2019, Número 1
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Biotecnol Apl 2019; 36 (1)
Estudio de caracterización epitópica, acoplamiento molecular y simulación dinámica molecular de dos proteínas inmunogénicas principales del virus de la viruela del canario
Mohammadi E, Pirkhezranian Z, Monhemi H, Razmyar J, Tahmoorespur M, Sekhavati MH
Idioma: Ingles.
Referencias bibliográficas: 52
Paginas: 1211-1218
Archivo PDF: 1750.74 Kb.
RESUMEN
El virus de la viruela del canario (CNPV) infecta a estas aves, con alta mortalidad y pérdidas económicas significativas especialmente en los países del Medio Oriente. Existen reportes de importaciones no autorizadas e ilegales de vacunas contra el CNPV propagadas en embriones, liofilizadas y vivas para su uso contra la enfermedad en Irán y en la región. El propósito de este trabajo fue preparar las condiciones para el diseño de una vacuna peptídica contra la enfermedad causada por el CNPV. Se seleccionaron dos proteínas inmunogénicas del CNPV homólogas a los antígenos de Poxine®, HP1-440 y las cepas de virus fowlpox. Se identificó a los péptidos específicos por el MHC II mediante varias herramientas bioinformáticas, los que se modelaron y acoplaron a los receptores HLA-DRB1 0101, 0301, 0401, 0405 y 1501. La estabilidad de los complejos acoplados se evaluó mediante simulaciones de dinámica molecular. También se seleccionó un epitopo experimental del virus Vaccinia para los receptores del MHC I, y su epitopo homólogo en CNPV se acopló a dos receptores BF de pollos. De los 13 epitopos predichos para los receptores del MHC II e identificados mediante acoplamiento y dinámica molecular se escogieron cuatro: IFNAIILWITYAL, LRQLYDVIIPPR, YYNRITSIHM y YRHDDIIAT. El epitopo homólogo al epitopo experimental VP35#1 del virus Vaccinia del canario se seleccionó, dada su respuesta de células T CD8+ de memoria de larga duración, y se propuso el epitopo SLSAYIVSK. Los epitopos candidatos de alta afinidad de unión pudieran incluirse como los más efectivos para diseñar vacunas peptídicas contra la infección por el CNPV.
REFERENCIAS (EN ESTE ARTÍCULO)
Moss B. Chapter 74: Poxviridae: The viruses and their replication. In: Fields Virology Fourth Edition. DM Knipe, PM Howley, editors. Philadelphia: Lippincott Williams & Wilkins; 2001. p. 2849-83.
Moyer R, Arif B, Black D, Boyle D, Buller R, Dumbell K, et al. Family Poxviridae. In: van Regenmortel MHV, Fauquet CM, Bishop DHL, Carstens EB, Estes MK, Lemon SM, et al., editors. Virus Taxonomy: Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press Inc.; 1999.
Tripathy DN, Schnitzlein WM, Morris PJ, Janssen DL, Zuba JK, Massey G, et al. Characterization of poxviruses from forest birds in Hawaii. J Wildl Dis. 2000;36(2):225-30.
Bolte AL, Meurer J, Kaleta EF. Avian host spectrum of avipoxviruses. Avian Pathol. 1999;28(5):415-32.
Giddens WE, Jr., Swango LJ, Henderson JD, Lewis RA, Farner DS, Carlos A, et al. Canary pox in sparrows and canaries (Fringillidae and in weavers (Ploceidae). Pathology and host specificity of the virus. Vet Pathol. 1971;8(3):260-80.
Naz RK, Dabir P. Peptide vaccines against cancer, infectious diseases, and conception. Front Biosci. 2007;12:1833-44.
Jacob CO, Leitner M, Zamir A, Salomon D, Arnon R. Priming immunization against cholera toxin and E. coli heat-labile toxin by a cholera toxin short peptide-betagalactosidase hybrid synthesized in E. coli. EMBO J. 1985;4(12):3339-43.
Schook LB, Lamont SJ. The major histocompatibility complex region of domestic animal species. Boca Raton: CRC Press; 1996.
Ghaffar A, Tariq A. In-silico analysis of Pasteurella multocida to identify common epitopes between fowl, goat and buffalo. Gene. 2016;580(1):58-66.
Xu R, Li K, Chen G, Xu H, Qiang B, Li C, et al. Characterization of genetic polymorphism of novel MHC B-LB II alleles in Chinese indigenous chickens. J Genet Genomics. 2007;34(2):109-18.
