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Immunological Investigations
A Journal of Molecular and Cellular Immunology
Volume 51, 2022 - Issue 1
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Research Article

In Silico and in Vivo Analysis of HIV-1 Rev Regulatory Protein for Evaluation of a Multiepitope-based Vaccine Candidate

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References

  • Abdulla F, Adhikari UK, Uddin MK. 2019. Exploring T and B-cell epitopes and designing multi-epitope subunit vaccine targeting integration step of HIV-1 lifecycle using immunoinformatics approach. Microb Pathog. 137:103791.
  • Addo MM, Altfeld M, Rosenberg ES, Eldridge RL, Philips MN, Habeeb K, Khatri A, Brander C, Robbins GK, Mazzara GP, et al. 2001. The HIV-1 regulatory proteins Tat and Rev are frequently targeted by cytotoxic T lymphocytes derived from HIV-1-infected individuals. Proc Natl Acad Sci. 98(4):1781–86.
  • Ahmed T, Borthwick NJ, Gilmour J, Hayes P, Dorrell L, Hanke T. 2016. Control of HIV-1 replication in vitro by vaccine-induced human CD8+ T cells through conserved subdominant Pol epitopes. Vaccine. 34(9):1215–24.
  • Ali M, Pandey RK, Khatoon N, Narula A, Mishra A, Prajapati VK. 2017. Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection. Sci Rep. 7(1):1–3.
  • Almeida RR, Rosa DS, Ribeiro SP, Santana VC, Kallas EG, Sidney J, Sette A, Kalil J, Cunha-Neto E. 2012. Broad and cross-clade CD4+ T-cell responses elicited by a DNA vaccine encoding highly conserved and promiscuous HIV-1 M-group consensus peptides. PLoS One. 7(9):e45267.
  • Apostólico JDS, Lunardelli VAS, Yamamoto MM, Souza HFS, Cunha-Neto E, Boscardin SB, Rosa DS. 2017. Dendritic cell targeting effectively boosts T cell responses elicited by an HIV multiepitope DNA vaccine. Front Immunol. 8:101.
  • Arya S, Lal P, Singh P, Kumar A. 2015. Recent advances in diagnosis of HIV and future prospects. Indian J Biotechnol. 14:9–18.
  • Bazhan SI, Antonets DV, Karpenko LI, Oreshkova SF, Kaplina ON, Starostina EV, Dudko SG, Fedotova SA, Ilyichev AA. 2019. In silico designed Ebola virus T-cell multi-epitope DNA vaccine constructions are immunogenic in mice. Vaccines. 7(2):34.
  • Black M, Trent A, Tirrell M, Olive C. 2010. Advances in the design and delivery of peptide subunit vaccines with a focus on toll-like receptor agonists. Expert Rev Vaccines. 9(2):157–73.
  • Boffito M, Fox J, Bowman C, Orkin C, Wilkins E, Jackson A, Pleguezuelos O, Robinson S, Stoloff GA, Caparrós-Wanderley W. 2013. Safety, immunogenicity and efficacy assessment of HIV immunotherapy in a multi-centre, double-blind, randomised, Placebo-controlled Phase Ib human trial. Vaccine. 31(48):5680–86.
  • Bolesta E, Gzyl J, Wierzbicki A, Kmieciak D, Kowalczyk A, Kaneko Y, Srinivasand A, Kozbora D. 2005. Clustered epitopes within the Gag-Pol fusion protein DNA vaccine enhance immune responses and protection against challenge with recombinant vaccinia viruses expressing HIV-1 Gag and Pol antigens. Virology. 332(2):467–79.
  • Chen C, Li Z, Huang H, Suzek BE, Wu CH. 2013. A fast peptide match service for UniProt knowledgebase. Bioinformatics. 29(21):2808–09.
  • Chiarella P, Massi E, De Robertis M, Fazio VM, Signori E. 2009. Recent advances in epitope design for immunotherapy of cancer. Recent Pat Anti-Cancer Drug Discovery. 4(3):227–40.
  • Cristillo AD, Wang S, Caskey MS, Unangst T, Hocker L, He L, Hudacik L, Whitney S, Keen T, Chou TW. 2006. Preclinical evaluation of cellular immune responses elicited by a polyvalent DNA prime/protein boost HIV-1 vaccine. Virology. 346(1):151–68.
