Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties

Vaccine

Volumn 25, Issue 5, 2007, Pages 856-866

  Doytchinova, Irini A ^a   Flower, Darren R ^b  

^a MEDICAL UNIVERSITY OF SOFIA   (Bulgaria)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Antigen prediction; Vaccine

Indexed keywords

AMINO ACID; ASPARTIC PROTEINASE; BACTERIAL ANTIGEN; BACTERIAL PROTEIN; BACTERIAL TOXIN; COPPER ZINC SUPEROXIDE DISMUTASE; DECORIN BINDING PROTEIN A; EG95 HOST PROTECTIVE VACCINE ANTIGEN; ENTEROTOXIN; EPSILON TOXIN; FLAGELLIN; HEAT LABILE ENTEROTOXIN B SUBUNIT; HEAT SHOCK PROTEIN 60; OUTER MEMBRANE PORIN PROTEIN OMS28; OUTER MEMBRANE PROTEIN; OUTER SURFACE PROTEIN A; OUTER SURFACE PROTEIN B; OUTER SURFACE PROTEIN C; PERTACTIN; PERTUSSIS TOXIN; PHOSPHOLIPASE C; PHOSPHOLIPASE D; PORIN; PROTEIN FIMH; PROTEIN SUBUNIT; RIBOSOME PROTEIN; SUBUNIT VACCINE; TETANUS TOXIN; UREASE;

ACCURACY; AMINO ACID SEQUENCE; ANTIGEN RECOGNITION; ARTICLE; COMPUTER MODEL; DRUG IDENTIFICATION; METHODOLOGY; PREDICTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE; VALIDATION PROCESS;

ALGORITHMS; AMINO ACID SEQUENCE; ANTIGENS, BACTERIAL; BACTERIAL VACCINES; MODELS, STATISTICAL; SENSITIVITY AND SPECIFICITY; VACCINES, SUBUNIT;

EID: 33845195440     PISSN: 0264410X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.vaccine.2006.09.032     Document Type: Article

References (63)

