[1]
Koff WC. A shot at AIDS. Curr Opin Biotechnol 2016; 42: 147-51.
[2]
HIV/AIDS JUNPo. UNAIDS. 2017.
[3]
Baeten JM, Donnell D, Ndase P, et al. Antiretroviral prophylaxis for HIV prevention in heterosexual men and women. N Engl J Med 2012; 367(5): 399-410.
[4]
Shin SY. Recent update in HIV vaccine development. Clin Exp Vaccine Res 2016; 5(1): 6-11.
[5]
Pollara J, Easterhoff D, Fouda GG. Lessons learned from human HIV vaccine trials. Curr Opin HIV AIDS 2017; 12(3): 216-21.
[6]
M Barry S. Trial, Error, and Breakthrough: A Review of HIV Vaccine Development. J AIDS Clin Res 2014; 05(11)
[7]
Fischer W, Perkins S, Theiler J, et al. Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants. Nat Med 2006; 13: 100-6.
[8]
David M. Knipe PH. Fields Virology sixth edition 2013.
[9]
Katlama C, Deeks SG, Autran B, et al. Barriers to a cure for HIV: new ways to target and eradicate HIV-1 reservoirs. Lancet 2013; 381(9883): 2109-17.
[10]
Bayon E, Morlieras J, Dereuddre-Bosquet N, et al. Overcoming immunogenicity issues of HIV p24 antigen by the use of innovative nanostructured lipid carriers as delivery systems: evidences in mice and non-human primates. NPJ Vaccines 2018; 3(1): 46.
[11]
Yasmin T, Akter S, Debnath M, et al. In silico proposition to predict cluster of B- and T-cell epitopes for the usefulness of vaccine design from invasive, virulent and membrane associated proteins of C. jejuni. In Silico Pharmacol 2016; 4(1): 5.
[12]
Munson P, Liu Y, Bratt D, et al. Therapeutic conserved elements (CE) DNA vaccine induces strong T-cell responses against highly conserved viral sequences during simian-human immunodeficiency virus infection. Hum Vaccin Immunother 2018; 14(7): 1820-31.
[13]
Shamriz S, Ofoghi H. Design, structure prediction and molecular dynamics simulation of a fusion construct containing malaria pre-erythrocytic vaccine candidate, PfCelTOS, and human interleukin 2 as adjuvant. BMC Bioinformatics 2016; 17: 71.
[14]
Liu Y, Rao U, McClure J, et al. Impact of mutations in highly conserved amino acids of the HIV-1 Gag-p24 and Env-gp120 proteins on viral replication in different genetic backgrounds. PLoS One 2014; 9(4): e94240.
[15]
Courant T, Bayon E, Reynaud-Dougier HL, et al. Tailoring nanostructured lipid carriers for the delivery of protein antigens: Physicochemical properties versus immunogenicity studies. Biomaterials 2017; 136: 29-42.
[16]
McMichael AJ, Haynes BF. Lessons learned from HIV-1 vaccine trials: new priorities and directions. Nat Immunol 2012; 13: 423.
[17]
Viraj Kulkarni AV. Margherita Rosati, Morgane Rolland, James I. Mullins, George N. Pavlakis. HIV-1 Conserved Elements p24CE DNA Vaccine Induces Humoral Immune Responses with Broad Epitope Recognition in Macaques. PLoS One 2014; 9(10)
[18]
Rolland M, Heckerman D, Deng W, et al. Broad and Gag-Biased HIV-1 Epitope Repertoires Are Associated with Lower Viral Loads. PLoS One 2008; 3(1): e1424.
[19]
Awad-Elkareem MA-E, Osman SA, Mohamed HA, et al. Prediction and Conservancy Analysis of Multiepitope Based Peptide Vaccine Against Merkel Cell Polyomavirus: An Immunoinformatics Approach. Immunol Res 2017; 13: 134.
[20]
He L, Zhu J. Computational tools for epitope vaccine design and evaluation. Curr Opin Virol 2015; 11: 103-12.
