Skip to content
2000
image of Immunoinformatics Analysis of Potent Therapeutic Formulations for the Development of HIV-1 Nefmut-Carrying Engineered Exosomes

Abstract

Background

The concept of designer exosomes involves developing engineered exosomes to overcome the limitations of natural exosomes in targeted drug delivery and vaccine development.

Methods

In this study, the multiepitope constructs were designed based on immunogenic regions of mutant Nef protein of Human Immunodeficiency Virus-1 (HIV-1 Nefmut) that were prone to high Post-Translational Modifications (PTMs), such as palmitoylation and myristoylation. These constructs with high scores in PTMs were selected for interactions with molecules involved in exosome biogenesis, anchoring of a protein in membranes, and enzymes involved in PTMs (, the mutant enzyme ZDHHC21 p.T209S). Moreover, the selected multiepitope construct with the highest PTM score and stable linkage with these molecules was fused to the first exon of the HIV-1 Tat protein as an antigen candidate, and to GFP as a tracking tool for evaluating their effects on the PTM scores and affinity binding with various molecules.

Results

Our data demonstrated that the multiepitope construct No.13 had better scores for incorporation into exosomes compared to the whole sequences of Nefmut and wild-type Nef protein (Nefwt). Furthermore, the linkage of Tat protein to construct No. 13 did not hinder its loading in exosomes compared to GFP, suggesting the use of this construct in vaccine development.

Conclusion

The multiepitope construct No.13 harboring potent Nefmut epitopes can be applied for linkage with other viral antigens, enhancing their delivery into exosomes for therapeutic applications.

Loading

Article metrics loading...

/content/journals/chr/10.2174/011570162X361821250512115612
2025-05-21
2025-09-04
Loading full text...

Full text loading...

