Login Register Cart 0
Generic placeholder image

Protein & Peptide Letters

Editor-in-Chief

ISSN (Print): 0929-8665
ISSN (Online): 1875-5305

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
General Research Article

Beyond B-Cell Epitopes: Curating Positive Data on Antipeptide Paratope Binding to Support Peptide-Based Vaccine Design

Author(s): Salvador Eugenio C. Caoili*

Volume 28, Issue 8, 2021

Published on: 18 February, 2021

Page: [953 - 962] Pages: 10

DOI: 10.2174/0929866528666210218215624

Price: $65

Abstract

Background: B-cell epitope prediction is a computational approach originally developed to support the design of peptide-based vaccines for inducing protective antibody-mediated immunity, as exemplified by neutralization of biological activity (e.g., pathogen infectivity). Said approach is benchmarked against experimentally obtained data on paratope-epitope binding; but such data are curated primarily on the basis of immune-complex structure, obscuring the role of antigen conformational disorder in the underlying immune recognition process.

Objective: This work aimed to critically analyze the curation of epitope-paratope binding data that are relevant to B-cell epitope prediction for peptide-based vaccine design.

Methods: Database records on neutralizing monoclonal antipeptide antibody immune-complex structure were retrieved from the Immune Epitope Database (IEDB) and analyzed in relation to other data from both IEDB and external sources including the Protein Data Bank (PDB) and published literature, with special attention to data on conformational disorder among paratope-bound and unbound peptidic antigens.

Results: Data analysis revealed key examples of antipeptide antibodies that recognize conformationally disordered B-cell epitopes and thereby neutralize the biological activity of cognate targets (e.g., proteins and pathogens), with inconsistency noted in the mapping of some epitopes due to reliance on immune-complex structural details, which vary even among experiments utilizing the same paratope-epitope combination (e.g., with the epitope forming part of a peptide or a protein).

Conclusion: The results suggest an alternative approach to curating paratope-epitope binding data based on neutralization of biological activity by polyclonal antipeptide antibodies, with reference to immunogenic peptide sequences and their conformational disorder in unbound antigen structures.

Keywords: Epitopes, paratopes, antigens, antibodies, peptides, proteins, vaccines, conformational disorder.