[21]
Hekmat SS, Siadat SD, Aghasadeghi MR, et al. From in-silico immunogenicity verification to in vitro expression of recombinant Core-NS3 fusion protein of HCV. Bratisl Med J 2017; 118(04): 189-95.
[22]
Steers NJ, Peachman KK, McClain SR, Alving CR, Rao M. Human Immunodeficiency Virus Type 1 Gag p24 Alters the Composition of Immunoproteasomes and Affects Antigen Presentation. J Virol 2009; 83: 7049-61.
[23]
Krupkaa M, Zachova K, Cahlikovaa R, et al. Endotoxin-minimized HIV-1 p24 fused to murine hsp70 activatesdendritic cells, facilitates endocytosis and p24-specific Th1 responsein mice. Immunol Lett 2015; 166: 36-44.
[24]
Gandhi RT, Kwon DS, Macklin EA, et al. Immunization of HIV-1-Infected Persons With Autologous Dendritic Cells Transfected With mRNA Encoding HIV-1 Gag and Nef: Results of a Randomized, Placebo-Controlled Clinical Trial. J Acquir Immune Defic Syndr 2016; 71(3): 246-53.
[25]
Pankrac J, Klein K, McKay PF, et al. A heterogeneous human immunodeficiency virus-like particle (VLP) formulation produced by a novel vector system. NPJ Vaccin 2018; 3(1): 40-6.
[26]
Freed EO. HIV-1 assembly, release and maturation. Nat Rev Microbiol 2015; 13: 484.
[27]
Dai B, Xiao L, Bryson PD, Fang J, Wang P. PD-1/PD-L1 blockade can enhance HIV-1 Gag-specific T cell immunity elicited by dendritic cell-directed lentiviral vaccines. Mol Ther 2012; 20(9): 1800-9.
[28]
Molly A. Accola SHG, Heinrich G. Go Ttlinger. A Putative a-Helical Structure Which Overlaps the Capsid-p2 Boundary in the Human Immunodeficiency Virus Type 1 Gag Precursor Is Crucial for Viral Particle Assembly. J Virol 1998; 72: 2072-8.
[29]
Bowzard JB, Bennett RP, Krishna NK, Ernst SM, Rein A, Wills JW. Importance of Basic Residues in the Nucleocapsid Sequence for Retrovirus Gag Assembly and Complementation Rescue. J Virol 1998; 72: 9034-44.
[30]
Alin K, Goff SP. Amino Acid Substitutions in the CA Protein of Moloney Murine Leukemia Virus That Block Early Events in Infection. Virology 1996; 222: 339-51.
[31]
Foster JL, Garcia JV. HIV-1 Nef: at the crossroads. Retrovirology 2008; 5: 84.
[32]
Foster JL, Garcia JV. Role of Nef in HIV-1 replication and pathogenesis. Adv Pharmacol 2007; 55: 389-409.
[33]
Simmons A, Aluviahare V, McMichael A. Nef Triggers a Transcriptional Program in T Cells Imitating Single-Signal T Cell Activation and Inducing HIV Virulence Mediators. Immunity 2001; 14: 763-77.
[34]
Maccormac LPJ. Jean-Marc Chain, Benjamin. The functional consequences of delivery of HIV-1 Nef to dendritic cells using an adenoviral vector. Vaccine 2004; 22(3-4): 528-35.
[35]
Chen DY, Balamurugan A, Ng HL, Cumberland WG, Yang OO. Epitope targeting and viral inoculum are determinants of Nef-mediated immune evasion of HIV-1 from cytotoxic T lymphocytes. Blood 2012; 120(1): 100.
[36]
Shinya E, Owaki A, Shimizu M, et al. Endogenously expressed HIV-1 nef down-regulates antigen-presenting molecules, not only class I MHC but also CD1a, in immature dendritic cells. Virology 2004; 326(1): 79-89.