References

  1. Welch J.L. Stapleton J.T. Okeoma C.M. Vehicles of intercellular communication: Exosomes and HIV-1. J. Gen. Virol. 2019 100 3 350 366 10.1099/jgv.0.001193 30702421
    [Google Scholar]
  2. Teow S.Y. Liew K. Khoo A.S.B. Peh S.C. Pathogenic role of exosomes in epstein-barr virus (EBV)-associated cancers. Int. J. Biol. Sci. 2017 13 10 1276 1286 10.7150/ijbs.19531 29104494
    [Google Scholar]
  3. Lu Y. Mai Z. Cui L. Zhao X. Engineering exosomes and biomaterial-assisted exosomes as therapeutic carriers for bone regeneration. Stem Cell Res. Ther. 2023 14 1 55 10.1186/s13287‑023‑03275‑x 36978165
    [Google Scholar]
  4. Paolicelli R.C. Bergamini G. Rajendran L. Cell-to-cell communication by extracellular vesicles: Focus on microglia. Neuroscience 2019 405 148 157 10.1016/j.neuroscience.2018.04.003 29660443
    [Google Scholar]
  5. Xu M. Yang Q. Sun X. Wang Y. Recent advancements in the loading and modification of therapeutic exosomes. Front. Bioeng. Biotechnol. 2020 8 586130 10.3389/fbioe.2020.586130 33262977
    [Google Scholar]
  6. Jafari D. Shajari S. Jafari R. Designer exosomes: A new platform for biotechnology therapeutics. BioDrugs 2020 34 5 567 586 10.1007/s40259‑020‑00434‑x 32754790
    [Google Scholar]
  7. Madison M. Okeoma C. Exosomes: Implications in HIV-1 Pathogenesis. Viruses 2015 7 7 4093 4118 10.3390/v7072810 26205405
    [Google Scholar]
  8. Raab-Traub N. Dittmer D.P. Viral effects on the content and function of extracellular vesicles. Nat. Rev. Microbiol. 2017 15 9 559 572 10.1038/nrmicro.2017.60 28649136
    [Google Scholar]
  9. Lenassi M. Cagney G. Liao M. HIV Nef is secreted in exosomes and triggers apoptosis in bystander CD4+ T cells. Traffic 2010 11 1 110 122 10.1111/j.1600‑0854.2009.01006.x 19912576
    [Google Scholar]
  10. Coleman S.H. Day J.R. Guatelli J.C. The HIV-1 Nef protein as a target for antiretroviral therapy. Emerg. Ther. Targets 2001 5 1 1 22 10.1517/14728222.5.1.1 15992165
    [Google Scholar]
  11. Lattanzi L. Federico M. A strategy of antigen incorporation into exosomes: Comparing cross-presentation levels of antigens delivered by engineered exosomes and by lentiviral virus-like particles. Vaccine 2012 30 50 7229 7237 10.1016/j.vaccine.2012.10.010 23099330
    [Google Scholar]
  12. Bonito P. Ridolfi B. Columba-Cabezas S. HPV-E7 delivered by engineered exosomes elicits a protective CD8+ T cell-mediated immune response. Viruses 2015 7 3 1079 1099 10.3390/v7031079 25760140
    [Google Scholar]
  13. Di Bonito P. Chiozzini C. Arenaccio C. Antitumor HPV E7-specific CTL activity elicited by in vivo engineered exosomes produced through DNA inoculation. Int. J. Nanomedicine 2017 12 4579 4591 10.2147/IJN.S131309 28694699
    [Google Scholar]
  14. de Gassart A. Géminard C. Février B. Raposo G. Vidal M. Lipid raft-associated protein sorting in exosomes. Blood 2003 102 13 4336 4344 12881314
    [Google Scholar]
  15. Manfredi F. Di Bonito P. Arenaccio C. Anticoli S. Federico M. Incorporation of heterologous proteins in engineered exosomes. Methods Mol. Biol. 2016 1448 249 260 10.1007/978‑1‑4939‑3753‑0_18 27317186
    [Google Scholar]
  16. Costa L.J. Chen N. Lopes A. Interactions between Nef and AIP1 proliferate multivesicular bodies and facilitate egress of HIV-1. Retrovirology 2006 3 33 10.1186/1742‑4690‑3‑33 16764724
    [Google Scholar]
  17. Han Q.F. Li W.J. Hu K.S. Exosome biogenesis: Machinery, regulation, and therapeutic implications in cancer. Mol. Cancer 2022 21 1 207 10.1186/s12943‑022‑01671‑0 36320056
    [Google Scholar]
