mRNA Vaccine Design Modifications and Their Implications for Next-Generation Vaccines: Lessons from COVID-19
DOI:
https://doi.org/10.24002/biota.v11i2.13298Keywords:
COVID-19, mRNA vaccine, mRNA modification, LNPAbstract
The COVID-19 pandemic accelerated rapid advances in vaccine development and underscored the need for platforms that can be rapidly engineered, highly effective, and adaptable to evolving pathogens. Messenger RNA (mRNA) vaccines have demonstrated exceptional efficacy and safety, establishing a significant milestone in modern vaccinology. This review aims to synthesize recent molecular engineering innovations that determine mRNA vaccine performance, focusing on nucleoside modification, spike protein prefusion stabilization, codon and untranslated region (UTR) optimization, and lipid nanoparticle (LNP) delivery systems. A literature search was conducted using PubMed and Google Scholar for studies published between 2020 and 2023, and selected publications were analyzed to identify key molecular determinants shaping vaccine function. Findings indicate that incorporation of N1-methyl-pseudouridine enhances mRNA stability, improves translational output, and reduces innate immune activation. The double-proline modification maintains the spike protein’s prefusion conformation, while codon and UTR optimization further elevate antigen expression. LNP encapsulation provides structural protection and supports efficient intracellular delivery. Collectively, these engineering strategies enhance immunogenicity, ensure favorable tolerability, and allow rapid adaptation to emerging variants. Overall, integrated molecular design and advanced delivery technologies position mRNA vaccines as a transformative platform for next-generation vaccine development and strengthened global pandemic preparedness.
References
Adams, K., Rhoads, J. P., Surie, D., Gaglani, M., Ginde, A. A., McNeal, T., Talbot, H. K., Casey, J. D., Zepeski, A., Shapiro, N. I., Gibbs, K. W., Files, D. C., Hager, D. N., Frosch, A. E., Exline, M. C., Mohamed, A., Johnson, N. J., Steingrub, J. S., Peltan, I. D., … Self, W. H. (2022). Vaccine effectiveness of primary series and booster doses against covid-19 associated hospital admissions in the United States: Living test negative design study. The BMJ. https://doi.org/10.1136/bmj-2022-072065
Ali, K., Berman, G., Zhou, H., Deng, W., Faughnan, V., Coronado-Voges, M., Ding, B., Dooley, J., Girard, B., Hillebrand, W., Pajon, R., Miller, J. M., Leav, B., & McPhee, R. (2021). Evaluation of mRNA-1273 SARS-CoV-2 Vaccine in Adolescents. New England Journal of Medicine, 385(24), 2241–2251. https://doi.org/10.1056/nejmoa2109522
Baden, L. R., El Sahly, H. M., Essink, B., Kotloff, K., Frey, S., Novak, R., Diemert, D., Spector, S. A., Rouphael, N., Creech, C. B., McGettigan, J., Khetan, S., Segall, N., Solis, J., Brosz, A., Fierro, C., Schwartz, H., Neuzil, K., Corey, L., … Zaks, T. (2021). Efficacy and Safety of the mRNA-1273 SARS-CoV-2 Vaccine. New England Journal of Medicine, 384(5), 403–416. https://doi.org/10.1056/nejmoa2035389
Corbett, K. S., Edwards, D. K., Leist, S. R., Abiona, O. M., Boyoglu-Barnum, S., Gillespie, R. A., Himansu, S., Schäfer, A., Ziwawo, C. T., DiPiazza, A. T., Dinnon, K. H., Elbashir, S. M., Shaw, C. A., Woods, A., Fritch, E. J., Martinez, D. R., Bock, K. W., Minai, M., Nagata, B. M., … Graham, B. S. (2020). SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness. Nature, 586(7830), 567–571. https://doi.org/10.1038/s41586-020-2622-0
Corbett, K. S., Flynn, B., Foulds, K. E., Francica, J. R., Boyoglu-Barnum, S., Werner, A. P., Flach, B., O’Connell, S., Bock, K. W., Minai, M., Nagata, B. M., Andersen, H., Martinez, D. R., Noe, A. T., Douek, N., Donaldson, M. M., Nji, N. N., Alvarado, G. S., Edwards, D. K., … Graham, B. S. (2020). Evaluation of the mRNA-1273 Vaccine against SARS-CoV-2 in Nonhuman Primates. New England Journal of Medicine, 383(16), 1544–1555. https://doi.org/10.1056/nejmoa2024671
Creech, C. B., Anderson, E., Berthaud, V., Yildirim, I., Atz, A. M., Melendez Baez, I., Finkelstein, D., Pickrell, P., Kirstein, J., Yut, C., Blair, R., Clifford, R. A., Dunn, M., Campbell, J. D., Montefiori, D. C., Tomassini, J. E., Zhao, X., Deng, W., Zhou, H., … Schnyder Ghamloush, S. (2022). Evaluation of mRNA-1273 Covid-19 Vaccine in Children 6 to 11 Years of Age. New England Journal of Medicine, 386(21), 2011–2023. https://doi.org/10.1056/nejmoa2203315