Wyatt LS, Earl PL, Eller LA, Moss B. Highly attenuated smallpox vaccine protects mice with and without immune deficiencies against pathogenic vaccinia virus challenge. Proc Natl Acad Sci U S A. 2004;101(13):4590-5.
Drexler I, Staib C, Kastenmuller W, Stevanovic S, Schmidt B, Lemonnier FA, et al. Identification of vaccinia virus epitope-specific HLA-A*0201-restricted T cells and comparative analysis of smallpox vaccines. Proc Natl Acad Sci U S A. 2003;100(1):217-22.
Abualrous ET, Fritzsche S, Hein Z, Al-Balushi MS, Reinink P, Boyle LH, et al. F pocket flexibility influences the tapasin dependence of two differentially diseaseassociated MHC Class I proteins. Eur J Immunol. 2015;45(4):1248-57.
Boulanger D, Green P, Jones B, Henriquet G, Hunt LG, Laidlaw SM, et al. Identification and characterization of three immunodominant structural proteins of fowlpox virus. J Virol. 2002;76(19):9844- 55.
Osman MM, ElAmin EE, Al-Nour MY, Alam SS, Adam RS, Ahmed AA, et al. In Silico design of epitope based peptide vaccine against virulent strains of HN-Newcastle Disease Virus (NDV) in poultry species. Int J Multidisciplin Curr Res. 2016;4:868-78.
Tang ST, Wang M, Lamberth K, Harndahl M, Dziegiel MH, Claesson MH, et al. MHC-I-restricted epitopes conserved among variola and other related orthopoxviruses are recognized by T cells 30 years after vaccination. Arch Virol. 2008;153(10):1833-44.
Tulman ER, Afonso CL, Lu Z, Zsak L, Kutish GF, Rock DL. The genome of canarypox virus. J Virol. 2004;78(1):353-66.
Backert L, Kohlbacher O. Immunoinformatics and epitope prediction in the age of genomic medicine. Genome Med. 2015;7:119.
Patronov A, Doytchinova I. T-cell epitope vaccine design by immunoinformatics. Open Biol. 2013;3(1):120139.
Sekhavati MH, Heravi RM, Tahmoorespur M, Yousefi S, Abbassi-Daloii T, Akbari R. Cloning, molecular analysis and epitopics prediction of a new chaperone GroEL Brucella melitensis antigen. Iran J Basic Med Sci. 2015;18(5):499-505.
Mohammad Hasani S, Mohammadi E, Sekhavati MH. Region-based epitope prediction, docking and dynamic studies of OMP31 as a dominant antigen in human and sheep Brucella. Int J Pept Res Ther. 2019. DOI: 10.1007/s10989- 019-09847-x.
Schuler MM, Nastke M-D, Stevanovikć S. SYFPEITHI: database for searching and T-cell epitope prediction. Methods Mol Biol. 2007;409:75-93.
Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, Cantrell JR, et al. The immune epitope database (IEDB) 3.0. Nucleic Acids Res. 2015;43(Database issue):D405-12.
Thevenet P, Shen Y, Maupetit J, Guyon F, Derreumaux P, Tuffery 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):W288-93.
Berendsen HJ, van der Spoel D, van Drunen R. GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun. 1995;91(1- 3):43-56.
Schmid N, Eichenberger AP, Choutko A, Riniker S, Winger M, Mark AE, et al. Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur Biophys J. 2011;40(7):843-56.
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605-12.
Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31(2):455-61.
Corbeil CR, Williams CI, Labute P. Variability in docking success rates due to dataset preparation. J Comput Aided Mol Des. 2012;26(6):775-86.
Mirza MU, Rafique S, Ali A, Munir M, Ikram N, Manan A, et al. Towards peptide vaccines against Zika virus: Immunoinformatics combined with molecular dynamics simulations to predict antigenic epitopes of Zika viral proteins. Sci Rep. 2016;6:37313.
DeLano WL. The PyMOL molecular graphics system. California: Delano Scientific LLC.; 2002 [cited 2018 March 25]. Available from: http://pymol.org
Shityakov S, Forster C. In silico predictive model to determine vector-mediated transport properties for the blood-brain barrier choline transporter. Adv Appl Bioinform Chem. 2014;7:23-36.
Yousefi S, Sekhavati MH, Tahmoorespur M, Abbassi-Daloii T. Cloning and molecular characterization of Omp31 gene from Brucella melitensis Rev 1 strain. Archives Razi Institute. 2016;71:117-124.
Boulanger D, Green P, Smith T, Czerny CP, Skinner MA. The 131-amino-acid repeat region of the essential 39-kilodalton core protein of fowlpox virus FP9, equivalent to vaccinia virus A4L protein, is nonessential and highly immunogenic. J Virol. 1998;72(1):170-9.
