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Research Article

In silico development of a novel anti-mutation, multi-epitope mRNA vaccine against MPXV variants of emerging lineage and sub-lineages by using immunoinformatics approaches

, , &
Received 26 Oct 2023, Accepted 24 Feb 2024, Published online: 07 Mar 2024

References

  • Alexander, J., del Guercio, M. F., Maewal, A., Qiao, L., Fikes, J., Chesnut, R. W., Paulson, J., Bundle, D. R., DeFrees, S., & Sette, A. (2000). Linear PADRE T helper epitope and carbohydrate B cell epitope conjugates induce specific high titer IgG antibody responses. Journal of Immunology (Baltimore, Md.: 1950), 164(3), 1625–1633. https://doi.org/10.4049/jimmunol.164.3.1625
  • Andreatta, M., & Nielsen, M. (2016). Gapped sequence alignment using artificial neural networks: Application to the MHC class I system. Bioinformatics (Oxford, England), 32(4), 511–517. https://doi.org/10.1093/bioinformatics/btv639
  • Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., Millán, C., Park, H., Adams, C., Glassman, C. R., DeGiovanni, A., Pereira, J. H., Rodrigues, A. V., van Dijk, A. A., Ebrecht, A. C., … Baker, D. (2021). Accurate prediction of protein structures and interactions using a three-track neural network. Science (New York, N.Y.), 373(6557), 871–876. https://doi.org/10.1126/science.abj8754
  • Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
  • Buchan, D. W. A., & Jones, D. T. (2019). The PSIPRED protein analysis workbench: 20 years on. Nucleic Acids Research, 47(W1), W402–w407. https://doi.org/10.1093/nar/gkz297
  • Calis, J. J. A., Maybeno, M., Greenbaum, J. A., Weiskopf, D., De Silva, A. D., Sette, A., Keşmir, C., & Peters, B. (2013). Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Computational Biology, 9(10), e1003266. https://doi.org/10.1371/journal.pcbi.1003266
  • Cancro, M. P., & Tomayko, M. M. (2021). Memory B cells and plasma cells: The differentiative continuum of humoral immunity. Immunological Reviews, 303(1), 72–82. https://doi.org/10.1111/imr.13016
  • Chen, C., Li, Z., Huang, H., Suzek, B. E., & Wu, C. H, UniProt Consortium. (2013). A fast peptide match service for UniProt knowledgebase. Bioinformatics (Oxford, England), 29(21), 2808–2809. https://doi.org/10.1093/bioinformatics/btt484
  • Chen, X., Zaro, J. L., & Shen, W. C. (2013). Fusion protein linkers: Property, design and functionality. Advanced Drug Delivery Reviews, 65(10), 1357–1369. https://doi.org/10.1016/j.addr.2012.09.039
  • Chung, C. S., Huang, C. Y., & Chang, W. (2005). Vaccinia virus penetration requires cholesterol and results in specific viral envelope proteins associated with lipid rafts. Journal of Virology, 79(3), 1623–1634. https://doi.org/10.1128/jvi.79.3.1623-1634.2005
  • Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science: A Publication of the Protein Society, 2(9), 1511–1519. https://doi.org/10.1002/pro.5560020916
  • Dhanda, S. K., Vir, P., & Raghava, G. P. (2013). Designing of interferon-gamma inducing MHC class-II binders. Biology Direct, 8(1), 30. https://doi.org/10.1186/1745-6150-8-30
  • Dimitrov, I., Bangov, I., Flower, D. R., & Doytchinova, I. (2014). AllerTOP v.2–a server for in silico prediction of allergens. Journal of Molecular Modeling, 20(6), 2278. https://doi.org/10.1007/s00894-014-2278-5
  • Doceul, V., Hollinshead, M., Breiman, A., Laval, K., & Smith, G. L. (2012). Protein B5 is required on extracellular enveloped vaccinia virus for repulsion of superinfecting virions. The Journal of General Virology, 93(Pt 9), 1876–1886. https://doi.org/10.1099/vir.0.043943-0