Cucinotta, D., & Vanelli, M. (2020). WHO declares COVID-19 a pandemic. In Acta Biomedica (Vol. 91, Issue 1, pp. 157–160). Mattioli 1885. https://doi.org/10.23750/abm.v91i1.9397
Dagan, N., Barda, N., Kepten, E., Miron, O., Perchik, S., Katz, M. A., Hernán, M. A., Lipsitch, M., Reis, B., & Balicer, R. D. (2021). BNT162b2 mRNA Covid-19 Vaccine in a Nationwide Mass Vaccination Setting. New England Journal of Medicine, 384(15), 1412–1423. https://doi.org/10.1056/nejmoa2101765
Dai, L., Gao, L., Tao, L., Hadinegoro, S. R., Erkin, M., Ying, Z., He, P., Girsang, R. T., Vergara, H., Akram, J., Satari, H. I., Khaliq, T., Sughra, U., Celi, A. P., Li, F., Li, Y., Jiang, Z., Dalimova, D., Tuychiev, J., … Gao, G. F. (2022). Efficacy and Safety of the RBD-Dimer–Based Covid-19 Vaccine ZF2001 in Adults. New England Journal of Medicine, 386(22), 2097–2111. https://doi.org/10.1056/nejmoa2202261
Deplanque, D., & Launay, O. (2021). Efficacy of COVID-19 vaccines: From clinical trials to real life. Therapies, 76(4), 277–283. https://doi.org/10.1016/j.therap.2021.05.004
El Sahly, H. M., Baden, L. R., Essink, B., Montefiori, D., McDermont, A., Rupp, R., Lewis, M., Swaminathan, S., Griffin, C., Fragoso, V., Miller, V. E., Girard, B., Paila, Y. D., Deng, W., Tomassini, J. E., Paris, R., Schödel, F., Das, R., August, A., … Pajon, R. (2022). Humoral Immunogenicity of the mRNA-1273 Vaccine in the Phase 3 Coronavirus Efficacy (COVE) Trial. Journal of Infectious Diseases, 226(10), 1731–1742. https://doi.org/10.1093/infdis/jiac188
Ferdinands, J. M., Rao, S., Dixon, B. E., Mitchell, P. K., Desilva, M. B., Irving, S. A., Lewis, N., Natarajan, K., Stenehjem, E., Grannis, S. J., Han, J., McEvoy, C., Ong, T. C., Naleway, A. L., Reese, S. E., Embi, P. J., Dascomb, K., Klein, N. P., Griggs, E. P., … Fireman, B. (2022). Waning of vaccine effectiveness against moderate and severe covid-19 among adults in the US from the VISION network: Test negative, case-control study. The BMJ. https://doi.org/10.1136/bmj-2022-072141
Frenck, R. W., Klein, N. P., Kitchin, N., Gurtman, A., Absalon, J., Lockhart, S., Perez, J. L., Walter, E. B., Senders, S., Bailey, R., Swanson, K. A., Ma, H., Xu, X., Koury, K., Kalina, W. V., Cooper, D., Jennings, T., Brandon, D. M., Thomas, S. J., … Gruber, W. C. (2021). Safety, Immunogenicity, and Efficacy of the BNT162b2 Covid-19 Vaccine in Adolescents. New England Journal of Medicine, 385(3), 239–250. https://doi.org/10.1056/nejmoa2107456
Heath, P. T., Galiza, E. P., Baxter, D. N., Boffito, M., Browne, D., Burns, F., Chadwick, D. R., Clark, R., Cosgrove, C., Galloway, J., Goodman, A. L., Heer, A., Higham, A., Iyengar, S., Jamal, A., Jeanes, C., Kalra, P. A., Kyriakidou, C., McAuley, D. F., … Toback, S. (2021). Safety and Efficacy of NVX-CoV2373 Covid-19 Vaccine. New England Journal of Medicine, 385(13), 1172–1183. https://doi.org/10.1056/nejmoa2107659
Jackson, L. A., Anderson, E. J., Rouphael, N. G., Roberts, P. C., Makhene, M., Coler, R. N., McCullough, M. P., Chappell, J. D., Denison, M. R., Stevens, L. J., Pruijssers, A. J., McDermott, A., Flach, B., Doria-Rose, N. A., Corbett, K. S., Morabito, K. M., O’Dell, S., Schmidt, S. D., Swanson, P. A., … Beigel, J. H. (2020). An mRNA Vaccine against SARS-CoV-2 — Preliminary Report. New England Journal of Medicine, 383(20), 1920–1931. https://doi.org/10.1056/nejmoa2022483
Jiao, K. (2022). A brief introduction and evaluation of typical mRNA vaccine, inactivated vaccine, vectored vaccine, sub-unit vaccine for COVID protection. Advances in Social Science, Education and Humanities Research, 664, 279–285. https://doi.org/10.2991/assehr.k.220504.052
Khobragade, A., Bhate, S., Ramaiah, V., Deshpande, S., Giri, K., Phophle, H., Supe, P., Godara, I., Revanna, R., Nagarkar, R., Sanmukhani, J., Dey, A., Chozhavel Rajanathan, T. M., Kansagra, K., & Koradia, P. (2022). Efficacy, safety, and immunogenicity of the DNA SARS-CoV-2 vaccine (ZyCoV-D): The interim efficacy results of a phase 3, randomised, double-blind, placebo-controlled study in India. The Lancet, 399(10332), 1313–1321.