  • De Rose R, Kent SJ, Ranasinghe C. 2015. Prime-boost vaccination: impact on the HIV-1 vaccine field. In: Novel approaches and strategies for biologics, vaccines and cancer therapies. The University of Melbourne, Academic Press; p. 289–313. doi: https://doi.org/10.1016/B978-0-12-416603-5.00012-2.
  • Deshayes S, Gerbal-Chaloin S, Morris MC, Aldrian-Herrada G, Charnet P, Divita G, Heitz F. 2004. On the mechanism of non-endosomial peptide-mediated cellular delivery of nucleic acids. Biochim Et Biophys Acta (Bba)-biomembr. 1667(2):141–47.
  • DeVico AL, Gallo RC. 2004. Control of HIV-1 infection by soluble factors of the immune response. Nat Rev Microbiol. 2(5):401–13.
  • Dhanda SK, Gupta S, Vir P, Raghava GP. 2013a. Prediction of IL4 inducing peptides. Clin Dev Immunol. 2013:1–9.
  • Dhanda SK, Vir P, Raghava GP. 2013b. Designing of interferon-gamma inducing MHC class-II binders. Biol Direct. 8(1):30.
  • Falk K, Rötzschke O, Stevanovié S, Jung G, Rammensee HG. 1991. Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature. 351(6324):290–96.
  • Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A. 2005. Protein identification and analysis tools on the ExPASy server. In: The proteomics protocols handbook. The Springer Protocols Handbooks book series (SPH). Humana press; p. 571–607.
  • Gautam A, Chaudhary K, Kumar R, Raghava GP. 2015. Computer-aided virtual screening and designing of cell-penetrating peptides. In: Cell-penetrating peptides. The Methods in Molecular Biology book series (MIMB, Vol. 1324), Springer. New York (NY): Humana press; p. 59–69.
  • Gautam A, Chaudhary K, Singh S. 2014. Hemolytik: a database of experimentally determined hemolytic and non-hemolytic peptides. Nucleic Acids Res. 42(D1):D444–9.
  • Gonzalez‐Rabade N, McGowan EG, Zhou F, Ralph Bock MSM, Dix PJ, Gray JC, Ma JKC. 2011. Immunogenicity of chloroplast‐derived HIV‐1 p24 and a p24‐Nef fusion protein following subcutaneous and oral administration in mice. Plant Biotechnol J. 9(6):629–38.
  • Gros E, Deshayes S, Morris MC, Aldrian-Herrada G, Depollier J, Heitz F, Divita G. 2006. A non-covalent peptide-based strategy for protein and peptide nucleic acid transduction. Biochim Et Biophys Acta (Bba)-biomembr. 1758(3):384–93.
  • Gupta S, Kapoor P, Chaudhary K, Gautam A, Kumar R, Raghava GP. 2013. In silico approach for predicting toxicity of peptides and proteins. PLoS One. 8(9):e73957.
  • Hebditch M, Carballo-Amador MA, Charonis S, Curtis R, Warwicker J. 2017. Protein–Sol: a web tool for predicting protein solubility from sequence. Bioinformatics. 33(19):3098–100.
  • Ikram A, Zaheer T, Awan FM, Obaid A, Naz A, Hanif R, Zafar Paracha R, Ali A, Naveed A, Janjua HA. 2018. Exploring NS3/4A, NS5A and NS5B proteins to design conserved subunit multiepitope vaccine against HCV utilizing immunoinformatics approaches. Sci Rep. 8(1):1–4.
  • Kardani K, Bolhassani A, Namvar A. 2020. An overview of in silico vaccine design against different pathogens and cancer. Expert Rev Vaccines. 19(8):699–726.
  • Kardani K, Hashemi A, Bolhassani A. 2019. Comparison of HIV-1 Vif and Vpu accessory proteins for delivery of polyepitope constructs harboring Nef, Gp160 and P24 using various cell penetrating peptides. PLoS One. 14(10):e0223844.