1. Rappuoli R. Reverse vaccinology, a genome-based approach to vaccine development. Vaccine 19 (2001) 2688
2. Pizza M., Scarlato V., Masignani V., Giuliani M.M., Arico B., Comanducci M., et al. Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 287 (2000) 1816
3. Mora M., Veggi D., Santini L., Pizza M., and Rappuoli R. Reverse vaccinology. Drug Discov Today 8 (2003) 459
4. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J Mol Biol 215 (1990) 403
5. Lipman D.J., and Pearson W.R. Rapid and sensitive protein similarity searches. Science 227 (1985) 1435
6. Nakai K., and Kanehisa M. Expert system for predicting protein localization sites in gram-negative bacteria. Proteins 11 (1991) 95
7. Bendtsen J.D., Nielsen H., von Heijne G., and Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340 (2004) 783
8. Accelrys GCG 11.0, July 2005.
9. Petsko G.A., and Ringe D. Protein structure and function (2004), Blackwell Publishing
10. Wold S., Jonsson J., Sjöström M., Sandberg M., and Rännar S. DNA and peptide sequences and chemical processes multivariately modeled by principal component analysis and partial least-squares projections to latent structures. Anal Chim Acta 277 (1993) 239
11. Andersson P.M., Sjöström M., and Lundstedt T. Preprocessing peptide sequences for multivariate sequence-property analysis. Chemometr Intell Lab 42 (1998) 41
12. Nyström A., Andersson P.M., and Lundstedt T. Multivariate data analysis of topographically modified α-melanotropin analoques using auto and cross auto covariances (ACC). Quant Struct-Act Rel 19 (2000) 264
13. Lapinsh M., Gutcaits A., Prusis P., Post C., Lundstedt T., and Wikberg J.E.S. Classification of G-protein coupled receptors by alignment-independent extraction of principal chemical properties of primary amino acid sequences. Protein Sci 11 (2002) 795
14. Mayers C., Duffield M., Rowe S., Miller J., Lingard B., Hayward S., et al. Analysis of known bacterial protein vaccine antigens reveals biased physical properties and amino acid composition. Comp Funct Genom 4 (2003) 468
15. Probert W.S., and LeFebvre R.B. Protection of C3H/HeN mice from challenge with Borrelia burgdorferi through active immunization with OspA, OspB, or OspC, but not with OspD or the 83-kilodalton antigen. Infect Immun 62 (1994) 1920
16. Lee L.H., Burg III E., Baqar S., Bourgeois A.L., Burr D.H., Ewing C.P., et al. Evaluation of a truncated recombinant flagellin subunit vaccine against Campylobacter jejuni. Infect Immun 67 (1999) 5799
17. Igietseme J.U., and Murdin A. Induction of protective immunity against Chlamydia trachomatis genital infection by a vaccine based on major outer membrane protein-lipophilic immune response-stimulating complexes. Infect Immun 68 (2000) 6798
18. Li K., Yu J., Hung C., Lehmann P.F., and Cole G.T. Recombinant urease and urease DNA of Coccidioides immitis elicit an immunoprotective response against coccidioidomycosis in mice. Infect Immun 69 (2001) 2878
19. Tarcha E.J., Basrur V., Hung C., Gardner M.J., and Cole G.T. A recombinant aspartyl protease of Coccidioides posadasii induces protection against pulmonary coccidioidomycosis in mice. Infect Immun 74 (2006) 516
20. Woollard D.J., Gauci C.G., Heath D.D., and Lightowlers M.W. Protection against hydatid disease induced with the EG95 vaccine is associated with conformational epitopes. Vaccine 19 (2001) 498
21. Bolduc G.R., Bouchet V., Jiang R., Geisselsoder J., Truong-Bolduc Q.C., Rice P.A., et al. Variability of outer membrane protein P1 and its evaluation as a vaccine candidate against experimental otitis media due to nontypeable Haemophilus influenzae: an unambiguous, multifaceted approach. Infect Immun 68 (2000) 4505
22. Dunkley M.L., Harris S.J., McCoy R.J., Musicka M.J., Eyers F.M., Beagley L.G., et al. Protection against Helicobacter pylori infection by intestinal immunization with a 50/52-kDa subunit protein. FEMS Immunol Med Mic 24 (1999) 221
23. Ermak T.H., Giannasca P.J., Nichols R., Myers G.A., Nedrud J., Weltzin R., et al. Immunization of mice with urease vaccine affords protection against Helicobacter pylori infection in the absence of antibodies and is mediated by MHC class II-restricted responses. J Exp Med 188 (1998) 2277