  • Doytchinova, I. A., & Flower, D. R. (2007). VaxiJen: A server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics, 8(1), 4. https://doi.org/10.1186/1471-2105-8-4
  • Engelstad, M., Howard, S. T., & Smith, G. L. (1992). A constitutively expressed vaccinia gene encodes a 42-kDa glycoprotein related to complement control factors that forms part of the extracellular virus envelope. Virology, 188(2), 801–810. https://doi.org/10.1016/0042-6822(92)90535-w
  • Fantini, J., Chahinian, H., & Yahi, N. (2022). A vaccine strategy based on the identification of an annular ganglioside binding motif in monkeypox virus protein E8L. Viruses, 14(11), 2531. https://doi.org/10.3390/v14112531
  • Fine, P. E., Jezek, Z., Grab, B., & Dixon, H. (1988). The transmission potential of monkeypox virus in human populations. International Journal of Epidemiology, 17(3), 643–650. https://doi.org/10.1093/ije/17.3.643
  • Foo, C. H., Lou, H., Whitbeck, J. C., Ponce-de-León, M., Atanasiu, D., Eisenberg, R. J., & Cohen, G. H. (2009). Vaccinia virus L1 binds to cell surfaces and blocks virus entry independently of glycosaminoglycans. Virology, 385(2), 368–382. https://doi.org/10.1016/j.virol.2008.12.019
  • Gilchuk, I., Gilchuk, P., Sapparapu, G., Lampley, R., Singh, V., Kose, N., Blum, D. L., Hughes, L. J., Satheshkumar, P. S., Townsend, M. B., Kondas, A. V., Reed, Z., Weiner, Z., Olson, V. A., Hammarlund, E., Raue, H.-P., Slifka, M. K., Slaughter, J. C., Graham, B. S., … Crowe, J. E. Jr. (2016). Cross-neutralizing and protective human antibody specificities to poxvirus infections. Cell, 167(3), 684–694.e689. https://doi.org/10.1016/j.cell.2016.09.049
  • Grote, A., Hiller, K., Scheer, M., Münch, R., Nörtemann, B., Hempel, D. C., & Jahn, D. (2005). JCat: A novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Research, 33(Web Server issue), W526–531. https://doi.org/10.1093/nar/gki376
  • Gruber, A. R., Lorenz, R., Bernhart, S. H., Neuböck, R., & Hofacker, I. L. (2008). The Vienna RNA websuite. Nucleic Acids Research, 36(Web Server issue), W70–74. https://doi.org/10.1093/nar/gkn188
  • Gruber, M. F. (2022). Current status of monkeypox vaccines. NPJ Vaccines, 7(1), 94. https://doi.org/10.1038/s41541-022-00527-4
  • Gu, Y., Yang, J., He, C., Zhao, T., Lu, R., Liu, J., Mo, X., Wen, F., & Shi, H. (2023). Incorporation of a Toll-like receptor 2/6 agonist potentiates mRNA vaccines against cancer and infectious diseases. Signal Transduction and Targeted Therapy, 8(1), 273. https://doi.org/10.1038/s41392-023-01479-4
  • Hallgren, J., Tsirigos, K., Pedersen, M. D., Almagro Armenteros, J. J., Marcatili, P., Nielsen, H., … Winther, O. (2022). DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. bioRxiv. https://doi.org/10.1101/2022.04.08.487609
  • Hou, F., Zhang, Y., Liu, X., Murad, Y. M., Xu, J., Yu, Z., Hua, X., Song, Y., Ding, J., Huang, H., Zhao, R., Jia, W., & Yang, X. (2023). mRNA Vaccines encoding fusion proteins of monkeypox virus antigens protect mice from vaccinia virus challenge. Nature Communications, 14(1), 5925. https://doi.org/10.1038/s41467-023-41628-5
  • Janeway, C. A., Jr, Travers, P., & Walport, M. (2001). Immunobiology: The immune system in health and disease (5th ed.). Garland Science. The major histocompatibility complex and its functions. https://www.ncbi.nlm.nih.gov/books/NBK27156/.