  • Karpenko LI, Bazhan SI, Bogryantseva MP, Ryndyuk NN, Ginko ZI, Kuzubov VI, Lebedev LR, Kaplina ON, Reguzova A, Ryzhikov AB, et al. 2016. Results of phase I clinical trials of a combined vaccine against HIV-1 based on synthetic polyepitope immunogens. Russ J Bioorg Chem. 42(2):170–82.
  • Khairkhah N, Namvar A, Kardani K, Bolhassani A. 2018. Prediction of cross‐clade HIV‐1 T‐cell epitopes using immunoinformatics analysis. Proteins Struct Funct Bioinf. 86(12):1284–93.
  • Kuck D, Lau T, Leuchs B, Kern A, Müller M, Gissmann L, Kleinschmidt JA. 2006. Intranasal vaccination with recombinant adeno-associated virus type 5 against human papillomavirus type 16 L1. J Virol. 80(6):2621–30.
  • Kühn R, Löhler J, Rennick D, Rajewsky K, Müller W. 1993. Interleukin-10-deficient mice develop chronic enterocolitis. Cell. 75:263–74.
  • Kumar Pandey R, Ojha R, Mishra A, Kumar Prajapati V. 2018. Designing B‐and T‐cell multi‐epitope based subunit vaccine using immunoinformatics approach to control Zika virus infection. J Cell Biochem. 119(9):7631–42.
  • Leal L, Lucero C, Gatell JM, Gallart T, Plana M, García F. 2017. New challenges in therapeutic vaccines against HIV infection. Expert Rev Vaccines. 16(6):587–600.
  • Liu BR, Chen HH, Chan MH, Huang YW, Aronstam RS, Lee HJ. 2015. Three arginine-rich cell-penetrating peptides facilitate cellular internalization of red-emitting quantum dots. J Nanosci Nanotechnol. 15(3):2067–78.
  • Liu BR, Huang YW, Winiarz JG, Chiang HJ, Lee HJ. 2011. Intracellular delivery of quantum dots mediated by a histidine-and arginine-rich HR9 cell-penetrating peptide through the direct membrane translocation mechanism. Biomaterials. 32(13):3520–37.
  • Meza B, Ascencio F, Sierra-Beltrán AP, Torres J, Angulo C. 2017. A novel design of a multi-antigenic, multistage and multi-epitope vaccine against Helicobacter pylori: an in silico approach. Infect Genet Evol. 49:309–17.
  • Morris MC, Chaloin L, Méry J, Heitz F, Divita G. 1999. A novel potent strategy for gene delivery using a single peptide vector as a carrier. Nucleic Acids Res. 27(17):3510–17.
  • Nabel GJ, Kwong PD, Mascola JR. 2011. Progress in the rational design of an AIDS vaccine. Phil Trans R Soc B. 366:2759–65.
  • Namazi F, Bolhassani A, Sadat SM, Irani S. 2019. Delivery of HIV-1 polyepitope constructs using cationic and amphipathic cell penetrating peptides into mammalian cells. Curr HIV Res. 17(6):408–28.
  • Ng PC, Li K, Wong RPO, Chui K, Wong E, Li G, Fok TF. 2003. Proinflammatory and anti-inflammatory cytokine responses in preterm infants with systemic infections. Arch Dis Child Fetal Neonatal Ed. 88:F209–13.
  • Nosrati M, Mohabatkar H, Behbahani M. 2017. A novel multi-epitope vaccine for cross protection against hepatitis C virus (HCV): an immunoinformatics approach. Res Mol Med. 5(1):17–26.
  • Okuda K, Bukawa H, Hamajima K, Kawamoto S, Sekigawa K, Yamada Y, Tanaka S, Ishi N, Aoki I, Nakamura M. 1995. Induction of potent humoral and cell-mediated immune responses following direct injection of DNA encoding the HIV type 1 env and rev gene products. AIDS Res Hum Retroviruses. 11:933–43.
  • Pandey RK, Ojha R, Aathmanathan VS, Krishnan M, Prajapati VK. 2018. Immunoinformatics approaches to design a novel multi-epitope subunit vaccine against HIV infection. Vaccine. 36(17):2262–72.
  • Ponnappan N, Budagavi DP, Chugh A. 2017. CyLoP-1: membrane-active peptide with cell-penetrating and antimicrobial properties. Biochim Et Biophys Acta (Bba)-biomembr. 1859(2):167–76.