« Previous
Graphical Abstract

[1]
Caoili, S.E. Antibodies, synthetic peptides and related constructs for planetary health based on green chemistry in the Anthropocene. Future Sci. OA, 2018, 4(3), FSO275.
[http://dx.doi.org/10.4155/fsoa-2017-0101] [PMID: 29568564]
[2]
Nandy, A.; Dey, S.; Roy, P.; Basak, S.C. Epidemics and peptide vaccine response: a brief review. Curr. Top. Med. Chem., 2018, 18(26), 2202-2208.
[http://dx.doi.org/10.2174/1568026618666181112144745] [PMID: 30417788]
[3]
Arnon, R. Synthetic vaccines--a dream or reality. Adv. Exp. Med. Biol., 1972, 31(0), 209-222.
[http://dx.doi.org/10.1007/978-1-4684-3225-1_17] [PMID: 4137226]
[4]
Malonis, R.J.; Lai, J.R.; Vergnolle, O. Peptide-based vaccines: current progress and future challenges. Chem. Rev., 2020, 120(6), 3210-3229.
[http://dx.doi.org/10.1021/acs.chemrev.9b00472] [PMID: 31804810]
[5]
Johnson, A.T. The technology hype cycle. IEEE Pulse, 2015, 6(2), 50.
[http://dx.doi.org/10.1109/MPUL.2014.2386491] [PMID: 25946758]
[6]
Shinnick, T.M.; Sutcliffe, J.G.; Green, N.; Lerner, R.A. Synthetic peptide immunogens as vaccines. Annu. Rev. Microbiol., 1983, 37, 425-446.
[http://dx.doi.org/10.1146/annurev.mi.37.100183.002233] [PMID: 6357058]
[7]
Brown, F. The Leeuwenhoek Lecture, 1993. Peptide vaccines: dream or reality? Philos. Trans. R. Soc. Lond. B Biol. Sci., 1994, 344(1308), 213-219.
[http://dx.doi.org/10.1098/rstb.1994.0062] [PMID: 7521966]
[8]
Hans, D.; Young, P.R.; Fairlie, D.P. Current status of short synthetic peptides as vaccines. Med. Chem., 2006, 2(6), 627-646.
[http://dx.doi.org/10.2174/1573406410602060627] [PMID: 17105445]
[9]
Trier, N.; Hansen, P.; Houen, G. Peptides, antibodies, peptide antibodies and more. Int. J. Mol. Sci., 2019, 20(24), 6289.
[http://dx.doi.org/10.3390/ijms20246289] [PMID: 31847088]
[10]
Potocnakova, L.; Bhide, M.; Pulzova, L.B. An introduction to B-cell epitope mapping and in silico epitope prediction. J. Immunol. Res., 2016, 2016, 6760830.
[http://dx.doi.org/10.1155/2016/6760830] [PMID: 28127568]
[11]
Sanchez-Trincado, J.L.; Gomez-Perosanz, M.; Reche, P.A. Fundamentals and methods for T- and B-cell epitope prediction. J. Immunol. Res., 2017, 2017, 2680160.
[http://dx.doi.org/10.1155/2017/2680160] [PMID: 29445754]
[12]
Hos, B.J.; Tondini, E.; van Kasteren, S.I.; Ossendorp, F. Approaches to improve chemically defined synthetic peptide vaccines. Front. Immunol., 2018, 9, 884.
[http://dx.doi.org/10.3389/fimmu.2018.00884] [PMID: 29755468]
[13]
Patronov, A.; Doytchinova, I. T-cell epitope vaccine design by immunoinformatics. Open Biol., 2013, 3(1), 120139.
[http://dx.doi.org/10.1098/rsob.120139] [PMID: 23303307]
[14]
Desai, D.V.; Kulkarni-Kale, U. T-cell epitope prediction methods: an overview. Methods Mol. Biol., 2014, 1184, 333-364.
[http://dx.doi.org/10.1007/978-1-4939-1115-8_19] [PMID: 25048134]
[15]
Oyarzun, P.; Kobe, B. Computer-aided design of T-cell epitope-based vaccines: addressing population coverage. Int. J. Immunogenet., 2015, 42(5), 313-321.
[http://dx.doi.org/10.1111/iji.12214] [PMID: 26211755]
[16]
Chen, S.W.; Van Regenmortel, M.H.; Pellequer, J.L. Structure-activity relationships in peptide-antibody complexes: implications for epitope prediction and development of synthetic peptide vaccines. Curr. Med. Chem., 2009, 16(8), 953-964.
[http://dx.doi.org/10.2174/092986709787581914] [PMID: 19275605]
[17]
MacRaild, C.A.; Richards, J.S.; Anders, R.F.; Norton, R.S. Antibody recognition of disordered antigens. Structure, 2016, 24(1), 148-157.