Binns M, Mason C, Boursnell M. A 39,000 Mr immunodominant protein of fowlpox virus contains multiple copies of a 12 amino acid repeat sequence. J Gen Virol. 1990;71 ( Pt 12):2883-8.
Moise L, Buller RM, Schriewer J, Lee J, Frey SE, Weiner DB, et al. VennVax, a DNA-prime, peptide-boost multi-T-cell epitope poxvirus vaccine, induces protective immunity against vaccinia infection by T cell response alone. Vaccine. 2011;29(3):501-11.
Xu R, Johnson AJ, Liggitt D, Bevan MJ. Cellular and humoral immunity against vaccinia virus infection of mice. J Immunol. 2004;172(10):6265-71.
Mohammadi E, Dashty S. Epitope prediction, modeling and docking studies for H3L protein as an agent of Smallpox. Biotechnologia. 2019;100:69-80.
Alcaide M, Munoz J, Martinez-de la Puente J, Soriguer R, Figuerola J. Extraordinary MHC class II B diversity in a non-passerine, wild bird: the Eurasian Coot Fulica atra (Aves: Rallidae). Ecol Evol. 2014;4(6):688-98.
Zhang J, Chen Y, Qi J, Gao F, Liu Y, Liu J, et al. Narrow groove and restricted anchors of MHC class I molecule BF2*0401 plus peptide transporter restriction can explain disease susceptibility of B4 chickens. J Immunol. 2012;189(9):4478-87.
Jardetzky TS, Gorga JC, Busch R, Rothbard J, Strominger JL, Wiley DC. Peptide binding to HLA-DR1: a peptide with most residues substituted to alanine retains MHC binding. EMBO J. 1990;9(6):1797-803.
O’Sullivan D, Arrhenius T, Sidney J, Del Guercio MF, Albertson M, Wall M, et al. On the interaction of promiscuous antigenic peptides with different DR alleles. Identification of common structural motifs. J Immunol. 1991;147(8):2663-9.
Hammer J, Takacs B, Sinigaglia F. Identification of a motif for HLA-DR1 binding peptides using M13 display libraries. J Exp Med. 1992;176(4):1007-13.
Brown JH, Jardetzky TS, Gorga JC, Stern LJ, Urban RG, Strominger JL, et al. Threedimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature. 1993;364(6432):33-9.
Stern LJ, Brown JH, Jardetzky TS, Gorga JC, Urban RG, Strominger JL, et al. Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature. 1994;368(6468):215-21.
Murthy VL, Stern LJ. The class II MHC protein HLA-DR1 in complex with an endogenous peptide: implications for the structural basis of the specificity of peptide binding. Structure. 1997;5(10):1385-96.
Barber LD, Bal V, Lamb JR, O’Hehir RE, Yendle J, Hancock RJ, et al. Contribution of T-cell receptor-contacting and peptidebinding residues of the class II molecule HLA-DR4 Dw10 to serologic and antigenspecific T-cell recognition. Hum Immunol. 1991;32(2):110-8.
Fu XT, Bono CP, Woulfe SL, Swearingen C, Summers NL, Sinigaglia F, et al. Pocket 4 of the HLA-DR(alpha,beta 1*0401) molecule is a major determinant of T cells recognition of peptide. J Exp Med. 1995;181(3):915-26. 48. Dessen A, Lawrence CM, Cupo S, Zaller DM, Wiley DC. X-ray crystal structure of HLADR4 (DRA*0101, DRB1*0401) complexed with a peptide from human collagen II. Immunity. 1997;7(4):473-81.
Madden DR. The three-dimensional structure of peptide-MHC complexes. Annu Rev Immunol. 1995;13:587-622.
Sieker F, Straatsma TP, Springer S, Zacharias M. Differential tapasin dependence of MHC class I molecules correlates with conformational changes upon peptide dissociation: a molecular dynamics simulation study. Mol Immunol. 2008;45(14):3714-22.
Sieker F, May A, Zacharias M. Predicting affinity and specificity of antigenic peptide binding to major histocompatibility class I molecules. Curr Protein Pept Sci. 2009;10(3):286-96.
Abualrous ET, Saini SK, Ramnarayan VR, Ilca FT, Zacharias M, Springer S. The carboxy terminus of the ligand peptide determines the stability of the MHC Class I molecule H-2Kb: A combined molecular dynamics and experimental study. PLoS One. 2015;10(8):e0135421.