[37]
Pawlak EN, Dikeakos JD. HIV-1 Nef: a master manipulator of the membrane trafficking machinery mediating immune evasion. Biochimica et Biophysica Acta (BBA) - General Subjects. Biochim Biophys Acta 2015; 1850(4): 733-41.
[38]
Mangasarian A, Piguet V, Wang JK, Chen YL, Trono D. Nef-Induced CD4 and Major Histocompatibility Complex Class I (MHC-I) Down-Regulation Are Governed by Distinct Determinants: N-Terminal Alpha Helix and Proline Repeat of Nef Selectively Regulate MHC-I Trafficking. J Virol 1999; 73: 1964-73.
[39]
Hung CH, Thomas L, Ruby CE, et al. HIV-1 Nef assembles a Src family kinase-ZAP-70/Syk-PI3K cascade to downregulate cell-surface MHC-I. Cell Host Microbe 2007; 19: 121-33.
[40]
Khalili S, Jahangiri A, Borna H, Ahmadi Zanoos K, Amani J. Computational vaccinology and epitope vaccine design by immunoinformatics. Acta Microbiol Immunol Hung 2014; 61(3): 285-307.
[41]
Wong TM, Ross TM. Use of computational and recombinant technologies for developing novel influenza vaccines. Exp Rev Vaccin 2016; 15(1): 41-51.
[42]
Tamura KSG, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol 2013; 30: 2725-9.
[43]
Reche PA, Glutting JP, Zhang H, Reinherz EL. Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles. Immunogenetics 2004; 56: 405-19.
[44]
Stranzl T, Larsen MV, Lundegaard C, Nielsen M. NetCTLpan: Pan-specific MHC class I pathway epitope predictions. Immunogenetics 2010; 62: 357-68.
[45]
Giguere S, Drouin A, Lacoste A, Marchand M, Corbeil J, Laviolette F. MHC-NP: Predicting peptides naturally processed by the MHC. J Immunol Methods 2013; 400-401: 30-6.
[46]
Abroun SFM. Iran Royan Cord Blood Bank: Royan Cord Blood Banking; 2010.
[47]
Shaiegan MYF, Abolghasemi H, Bagheri N, et al. Allele Frequencies of HLA-A, B and DRB1 among People of Fars Ethnicity Living in Tehran. IJBC 2011; pp. 55-9.
[48]
Esmaeili A, Rabe SZT, Mahmoudi M, Rastin M. Frequencies of HLA-A, B and DRB1 alleles in a large normal population living in the city of Mashhad, Northeastern Iran. Iran J Basic Med Sci 2017; 20(8): 940-3.
[49]
Doytchinova IA, Flower DR. Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties. Vaccine 2007; 25: 856-66.
[50]
Doytchinova IA, Flower DR. VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics 2007; 8: 4.
[51]
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: 361.
[52]
Gupta S, Kapoor P, Chaudhary K, et al. In Silico Approach for Predicting Toxicity of Peptides and Proteins. PlosS One 2013. 8(9): e73957.
[53]
Wilkins MR, Gasteiger E, Bairoch A, et al. Protein identification and analysis tools in the ExPASy server. Methods Mol Biol 1999; 112: 531-52.
[54]
Geourjon C. Deleage G. SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput Appl Biosci 1995; 11: 681-4.
[55]
Cuff JA, Clamp ME, Siddiqui AS, Finlay M, Barton GJ. JPred: a consensus secondary structure prediction server. Bioinformatics 1998; 14: 892-3.
[56]
Ferrè F, Clote P. DiANNA: a web server for disulfide connectivity prediction. Nucleic Acids Res 2005; 33: W230-2.
[57]
Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008; 9: 40.
[58]
Yuedong Yang YZ. Specific interactions for ab initio folding of protein terminal regions with secondary structures. Proteins 2008; 72: 793-803.
[59]
Laskowski RA, Macarthur MW, Moss DS, Thornton JM. PROCHECK -a program to check the stereochemical quality of protein structures. J Appl Cryst 1993; 26: 283-91.