[http://dx.doi.org/10.1016/j.str.2015.10.028] [PMID: 26712277]
[18]
Kaufmann, S.H.E. Immunology’s coming of age. Front. Immunol., 2019, 10, 684.
[http://dx.doi.org/10.3389/fimmu.2019.00684] [PMID: 31001278]
[19]
Jerne, N.K. Immunological speculations. Annu. Rev. Microbiol., 1960, 14, 341-358.
[http://dx.doi.org/10.1146/annurev.mi.14.100160.002013] [PMID: 13789973]
[20]
Van Regenmortel, M.H. What is a B-cell epitope? Methods Mol. Biol., 2009, 524, 3-20.
[http://dx.doi.org/10.1007/978-1-59745-450-6_1] [PMID: 19377933]
[21]
Skwarczynski, M.; Toth, I. Peptide-based synthetic vaccines. Chem. Sci. (Camb.), 2016, 7(2), 842-854.
[http://dx.doi.org/10.1039/C5SC03892H] [PMID: 28791117]
[22]
Van Regenmortel, M.H. From absolute to exquisite specificity. Reflections on the fuzzy nature of species, specificity and antigenic sites. J. Immunol. Methods, 1998, 216(1-2), 37-48.
[http://dx.doi.org/10.1016/S0022-1759(98)00069-6] [PMID: 9760214]
[23]
Martini, S.; Nielsen, M.; Peters, B.; Sette, A. The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook. Immunogenetics, 2020, 72(1-2), 57-76.
[http://dx.doi.org/10.1007/s00251-019-01137-6] [PMID: 31761977]
[24]
Caoili, S.E. Hybrid methods for B-cell epitope prediction. Methods Mol. Biol., 2014, 1184, 245-283.
[http://dx.doi.org/10.1007/978-1-4939-1115-8_14] [PMID: 25048129]
[25]
Burley, S.K.; Berman, H.M.; Bhikadiya, C.; Bi, C.; Chen, L.; Di Costanzo, L.; Christie, C.; Dalenberg, K.; Duarte, J.M.; Dutta, S.; Feng, Z.; Ghosh, S.; Goodsell, D.S.; Green, R.K.; Guranovic, V.; Guzenko, D.; Hudson, B.P.; Kalro, T.; Liang, Y.; Lowe, R.; Namkoong, H.; Peisach, E.; Periskova, I.; Prlic, A.; Randle, C.; Rose, A.; Rose, P.; Sala, R.; Sekharan, M.; Shao, C.; Tan, L.; Tao, Y.P.; Valasatava, Y.; Voigt, M.; Westbrook, J.; Woo, J.; Yang, H.; Young, J.; Zhuravleva, M.; Zardecki, C. RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. Nucleic Acids Res., 2019, 47(D1), D464-D474.
[http://dx.doi.org/10.1093/nar/gky1004] [PMID: 30357411]
[26]
Lu, Z. PubMed and beyond: a survey of web tools for searching biomedical literature. Database (Oxford), 2011, 2011, baq036.
[http://dx.doi.org/10.1093/database/baq036] [PMID: 21245076]
[27]
Kabsch, W.; Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 1983, 22(12), 2577-2637.
[http://dx.doi.org/10.1002/bip.360221211] [PMID: 6667333]
[28]
DeForte, S.; Uversky, V.N. Order, disorder, and everything in between. Molecules, 2016, 21(8), 1090.
[http://dx.doi.org/10.3390/molecules21081090] [PMID: 27548131]
[29]
Uversky, V.N. Flexibility of the “rigid” classics or rugged bottom of the folding funnels of myoglobin, lysozyme, RNase A, chymotrypsin, cytochrome c, and carboxypeptidase A1. Intrinsically Disord. Proteins, 2017, 5(1), e1355205.
[http://dx.doi.org/10.1080/21690707.2017.1355205] [PMID: 30250772]
[30]
Dauter, Z.; Wlodawer, A. Progress in protein crystallography. Protein Pept. Lett., 2016, 23(3), 201-210.
[http://dx.doi.org/10.2174/0929866523666160106153524] [PMID: 26732246]
[31]
Arai, M. Unified understanding of folding and binding mechanisms of globular and intrinsically disordered proteins. Biophys. Rev., 2018, 10(2), 163-181.
[http://dx.doi.org/10.1007/s12551-017-0346-7] [PMID: 29307002]
[32]
Shingler, K.L.; Cifuente, J.O.; Ashley, R.E.; Makhov, A.M.; Conway, J.F.; Hafenstein, S. The enterovirus 71 procapsid binds neutralizing antibodies and rescues virus infection in vitro. J. Virol., 2015, 89(3), 1900-1908.
[http://dx.doi.org/10.1128/JVI.03098-14] [PMID: 25428877]
[33]