  18. Federico M. From virus-like particles to engineered exosomes for a new generation of vaccines. Future Virol. 2012 7 5 473 482 10.2217/fvl.12.29
    [Google Scholar]
  19. Soltani N. Pakniya F. Parchami N. Behbahani M. Mohabatkar H. In-silico comparison of post-translational modifications of SARS-CoV and SARS-CoV-2 structural proteins. Shahrekord Univ. Med. Sci. J. 2021 23 4 168 173
    [Google Scholar]
  20. Resh M.D. Fatty acylation of proteins: New insights into membrane targeting of myristoylated and palmitoylated proteins. Biochim. Biophys. Acta 1999 1451 1 1 16 10.1016/s0167‑4889(99)00075‑0 10446384
    [Google Scholar]
  21. Blaskovic S. Blanc M. van der Goot F.G. What does S-palmitoylation do to membrane proteins? FEBS J. 2013 280 12 2766 2774 10.1111/febs.12263 23551889
    [Google Scholar]
  22. Boeske A. Schwarten M. Ma P. Direct binding to GABARAP family members is essential for HIV-1 Nef plasma membrane localization. Sci. Rep. 2017 7 1 5979 10.1038/s41598‑017‑06319‑4 28729737
    [Google Scholar]
  23. Li W. Pang Y. Wang Y. Aberrant palmitoylation caused by a ZDHHC21 mutation contributes to pathophysiology of Alzheimer’s disease. BMC Med. 2023 21 1 223 10.1186/s12916‑023‑02930‑7 37365538
    [Google Scholar]
  24. McNamara R.P. Costantini L.M. Myers T.A. Nef secretion into extracellular vesicles or exosomes is conserved across human and simian immunodeficiency viruses. MBio 2018 9 1 e02344 e17 10.1128/mBio.02344‑17 29437924
    [Google Scholar]
  25. Ensoli B. Moretti S. Borsetti A. New insights into pathogenesis point to HIV-1 Tat as a key vaccine target. Arch. Virol. 2021 166 11 2955 2974 10.1007/s00705‑021‑05158‑z 34390393
    [Google Scholar]
  26. Hill B.T. Skowronski J. Human N-myristoyltransferases form stable complexes with lentiviral nef and other viral and cellular substrate proteins. J. Virol. 2005 79 2 1133 1141 10.1128/JVI.79.2.1133‑1141.2005 15613341
    [Google Scholar]
  27. Liu B. Yang Z. Liu Q. Computational prediction of allergenic proteins based on multi-feature fusion. Front. Genet. 2023 14 1294159 10.3389/fgene.2023.1294159 37928245
    [Google Scholar]
  28. Fleri W. Paul S. Dhanda S.K. The immune epitope database and analysis resource in epitope discovery and synthetic vaccine design. Front. Immunol. 2017 8 278 10.3389/fimmu.2017.00278 28352270
    [Google Scholar]
  29. Xie Y. Zheng Y. Li H. GPS-Lipid: A robust tool for the prediction of multiple lipid modification sites. Sci. Rep. 2016 6 1 28249 10.1038/srep28249 27306108
    [Google Scholar]
  30. Shey R.A. Ghogomu S.M. Esoh K.K. In-silico design of a multi-epitope vaccine candidate against onchocerciasis and related filarial diseases. Sci. Rep. 2019 9 1 4409 10.1038/s41598‑019‑40833‑x 30867498
    [Google Scholar]
  31. Chiu J. Hogg P.J. Allosteric disulfides: Sophisticated molecular structures enabling flexible protein regulation. J. Biol. Chem. 2019 294 8 2949 5908 10.1074/jbc.REV118.005604 30635401
    [Google Scholar]
  32. Montgomerie S Cruz JA Shrivastava S Arndt D Berjanskii M Wishart DS PROTEUS2: A web server for comprehensive protein structure prediction and structure-based annotation. Nucleic Acids Res 2008 36Web ServerW202W209 10.1093/nar/gkn255 18483082
    [Google Scholar]
  33. Rapin N. Lund O. Castiglione F. Immune system simulation online. Bioinformatics 2011 27 14 2013 2014 10.1093/bioinformatics/btr335 21685045
    [Google Scholar]
  34. Sivalingam G.N. Shepherd A.J. An analysis of B-cell epitope discontinuity. Mol. Immunol. 2012 51 3-4 304 309 10.1016/j.molimm.2012.03.030 22520973
    [Google Scholar]
  35. Ponomarenko J. Bui H.H. Li W. ElliPro: A new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics 2008 9 1 514 10.1186/1471‑2105‑9‑514 19055730
