168 5 2371 2382 11859128
   PubMed Web of Science ®Google Scholar
• Kolaskar AS Tongaonkar PC A semi-empirical method for prediction of antigenic determinants on protein antigens FEBS Lett 1990 276 1–2 172 174 1702393
   PubMed Web of Science ®Google Scholar
• Emini EA Hughes JV Perlow DS Boger J Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide J Virol 1985 55 3 836 839 2991600
   PubMed Web of Science ®Google Scholar
• Karplus PA Schulz GE Prediction of chain flexibility in proteins Naturwissenschaften 1985 72 4 212 213
   Web of Science ®Google Scholar
• Larsen JE Lund O Nielsen M Improved method for predicting linear B-cell epitopes Immunome Res 2006 2 1 2 16635264
   PubMedGoogle Scholar
• Chou PY Fasman GD Empirical predictions of protein conformation Annu Rev Biochem 1978 47 251 276 354496
   PubMed Web of Science ®Google Scholar
• Rini JM Schulze-Gahmen U Wilson IA Structural evidence for induced fit as a mechanism for antibody-antigen recognition Science 1992 255 5047 959 965 1546293
   PubMed Web of Science ®Google Scholar
• Rose GD Gierasch L Smith JA Turns in peptides and proteins Adv Protein Chem 1985 37 1 109 2865874
   PubMedGoogle Scholar
• Novotný J Handschumacher M Haber E Antigenic determinants in proteins coincide with surface regions accessible to large probes (antibody domains) Proc Natl Acad Sci U S A 1986 83 2 226 230 2417241
   PubMed Web of Science ®Google Scholar
• Marshall SJ Developing countries face double burden of disease Bull World Health Organ 2004 82 7 556 15500291
   PubMed Web of Science ®Google Scholar
• De Groot AS Rappuoli R Genome-derived vaccines Expert Rev Vaccines 2004 3 1 59 76 14761244
   PubMedGoogle Scholar
• Korber B LaBute M Yusim K Immunoinformatics comes of age PLoS Comput Biol 2006 2 6 e71 16846250
   PubMed Web of Science ®Google Scholar
• Fauci AS Emerging and re-emerging infectious diseases: influenza as a prototype of the host-pathogen balancing act Cell 2006 124 4 665 670 16497575
   PubMed Web of Science ®Google Scholar
• Purcell AW McCluskey J Rossjohn J More than one reason to rethink the use of peptides in vaccine design Nat Rev Drug Discov 2007 6 5 404 414 17473845
   PubMed Web of Science ®Google Scholar
• Lapelosa M Gallicchio E Arnold GF Arnold E Levy RM In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes J Mol Biol 2009 385 2 675 691 19026659
   PubMed Web of Science ®Google Scholar
• Chakraborty S Chakravorty R Ahmed M A computational approach for identification of epitopes in dengue virus envelope protein: a step towards designing a universal dengue vaccine targeting endemic regions In Silico Biol 2010 10 5–6 235 246 22430357
   PubMedGoogle Scholar
• Islam R Sakib MS Zaman A A computational assay to design an epitope-based peptide vaccine against chikungunya virus Future Virol 2012 7 10 1029 1042
   Web of Science ®Google Scholar
• Hasan MA Hossain M Alam MJ A computational assay to design an epitope-based Peptide vaccine against Saint Louis encephalitis virus Bioinform Biol Insights 2013 7 347 355 24324329
   PubMedGoogle Scholar
• Twiddy SS Holmes EC Rambaut A Inferring the rate and time-scale of dengue virus evolution Mol Biol Evol 2003 20 1 122 129 12519914
   PubMed Web of Science ®Google Scholar
• Manzin A Solforosi L Petrelli E Evolution of hypervariable region 1 of hepatitis C virus in primary infection J Virol 1998 72 7 6271 6276 9621104
   PubMed Web of Science ®Google Scholar
• Christie JM Chapel H Chapman RW Rosenberg WM Immune selection and genetic sequence variation in core and envelope regions of hepatitis C virus Hepatology 1999 30 4 1037 1044 10498657
   PubMed Web of Science ®Google Scholar
• Ma C Li Y Wang L Intranasal vaccination with recombinant receptor-binding domain of MERS-CoV spike protein induces much stronger local mucosal immune responses than subcutaneous immunization: Implication for designing novel mucosal MERS vaccines Vaccine 2014 32 18 2100 2108 24560617
   PubMed Web of Science ®Google Scholar
• Yang ZY Kong WP Huang Y A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice Nature 2004 428 6982 561 564 15024391
   PubMed Web of Science ®Google Scholar
• Agnihothram S Gopal R Yount BL Platform strategies for rapid response against emerging coronaviruses: MERS-CoV serologic and antigenic relationships in vaccine design J Infect Dis [serial on the Internet] 11 2013 [cited May 16, 2014]. Available from: http://jid.oxfordjournals.org/content/early/2013/11/18/infdis.jit609 Accessed July 12, 2014
   Google Scholar
• Shrestha B Diamond MS Role of CD8+ T cells in control of West Nile virus infection J Virol 2004 78 15 8312 8321 15254203
   PubMed Web of Science ®Google Scholar
• Sharmin R Islam AB A highly conserved WDYPKCDRA epitope in the RNA directed RNA polymerase of human coronaviruses can be used as epitope-based universal vaccine design BMC Bioinformatics 2014 15 161 24884408
   PubMed Web of Science ®Google Scholar
• van der Hoek L Pyrc K Jebbink MF Identification of a new human coronavirus Nat Med 2004 10 4 368 373 15034574
   PubMed Web of Science ®Google Scholar
• Hofmann H Pyrc K van der Hoek L Geier M Berkhout B Pöhlmann S Human coronavirus NL63 employs the severe acute respiratory syndrome coronavirus receptor for cellular entry Proc Natl Acad Sci U S A 2005 102 22 7988 7993 15897467
   PubMed Web of Science ®Google Scholar
• Chiu SS Chan KH Chu KW Human coronavirus NL63 infection and other coronavirus infections in children hospitalized with acute respiratory disease in Hong Kong, China Clin Infect Dis 2005 40 12 1721 1729 15909257
   PubMed Web of Science ®Google Scholar
• McKeever TM Lewis SA Smith C Hubbard R Vaccination and allergic disease: a birth cohort study Am J Public Health 2004 94 6 985 989 15249303
   PubMed Web of Science ®Google Scholar
• Khan MK Zaman S Chakraborty S In silico predicted mycobacterial epitope elicits in vitro T-cell responses Mol Immunol 2014 61 1 16 22 24853589
   PubMed Web of Science ®Google Scholar