Grzesiek, S.; Döbeli, H.; Gentz, R.; Garotta, G.; Labhardt, A.M.; Bax, A. 1H, 13C, and 15N NMR backbone assignments and secondary structure of human interferon-gamma. Biochemistry, 1992, 31(35), 8180-8190.
[http://dx.doi.org/10.1021/bi00150a009] [PMID: 1525157]
[34]
Vanhaverbeke, C.; Simorre, J.P.; Sadir, R.; Gans, P.; Lortat-Jacob, H. NMR characterization of the interaction between the C-terminal domain of interferon-gamma and heparin-derived oligosaccharides. Biochem. J., 2004, 384(Pt 1), 93-99.
[http://dx.doi.org/10.1042/BJ20040757] [PMID: 15270718]
[35]
Liao, S.Y.; Fritzsching, K.J.; Hong, M. Conformational analysis of the full-length M2 protein of the influenza A virus using solid-state NMR. Protein Sci., 2013, 22(11), 1623-1638.
[http://dx.doi.org/10.1002/pro.2368] [PMID: 24023039]
[36]
Caruso, A.; Viani, E.; Tiberio, L.; Pollara, P.; Monti, E.; Bonfanti, C.; Gao, J.; Landolfo, S.; Balsari, A.; Turano, A. Inhibition of the biological activity of human interferon-gamma by antipeptide antibodies. J. Interferon Res., 1992, 12(1), 49-54.
[http://dx.doi.org/10.1089/jir.1992.12.49] [PMID: 1573282]
[37]
Caoili, S.E. Benchmarking B-cell epitope prediction for the design of peptide-based vaccines: problems and prospects. J. Biomed. Biotechnol., 2010, 2010, 910524.
[http://dx.doi.org/10.1155/2010/910524] [PMID: 20368996]
[38]
Caoili, S.E. An integrative structure-based framework for predicting biological effects mediated by antipeptide antibodies. J. Immunol. Methods, 2015, 427, 19-29.
[http://dx.doi.org/10.1016/j.jim.2015.09.002] [PMID: 26410103]
[39]
Grifoni, A.; Sidney, J.; Zhang, Y.; Scheuermann, R.H.; Peters, B.; Sette, A. A sequence homology and bioinformatic approach can predict candidate targets for immune responses to SARS-CoV-2. Cell Host Microbe, 2020, 27(4), 671-680.e2.
[http://dx.doi.org/10.1016/j.chom.2020.03.002] [PMID: 32183941]
[40]
Kalita, P.; Padhi, A.K.; Zhang, K.Y.J.; Tripathi, T. Design of a peptide-based subunit vaccine against novel coronavirus SARS-CoV-2. Microb. Pathog., 2020, 145, 104236.
[http://dx.doi.org/10.1016/j.micpath.2020.104236] [PMID: 32376359]
[41]
Lin, L.; Ting, S.; Yufei, H.; Wendong, L.; Yubo, F.; Jing, Z. Epitope-based peptide vaccines predicted against novel coronavirus disease caused by SARS-CoV-2. Virus Res., 2020, 288, 198082.
[http://dx.doi.org/10.1016/j.virusres.2020.198082] [PMID: 32621841]
[42]
Crooke, S.N.; Ovsyannikova, I.G.; Kennedy, R.B.; Poland, G.A. Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome. Sci. Rep., 2020, 10(1), 14179.
[http://dx.doi.org/10.1038/s41598-020-70864-8] [PMID: 32843695]
[43]
Singh, A.; Thakur, M.; Sharma, L.K.; Chandra, K. Designing a multi-epitope peptide based vaccine against SARS-CoV-2. Sci. Rep., 2020, 10(1), 16219.
[http://dx.doi.org/10.1038/s41598-020-73371-y] [PMID: 33004978]
[44]
Khairkhah, N.; Aghasadeghi, M.R.; Namvar, A.; Bolhassani, A. Design of novel multiepitope constructs-based peptide vaccine against the structural S, N and M proteins of human COVID-19 using immunoinformatics analysis. PLoS One, 2020, 15(10), e0240577.
[http://dx.doi.org/10.1371/journal.pone.0240577] [PMID: 33057358]
[45]
Di Natale, C.; Marasco, D.; La Manna, S.; De Benedictis, I.; Brandi, P. Perspectives in peptide-based vaccination strategies for SARS-CoV-2 pandemic. Front. Pharmacol., 2020, 11, 578382.
[http://dx.doi.org/10.3389/fphar.2020.578382] [PMID: 33343349]

Rights & Permissions Print Cite
Article Metrics
10
1
© 2024 Bentham Science Publishers | Privacy Policy