24. Radcliff F.J., Hazell S.L., Kolesnikow T., Doidge C., and Lee A. Catalase, a novel antigen for Helicobacter pylori vaccination. Infect Immun 65 (1997) 4668
25. Satin B., Del Giudice G., Della Bianca V., Dusi S., Laudanna C., Tonello F., et al. The neutrophil-activating protein (HP-NAP) of Helicobacter pylori is a protective antigen and a major virulence factor. J Exp Med 191 (2000) 1467
26. Weeratna R., Stamler D.A., Edelstein P.H., Ripley M., Marrie T., Hoskin D., et al. Human and guinea pig immune responses to Legionella pneumophila protein antigens OmpS and Hsp60. Infect Immun 62 (1994) 3454
27. Velaz-Faircloth M., Cobb A.J., Horstman A.L., Henry S.C., and Frothingham R. Protection against Mycobacterium avium by DNA vaccines expressing mycobacterial antigens as fusion proteins with green fluorescent protein. Infect Immun 67 (1999) 4243
28. Chambers M.A., Vordermeier H.M., Whelan A., Commander N., Tascon R., Lowrie D., et al. Vaccination of mice and cattle with plasmid DNA encoding the Mycobacterium bovis antigen MPB83. Clin Infect Dis 30 Suppl. 3 (2000) S283
29. Delogu G., Howard A., Collins F.M., and Morris S.L. DNA vaccination against tuberculosis: Expression of a ubiquitin-conjugated tuberculosis protein enhances antimycobacterial immunity. Infect Immun 68 (2000) 3097
30. Demangel C., Brodin P., Cockle P.J., Brosch R., Majlessi L., Leclerc C., et al. Cell envelope protein PPE68 contributes to Mycobacterium tuberculosis RD1 immunogenicity independently of a 10-kilodalton culture filtrate protein and ESAT-6. Infect Immun 72 (2004) 2170
31. Kamath A.T., Groat N.L., Bean A.G.D., and Britton W.J. Protective effect of DNA immunization against mycobacterial infection is associated with the early emergence of interferon-gamma (IFN-γ)-secreting lymphocytes. Clin Exp Immunol 120 (2000) 476
32. Li Z., Howard A., Kelley C., Delogu G., Collins F., and Morris S. Immunogenicity of DNA vaccines expressing tuberculosis proteins fused to tissue plasminogen activator signal sequences. Infect Immun 67 (1999) 4780
33. Morris S., Kelley C., Howard A., Li Z., and Collins F. The immunogenicity of single and combination DNA vaccines against tuberculosis. Vaccine 18 (2000) 2155
34. Tanghe A., Lefevre P., Denis O., D'Souza S., Braibant m., Lozes E., et al. Immunogenicity and protective efficacy of tuberculosis DNA vaccines encoding putative phosphate transport receptors. J Immunol 162 (1999) 1113
35. Martin D., Cadieux N., Hamel J., and Brodeur B.R. Highly conserved Neisseria meningitides surface protein confers protection against experimental infection. J Exp Med 185 (1997) 1173
36. West D., Reddin K., Matheson M., Heath R., Funnell S., Hudson M., et al. Recombinant Neisseria miningitidis transferring binding protein A protects against experimental meningococcal infection. Infect Immun 69 (2001) 1561
37. Denis-Mize K.S., Price B.M., Baker N.R., and Galloway D.R. Analysis of immunization with DNA encoding Pseudomonas aerginosa exotoxin A. FEMS Immunol Med Mic 27 (2000) 147
38. Gilleland Jr. H.E., Gilleland L.B., and Metthews-Greer J.M. Outer membrane protein F preparation of Pseudomonas aeruginosa as a vaccine against chronic pulmonary infection with heterologous immunotype strains in a rat model. Infect Immun 56 (1988) 1017
39. Holder I.A., Neely A.N., and Frank D.W. PcrV immunization enhances survival of burned Pseudomonas aeruginosa-infected mice. Infect Immun 69 (2001) 5908
40. Seong S., Huh M.S., Jang W.J., Park S.G., Kim J.G., Woo S.G., et al. Induction of homologous immune response to Rickettsia tsutsugamushi Boryong with a partial 56-kilodalton recombinant antigen fused with the maltose-binding protein MBP-Bor56. Infect Immun 65 (1997) 1541
41. Ohwada A., Sekiya M., hanaki H., Arai K.K., Nagaoka I., Hori S., et al. DNA vaccination by mecA sequence evokes an antibacterial immune response against methicillin-resistant Staphylococcus aureus. J Antimicrob Chemoth 44 (1999) 767