[60]
Colovos C, Yeates TO. Verification of protein structures: patterns of non-bonded atomic interactions. Protein Sci 1993; 9: 1511-9.
[61]
Bowie JU, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991; 253: 164-70.
[62]
Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem 2004; 25(13): 1605-12.
[63]
Nickle DC, Rolland M, Jensen MA, et al. Coping with Viral Diversity in HIV Vaccine Design. PLOS Comput Biol 2007; 3(4): e75.
[64]
Nandy A, Basak SC. A Brief Review of Computer-Assisted Approaches to Rational Design of Peptide Vaccines. Int J Mol Sci 2016; 17(5): 666.
[65]
Perez-Martinez AP, Ong E, Zhang L, Marrs CF, He Y, Yang Z. Conservation in gene encoding Mycobacterium tuberculosis antigen Rv2660 and a high predicted population coverage of H56 multistage vaccine in South Africa. Infection, Genetics and Evolution 2017; 55: 244-50.
[66]
Afzal S, Idrees M, Hussain M. De Novo modeling of Envelope 2 protein of HCV isolated from Pakistani patient and epitopes prediction for vaccine development. J Transl Med 2014; 12(1): 115.
[67]
Rappuoli R, Bottomley MJ, D’Oro U, Finco O, De Gregorio E. Reverse vaccinology 2.0: Human immunology instructs vaccine antigen design. JEM 2016; 213(4): 469.
[68]
Moyle PM, Toth I. Modern subunit vaccines: development, components, and research opportunities. ChemMedChem 2013; 8(3): 360-76.
[69]
Mahdavi M, Ebtekar M, Azadmanesh K, et al. HIV-1 Gag p24-Nef fusion peptide induces cellular and humoral immune response in a mouse model. Acta Virol 2010; 54: 131-6.
[70]
Gonzalez-Rabade N, McGown EG, Zhou F, et al. Immunogenicity of chloroplast-derived HIV-1 p24 and a p24-Nef fusion protein following subcutaneous and oral administration in mice. Plant Biotechnol J 2011; 9: 629-38.
[71]
Kuo LS, Baugh LL, Denial SJ, et al. Overlapping effector interfaces define the multiple functions of the HIV-1 Nef polyproline helix. Retrovirology 2012; 9: 47.
[72]
Popov S, Popova E, Inoue M, Gottlinger HG. Human immunodeficiency virus type 1 Gag engages the Bro1 domain of ALIX/AIP1 through the nucleocapsid. J Virol 2008; 82(3): 1389-98.
[73]
Jia X, Singh R, Homann S, et al. Structural basis of evasion of cellular adaptive immunity by HIV-1 Nef. Nat Struct Mol Biol 2012; 19: 701.
[74]
Wonderlich ER, Leonard JA, Collins KL. HIV immune evasion disruption of antigen presentation by the HIV Nef protein. Adv Virus Res 2011; 80: 103-27.
[75]
Hanna E, Hoyne GF. The Role of the Nef Protein in MHC-I Downregulation and Viral Immune Evasion by HIV-1. J Clin Cell Immunol 2015; 7: 375.
[76]
Abdel-Motal UM, Wang S, Awad A, et al. Increased immunogenicity of HIV-1 p24 and gp120 following immunization with gp120/p24 fusion protein vaccine expressing alpha-gal epitopes. Vaccine 2010; 28(7): 1758-65.
[77]
Piguet V, Wan L, Borel C, et al. HIV-1 Nef protein binds to the cellular protein PACS-1 to downregulate class I major histocompatibility complexes. Nat Cell Biol 2000; 2: 163-7.
[78]
Burinston MT, Cimarelli A, Colgan J, Curtis SP, Luban J. Human Immunodeficiency Virus Type 1 Gag Polyprotein Multimerization Requires the Nucleocapsid Domain and RNA and Is Promoted by the Capsid-Dimer Interface and the Basic Region of Matrix Protein. J Virol 1999; 73: 8527-40.
54
8
1
1