  • Ponnappan N, Chugh A. 2017. Cell-penetrating and cargo-delivery ability of a spider toxin-derived peptide in mammalian cells. Eur J Pharm Biopharm. 114:145–53.
  • Ramsey JD, Flynn NH. 2015. Cell-penetrating peptides transport therapeutics into cells. Pharmacol Ther. 154:78–86.
  • Ranasinghe S, Soghoian DZ, Lindqvist M, Ghebremichael M, Donaghey F, Carrington M, Seaman MS, Kaufmann DE, Walker BD, Porichis F. 2016. HIV-1 antibody neutralization breadth is associated with enhanced HIV-specific CD4+ T cell responses. J Virol. 90(5):2208–20.
  • Reguzova A, Antonets D, Karpenko L, Ilyichev A, Maksyutov R, Bazhan S. 2015. Design and evaluation of optimized artificial HIV-1 poly-T cell-epitope immunogens. PLoS One. 10(3):e0116412.
  • Rosa DS, Ribeiro SP, Almeida RR, Mairena EC, Posto E, Kalil J, Cunha-Neto E. 2011. A DNA vaccine encoding multiple HIV CD4 epitopes elicits vigorous polyfunctional, long-lived CD4+ and CD8+ T cell responses. PLoS One. 6(2):e16921.
  • Sabat R, Grütz G, Warszawska K, Kirsch S, Witte E, Wolk K, Geginat J. 2010. Biology of interleukin-10. Cytokine Growth Factor Rev. 21:331–44.
  • Saha S, Raghava GP. 2006a. AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. Nucleic Acids Res. 34(2):W202–9.
  • Saha S, Raghava GP. 2006b. Prediction of continuous B‐cell epitopes in an antigen using recurrent neural network. Proteins Struct Funct Bioinf. 65(1):40–48.
  • Sahni AK, Nagendra A. 2004. HIV vaccine strategies: an update. Med J Armed Forces India. 60(2):157.
  • Schoenborn JR, Wilson CB. 2007. Regulation of interferon-γ during innate and adaptive immune responses. Washington, USA: Adv Immunol Academic Press; p. 41–101.
  • Schuler MM, Nastke MD, Stevanović S. 2007. SYFPEITHI. In: Immunoinformatics. Springer Protocol. Humana Press; p. 75–93.
  • Slingluff CL. 2011. The present and future of peptide vaccines for cancer: single or multiple, long or short, alone or in combination? Cancer J. 17(5):343.
  • Spira S, Wainberg MA, Loemba H, Turner D, Brenner BG. 2003. Impact of clade diversity on HIV-1 virulence, antiretroviral drug sensitivity and drug resistance. J Antimicrob Chemother. 51(2):229–40.
  • Tähtinen M, Strengell M, Collings A, Pitkänen J, Kjerrström A, Hakkarainen K, Peterson P, Kohleisen B, Wahren B, Ranki A, et al. 2001. DNA vaccination in mice using HIV-1 nef, rev and tat genes in self-replicating pBN-vector. Vaccine. 19:2039–47.
  • Vardas E, Stanescu I, Leinonen M, Ellefsen K, Pantaleo G, Valtavaara M, Ustav M, Reijonen K. 2012. Indicators of therapeutic effect in FIT-06, a phase II trial of a DNA vaccine, GTU®-Multi-HIVB, in untreated HIV-1 infected subjects. Vaccine. 30(27):4046–54.
  • Verrier B, Le Grand R, Ataman-Önal Y, Terrat C, Guillon C, Durand PY, Hurtrel B, Aubertin AM, Sutter G, Erfle V, et al. 2002. Evaluation in rhesus macaques of Tat and rev-targeted immunization as a preventive vaccine against mucosal challenge with SHIV-BX08. DNA Cell Biol. 21(9):653–58.
  • Yoo JW, Doshi N, Mitragotri S. 2011. Adaptive micro and nanoparticles: temporal control over carrier properties to facilitate drug delivery. Adv Drug Delivery Rev. 63(14–15):1247–56.
  • Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J, et al. 2008. Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res. 36(2):W513–8.

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