42. Brodeur B.R., Boyer M., Charlebois I., Hamel J., Couture F., Rioux C.R., et al. Identification of group B streptococcal sip protein which elicits cross-protective immunity. Infect Immun 68 (2000) 5610
43. Briles D.E., Ades E., Paton J.C., Sampson J.S., Carlone G.M., Huebner R.C., et al. Intranasal immunization of mice with a mixture of the pneumococcal proteins PsaA and PspA is highly protective against nasopharyngeal carriage of Streptococcus pneumoniae. Infect Immun 68 (2000) 796
44. Ogunniyi A.D., Woodrow M.C., Poolman J.T., and Paton J.C. Protection against Streptococcus pneumoniae elicited by immunization with pneumolysin and CbpA. Infect Immun 69 (2001) 5997
45. Cameron C.E., Castro C., Lukehart S.A., and van Voorhis W.C. Function and proteictive capacity of Treponema pallidum subsp pallidum glycerophosphodiester phosphodiesterase. Infect Immun 66 (1998) 5763
46. Centurion-Lara A., Castro C., Barrett L., Cameron C., Mostowfi M., van Voorhis W.C., et al. Treponema pallidum major sheath protein homologue Tpr K is a target of opsonic antibody and the protective immune response. J Exp Med 189 (1999) 647
47. Wicher K., Schouls L.M., Wicher V., van Embden J.D.A., and Nakeeb S.S. Immunization of guinea pigs with recombinant TmpB antigen induces protection against challenge infection with Treponema pallidum Nichols. Infect Immun 59 (1991) 4343
48. Anderson Jr. G.W., Leary S.E.C., Williamson E.D., Titball R.W., Welkos S.L., Worsham P.L., et al. Recombinant V antigen protects mice against pneumonic and bubonic plague caused by F1-capsule-positive and -negative strains of Yersinia pepstis. Infect Immun 64 (1996) 4580
49. Elvin S.J., Eyles J.E., Howard K.A., Ravichandran E., Somavarappu S., Alpar H.O., et al. Protection against bubonic and pneumonic plague with a single dose microencapsulated sub-unit vaccine. Vaccine 24 (2006) 4433
50. Kurupati P., The B.K., Kumarasinghe G., and Poh C.L. Identification of vaccine candidate antigens of an ESBL producing Klebsiella pneumoniae clinical strain by immunoproteome analysis. Proteomics 6 (2006) 836
51. Andersen P., and Doherty T.M. TB subunit vaccines-putting the pieces together. Microbes Infect 7 (2005) 911
52. Wizemann T.M., Heinrichs J.H., Adamou J.E., Erwin A.L., Kunsch C., Choi G.H., et al. Use of a whole genome approach to identify vaccine molecules affording protection against Streptococcus pneumoniae infection. Infect Immun 69 (2001) 1593
53. Hellberg S., Sjöström M., Skagerberg B., and Wold S. Peptide quantitative structure-activity relationships, a multivariate approach. J Med Chem 30 (1987) 1126
54. Sandberg M., Eriksson L., Jonsson J., Sjöström M., and Wold S. New chemical descriptors relevant for the design of biologically active peptides A multivariate characterization of 87 amino acids. J Med Chem 41 (1998) 2481
55. Leardi R., Boggia R., and Terrile M. Genetic algorithms as a strategy for feature-selection. J Chemometrics 6 (1992) 267
56. MDL QSAR 2.2. 14600 Catalina St, San Leondro CA 94577.
57. SIMCA 8.0. Umetrics UK Ltd., Wokingham Road, RG42 1PL, Bracknell, UK.
58. Bradley A.P. The use of the area under the ROC curve in the evaluation of machine learning algorithms. Pattern Recogn 30 (1997) 1145
59. MacCallum R.M., Martin A.C.R., and Thornton J.M. Antibody-antigen interactions: contact analysis and binding site topography. J Mol Biol 262 (1996) 732
60. Collis A.V.J., Brouwer A.P., and Martin A.C.R. Analysis of the antigen combining site: correlations between length and sequence composition of the hypervariable loops and the nature of the antigen. J Mol Biol 325 (2003) 337
61. Mian I.S., Bradwell A.R., and Olson A.J. Structure, function and properties of antibody binding sites. J Mol Biol 217 (1991) 133
62. Chothia C., Lesk A.M., Tramontano A., Levitt M., Smith-Gill S.J., Air G., et al. Conformations of immunoglobulin hypervariable regions. Nature 342 (1989) 877
63. Doytchinova I.A., and Flower D.R. Modeling the peptide - T-cell receptor interaction by the comparative molecular similarity analysis - soft independent modeling of class analogy technique. J Med Chem 49 (2006) 2193