  • Jespersen, M. C., Peters, B., Nielsen, M., & Marcatili, P. (2017). BepiPred-2.0: Improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Research, 45(W1), W24–w29. https://doi.org/10.1093/nar/gkx346
  • Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., … Hassabis, D. (2021). Highly accurate protein structure prediction with AlphaFold. Nature, 596(7873), 583–589. https://doi.org/10.1038/s41586-021-03819-2
  • Kim, D. E., Chivian, D., & Baker, D. (2004). Protein structure prediction and analysis using the Robetta server. Nucleic Acids Research, 32(Web Server issue), W526–531. https://doi.org/10.1093/nar/gkh468
  • Kim, J., Yang, Y. L., Jeong, Y., & Jang, Y. S. (2020). Conjugation of human β-Defensin 2 to spike protein receptor-binding domain induces antigen-specific protective immunity against middle east respiratory syndrome coronavirus infection in human dipeptidyl peptidase 4 transgenic mice. Vaccines, 8(4). https://doi.org/10.3390/vaccines8040635
  • Kutzner, C., Páll, S., Fechner, M., Esztermann, A., de Groot, B. L., & Grubmüller, H. (2015). Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. Journal of Computational Chemistry, 36(26), 1990–2008. https://doi.org/10.1002/jcc.24030
  • Ladnyj, I., Ziegler, P., & Kima, E. (1972). A human infection caused by monkeypox virus in Basankusu Territory, Democratic Republic of the Congo. Bulletin of the World Health Organization, 46(5), 593–597.
  • Larsen, M. V., Lundegaard, C., Lamberth, K., Buus, S., Lund, O., & Nielsen, M. (2007). Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics, 8(1), 424. https://doi.org/10.1186/1471-2105-8-424
  • Laskowski, R. A., Jabłońska, J., Pravda, L., Vařeková, R. S., & Thornton, J. M. (2018). PDBsum: Structural summaries of PDB entries. Protein Science: A Publication of the Protein Society, 27(1), 129–134. https://doi.org/10.1002/pro.3289
  • Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
  • Lum, F. M., Torres-Ruesta, A., Tay, M. Z., Lin, R. T. P., Lye, D. C., Rénia, L., & Ng, L. F. P. (2022). Monkeypox: Disease epidemiology, host immunity and clinical interventions. Nature Reviews. Immunology, 22(10), 597–613. https://doi.org/10.1038/s41577-022-00775-4
  • Luna, N., Muñoz, M., Bonilla-Aldana, D. K., Patiño, L. H., Kasminskaya, Y., Paniz-Mondolfi, A., & Ramírez, J. D. (2023). Monkeypox virus (MPXV) genomics: A mutational and phylogenomic analyses of B.1 lineages. Travel Medicine and Infectious Disease, 52, 102551. https://doi.org/10.1016/j.tmaid.2023.102551
  • Magnan, C. N., Zeller, M., Kayala, M. A., Vigil, A., Randall, A., Felgner, P. L., & Baldi, P. (2010). High-throughput prediction of protein antigenicity using protein microarray data. Bioinformatics (Oxford, England), 26(23), 2936–2943. https://doi.org/10.1093/bioinformatics/btq551
  • Maisuradze, G. G., Liwo, A., & Scheraga, H. A. (2010). Relation between free energy landscapes of proteins and dynamics. Journal of Chemical Theory and Computation, 6(2), 583–595. https://doi.org/10.1021/ct9005745
  • Malik, S., Ahmed, A., Ahsan, O., Muhammad, K., & Waheed, Y. (2023). Monkeypox virus: A comprehensive overview of viral pathology, immune response, and antiviral strategies. Vaccines, 11(8). https://doi.org/10.3390/vaccines11081345
  • Marciani, D. J. (2003). Vaccine adjuvants: Role and mechanisms of action in vaccine immunogenicity. Drug Discovery Today, 8(20), 934–943. https://doi.org/10.1016/s1359-6446(03)02864-2
  • McCollum, A. M., & Damon, I. K. (2014). Human monkeypox. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, 58(2), 260–267. https://doi.org/10.1093/cid/cit703
  • Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2022). ColabFold: Making protein folding accessible to all. Nature Methods, 19(6), 679–682. https://doi.org/10.1038/s41592-022-01488-1
  • Nielsen, H., Tsirigos, K. D., Brunak, S., & von Heijne, G. (2019). A brief history of protein sorting prediction. The Protein Journal, 38(3), 200–216. https://doi.org/10.1007/s10930-019-09838-3
  • Olejnik, J., Hume, A. J., & Mühlberger, E. (2018). Toll-like receptor 4 in acute viral infection: Too much of a good thing. PLoS Pathogens, 14(12), e1007390. https://doi.org/10.1371/journal.ppat.1007390
  • Parrinello, M., & Rahman, A. (1982). Strain fluctuations and elastic constants. The Journal of Chemical Physics, 76(5), 2662–2666. https://doi.org/10.1063/1.443248
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Meng, E. C., Couch, G. S., Croll, T. I., Morris, J. H., & Ferrin, T. E. (2021). UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Science: A Publication of the Protein Society, 30(1), 70–82. https://doi.org/10.1002/pro.3943
  • Rapin, N., Lund, O., Bernaschi, M., & Castiglione, F. (2010). Computational immunology meets bioinformatics: The use of prediction tools for molecular binding in the simulation of the immune system. PloS One, 5(4), e9862. https://doi.org/10.1371/journal.pone.0009862
  • Saha, S., & Raghava, G. P. (2006). Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins, 65(1), 40–48. https://doi.org/10.1002/prot.21078
  • Sartorius, R., Trovato, M., Manco, R., D'Apice, L., & De Berardinis, P. (2021). Exploiting viral sensing mediated by Toll-like receptors to design innovative vaccines. NPJ Vaccines, 6(1), 127. https://doi.org/10.1038/s41541-021-00391-8
  • Services, U. S. D. O H. A H. (2022). Biden-Harris administration bolsters monkeypox response; HHS secretary Becerra declares public health emergency. https://www.hhs.gov/about/news/2022/08/04/biden-harris-administration-bolsters-monkeypox-response-hhs-secretary-becerra-declares-public-health-emergency.html
  • Sharma, N., Naorem, L. D., Jain, S., & Raghava, G. P. S. (2022). ToxinPred2: An improved method for predicting toxicity of proteins. Briefings in Bioinformatics, 23(5). https://doi.org/10.1093/bib/bbac174
  • Shchelkunov, S. N., Totmenin, A. V., Safronov, P. F., Mikheev, M. V., Gutorov, V. V., Ryazankina, O. I., Petrov, N. A., Babkin, I. V., Uvarova, E. A., Sandakhchiev, L. S., Sisler, J. R., Esposito, J. J., Damon, I. K., Jahrling, P. B., & Moss, B. (2002). Analysis of the monkeypox virus genome. Virology, 297(2), 172–194. https://doi.org/10.1006/viro.2002.1446
  • Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J. D., & Higgins, D. G. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7(1), 539. (Accession No. 21988835). https://doi.org/10.1038/msb.2011.75
  • Tan, C., Zhu, F., Pan, P., Wu, A., & Li, C. (2023). Development of multi-epitope vaccines against the monkeypox virus based on envelope proteins using immunoinformatics approaches. Frontiers in Immunology, 14, 1112816. https://doi.org/10.3389/fimmu.2023.1112816
  • Tian, C., Kasavajhala, K., Belfon, K. A. A., Raguette, L., Huang, H., Migues, A. N., Bickel, J., Wang, Y., Pincay, J., Wu, Q., & Simmerling, C. (2020). ff19SB: Amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution. Journal of Chemical Theory and Computation, 16(1), 528–552. https://doi.org/10.1021/acs.jctc.9b00591
  • Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021). gmx_MMPBSA: A new tool to perform end-state free energy calculations with GROMACS. Journal of Chemical Theory and Computation, 17(10), 6281–6291. https://doi.org/10.1021/acs.jctc.1c00645