    [Google Scholar]
  36. Jorgensen W.L. Madura J.D. Quantum and statistical mechanical studies of liquids. 25. Solvation and conformation of methanol in water. J. Am. Chem. Soc. 1983 105 6 1407 1413 10.1021/ja00344a001
    [Google Scholar]
  37. Bussi G. Donadio D. Parrinello M. Canonical sampling through velocity rescaling. J. Chem. Phys. 2007 126 1 014101 10.1063/1.2408420 17212484
    [Google Scholar]
  38. Ali M. Pandey R.K. Khatoon N. Narula A. Mishra A. Prajapati V.K. Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection. Sci. Rep. 2017 7 1 9232 10.1038/s41598‑017‑09199‑w 28835708
    [Google Scholar]
  39. Mustufa M.M. Chandra S. Wajid S. Homology modeling and molecular docking analysis of human RAC-alpha serine/threonine protein kinase. Int. J. Pharma Bio Sci. 2014 5 1033 1042
    [Google Scholar]
  40. Ikai A. Thermostability and aliphatic index of globular proteins. J. Biochem. 1980 88 6 1895 1898 7462208
    [Google Scholar]
  41. Dias M.V.S. Costa C.S. daSilva L.L.P. The ambiguous roles of extracellular vesicles in HIV replication and pathogenesis. Front. Microbiol. 2018 9 2411 10.3389/fmicb.2018.02411 30364166
    [Google Scholar]
  42. da Silva-Januário M.E. da Costa C.S. Tavares L.A. HIV-1 Nef changes the proteome of T cells extracellular vesicles depleting IFITMs and other antiviral factors. Mol. Cell. Proteomics 2023 22 12 100676 10.1016/j.mcpro.2023.100676 37940003
    [Google Scholar]
  43. Liu C. Su C. Design strategies and application progress of therapeutic exosomes. Theranostics 2019 9 4 1015 1028 10.7150/thno.30853 30867813
    [Google Scholar]
  44. Anticoli S. Manfredi F. Chiozzini C. An exosome-based vaccine platform imparts cytotoxic T lymphocyte immunity against viral antigens. Biotechnol. J. 2018 13 4 1700443 10.1002/biot.201700443 29274250
    [Google Scholar]
  45. Serrano L. Neira J.L. Sancho J. Fersht A.R. Effect of alanine versus glycine in α-helices on protein stability. Nature 1992 356 6368 453 455 10.1038/356453a0 1557131
    [Google Scholar]
  46. Chiozzini C. Manfredi F. Arenaccio C. Ferrantelli F. Leone P. Federico M. N-terminal fatty acids of Nefmut are required for the CD8+ T-cell immunogenicity of in vivo engineered extracellular vesicles. Vaccines 2020 8 2 243 10.3390/vaccines8020243 32456079
    [Google Scholar]
  47. Huda M.N. Nurunnabi M. Potential application of exosomes in vaccine development and delivery. Pharm. Res. 2022 39 11 2635 2671 10.1007/s11095‑021‑03143‑4 35028802
    [Google Scholar]
  48. Dyball L.E. Smales C.M. Exosomes: Biogenesis, targeting, characterization and their potential as “Plug & Play” vaccine platforms. Biotechnol. J. 2022 17 11 e2100646 35899790
    [Google Scholar]
  49. Mitchell D.A. Vasudevan A. Linder M.E. Deschenes R.J. Thematic review series: Lipid posttranslational modifications. Protein palmitoylation by a family of DHHC protein Sacyltransferases. J. Lipid Res. 2006 47 6 1118 1127 10.1194/jlr.R600007‑JLR200 16582420
    [Google Scholar]
  50. Greaves J. Chamberlain L.H. DHHC palmitoyl transferases: Substrate interactions and (patho)physiology. Trends Biochem. Sci. 2011 36 5 245 253 10.1016/j.tibs.2011.01.003 21388813
    [Google Scholar]
  51. Reddy K.D. Malipeddi J. DeForte S. Physicochemical sequence characteristics that influence S-palmitoylation propensity. J. Biomol. Struct. Dyn. 2017 35 11 2337 2350 10.1080/07391102.2016.1217275 27498722
    [Google Scholar]
  52. Khanal N. Pejaver V. Li Z. Radivojac P. Clemmer D.E. Mukhopadhyay S. Position of proline mediates the reactivity of S-palmitoylation. ACS Chem. Biol. 2015 10 11 2529 2536 10.1021/acschembio.5b00429 26255674