  • van Zundert, G. C. P., Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A. S. J., van Dijk, M., de Vries, S. J., & Bonvin, A. M. J. J. (2016). The HADDOCK2.2 Web Server: User-friendly integrative modeling of biomolecular complexes. Journal of Molecular Biology, 428(4), 720–725. https://doi.org/10.1016/j.jmb.2015.09.014
  • Vangone, A., & Bonvin, A. M. (2015). Contacts-based prediction of binding affinity in protein-protein complexes. eLife, 4, e07454. https://doi.org/10.7554/eLife.07454
  • Vijay, K. (2018). Toll-like receptors in immunity and inflammatory diseases: Past, present, and future. International Immunopharmacology, 59, 391–412. https://doi.org/10.1016/j.intimp.2018.03.002
  • Wang, P., Sidney, J., Kim, Y., Sette, A., Lund, O., Nielsen, M., & Peters, B. (2010). Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics, 11(1), 568. https://doi.org/10.1186/1471-2105-11-568
  • Wang, Y., Yang, K., & Zhou, H. (2023). Immunogenic proteins and potential delivery platforms for mpox virus vaccine development: A rapid review. International Journal of Biological Macromolecules, 245, 125515. https://doi.org/10.1016/j.ijbiomac.2023.125515
  • Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M., & Barton, G. J. (2009). Jalview Version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics (Oxford, England), 25(9), 1189–1191. https://doi.org/10.1093/bioinformatics/btp033
  • Weng, G., Wang, E., Wang, Z., Liu, H., Zhu, F., Li, D., & Hou, T. (2019). HawkDock: A web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA. Nucleic Acids Research, 47(W1), W322–w330. https://doi.org/10.1093/nar/gkz397
  • WHO. (2022a). Annexes to the vaccines and immunization for monkeypox interim guidance. https://www.who.int/publications/i/item/WHO-MPX-Immunization-Annexes-2022
  • WHO. (2022b). WHO Director—General declares ongoing monkeypox outbreak a Public health Emergency of International Concern. https://www.who.int/europe/news/item/23-07-2022-who-director-general-declares-the-ongoing-monkeypox-outbreak-a-public-health-event-of-international-concern
  • WHO. (2023). Multi-country outbreak of mpox, External situation report#29 – 20 October 2023. https://www.who.int/publications/m/item/multi-country-outbreak-of-mpox–external-situation-report-29–-20-october-2023
  • Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server issue), W407–410. https://doi.org/10.1093/nar/gkm290
  • Yan, Y., Zhang, D., Zhou, P., Li, B., & Huang, S. Y. (2017). HDOCK: A web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. Nucleic Acids Research, 45(W1), W365–w373. https://doi.org/10.1093/nar/gkx407
  • Zhan, X. Y., Zha, G. F., & He, Y. (2022). Evolutionary dissection of monkeypox virus: Positive Darwinian selection drives the adaptation of virus-host interaction proteins. Frontiers in Cellular and Infection Microbiology, 12, 1083234. https://doi.org/10.3389/fcimb.2022.1083234
  • Zhang, R.-R., Wang, Z.-J., Zhu, Y.-L., Tang, W., Zhou, C., Zhao, S.-Q., Wu, M., Ming, T., Deng, Y.-Q., Chen, Q., Jin, N.-Y., Ye, Q., Li, X., & Qin, C.-F. (2023). Rational development of multicomponent mRNA vaccine candidates against mpox. Emerging Microbes & Infections, 12(1), 2192815. https://doi.org/10.1080/22221751.2023.2192815
  • Zhou, R., Liu, L., & Wang, Y. (2021). Viral proteins recognized by different TLRs. Journal of Medical Virology, 93(11), 6116–6123. https://doi.org/10.1002/jmv.27265

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