    [Google Scholar]
  53. Wang B. Dai T. Sun W. Protein N-myristoylation: Functions and mechanisms in control of innate immunity. Cell. Mol. Immunol. 2021 18 4 878 888 10.1038/s41423‑021‑00663‑2 33731917
    [Google Scholar]
  54. Resh M.D. Regulation of cellular signalling by fatty acid acylation and prenylation of signal transduction proteins. Cell. Signal. 1996 8 6 403 412 10.1016/s0898‑6568(96)00088‑5 8958442
    [Google Scholar]
  55. Tan K.P. Singh K. Hazra A. Madhusudhan M.S. Peptide bond planarity constrains hydrogen bond geometry and influences secondary structure conformations. Curr. Res. Struct. Biol. 2020 3 1 8 10.1016/j.crstbi.2020.11.002 34382009
    [Google Scholar]
  56. Yuan Y. Li P. Li J. Zhao Q. Chang Y. He X. Protein lipidation in health and disease: Molecular basis, physiological function and pathological implication. Signal Transduct. Target. Ther. 2024 9 1 60 10.1038/s41392‑024‑01759‑7 38485938
    [Google Scholar]
  57. Pereira E.A. daSilva L.L. HIV-1 Nef: Taking control of protein trafficking. Traffic 2016 17 9 976 996 10.1111/tra.12412 27161574
    [Google Scholar]
  58. Staudt R.P. Alvarado J.J. Emert-Sedlak L.A. Structure, function, and inhibitor targeting of HIV-1 Nef-effector kinase complexes. J. Biol. Chem. 2020 295 44 15158 15171 10.1074/jbc.REV120.012317 32862141
    [Google Scholar]
  59. Udenwobele D.I. Su R.C. Good S.V. Ball T.B. Varma Shrivastav S. Shrivastav A. Myristoylation: An important protein modification in the immune response. Front. Immunol. 2017 8 751 10.3389/fimmu.2017.00751 28713376
    [Google Scholar]
  60. Byrne P.O. McLellan J.S. Principles and practical applications of structure-based vaccine design. Curr. Opin. Immunol. 2022 77 102209 10.1016/j.coi.2022.102209 35598506
    [Google Scholar]
  61. Cordeiro P.A.S. Assone T. Prates G. Tedeschi M.R.M. Fonseca L.A.M. Casseb J. The role of IFN-γ production during retroviral infections: An important cytokine involved in chronic inflammation and pathogenesis. Rev. Inst. Med. Trop. São Paulo 2022 64 e64 10.1590/s1678‑9946202264064 36197425
    [Google Scholar]
  62. Lee A.J. Ashkar A.A. The dual nature of type I and type II interferons. Front. Immunol. 2018 9 2061 10.3389/fimmu.2018.02061 30254639
    [Google Scholar]
  63. Brügger B. Krautkrämer E. Tibroni N. Human Immunodeficiency Virus Type 1 Nef protein modulates the lipid composition of virions and host cell membrane microdomains. Retrovirology 2007 4 1 70 10.1186/1742‑4690‑4‑70 17908312
    [Google Scholar]
  64. Fanales-Belasio E. Raimondo M. Suligoi B. Buttò S. HIV virology and pathogenetic mechanisms of infection: A brief overview. Ann. Ist. Super. Sanita 2010 46 1 5 14 10.1590/S0021‑25712010000100002 20348614
    [Google Scholar]
  65. Bentham M. Mazaleyrat S. Harris M. Role of myristoylation and N-terminal basic residues in membrane association of the human immunodeficiency virus type 1 Nef protein. J. Gen. Virol. 2006 87 3 563 571 10.1099/vir.0.81200‑0 16476977
    [Google Scholar]
  66. Buffalo C.Z. Iwamoto Y. Hurley J.H. Ren X. How H.I.V. Nef proteins hijack membrane traffic to promote infection? J. Virol. 2019 93 24 e01322 e19 10.1128/JVI.01322‑19 31578291
    [Google Scholar]
/content/journals/chr/10.2174/011570162X361821250512115612
Loading
/content/journals/chr/10.2174/011570162X361821250512115612
Loading

Data & Media loading...

Supplements

Supplementary material is available on the publisher's website along with the published article.

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error
Please enter a valid_number test