https://doi.org/10.1016/S0140-6736(22)00151-9
Logunov, D. Y., Dolzhikova, I. V., Shcheblyakov, D. V., Tukhvatulin, A. I., Zubkova, O. V., Dzharullaeva, A. S., Kovyrshina, A. V., Lubenets, N. L., Grousova, D. M., Erokhova, A. S., Botikov, A. G., Izhaeva, F. M., Popova, O., Ozharovskaya, T. A., Esmagambetov, I. B., Favorskaya, I. A., Zrelkin, D. I., Voronina, D. V., Shcherbinin, D. N., … Gintsburg, A. L. (2021). Safety and efficacy of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine: an interim analysis of a randomised controlled phase 3 trial in Russia. The Lancet, 397(10275), 671–681. https://doi.org/10.1016/S0140-6736(21)00234-8
Moreira, E. D., Kitchin, N., Xu, X., Dychter, S. S., Lockhart, S., Gurtman, A., Perez, J. L., Zerbini, C., Dever, M. E., Jennings, T. W., Brandon, D. M., Cannon, K. D., Koren, M. J., Denham, D. S., Berhe, M., Fitz-Patrick, D., Hammitt, L. L., Klein, N. P., Nell, H., … Jansen, K. U. (2022). Safety and Efficacy of a Third Dose of BNT162b2 Covid-19 Vaccine. New England Journal of Medicine, 386(20), 1910–1921. https://doi.org/10.1056/nejmoa2200674
Msemburi, W., Karlinsky, A., Knutson, V., Aleshin-Guendel, S., Chatterji, S., & Wakefield, J. (2023). The WHO estimates of excess mortality associated with the COVID-19 pandemic. Nature, 613(7942), 130–137. https://doi.org/10.1038/s41586-022-05522-2
Mulligan, M. J., Lyke, K. E., Kitchin, N., Absalon, J., Gurtman, A., Lockhart, S., Neuzil, K., Raabe, V., Bailey, R., Swanson, K. A., Li, P., Koury, K., Kalina, W., Cooper, D., Fontes-Garfias, C., Shi, P. Y., Türeci, Ö., Tompkins, K. R., Walsh, E. E., … Jansen, K. U. (2020). Phase I/II study of COVID-19 RNA vaccine BNT162b1 in adults. Nature, 586(7830), 589–593. https://doi.org/10.1038/s41586-020-2639-4
Noor, R. (2021). Developmental Status of the Potential Vaccines for the Mitigation of the COVID-19 Pandemic and a Focus on the Effectiveness of the Pfizer-BioNTech and Moderna mRNA Vaccines. https://doi.org/10.1007/s40588-021-00162-y/Published
Pardi, N., Hogan, M. J., Porter, F. W., & Weissman, D. (2018). mRNA vaccines-a new era in vaccinology. In Nature Reviews Drug Discovery (Vol. 17, Issue 4, pp. 261–279). Nature Publishing Group. https://doi.org/10.1038/nrd.2017.243
Park, J. W., Lagniton, P. N. P., Liu, Y., & Xu, R. H. (2021). Mrna vaccines for covid-19: What, why and how. In International Journal of Biological Sciences (Vol. 17, Issue 6, pp. 1446–1460). Ivyspring International Publisher. https://doi.org/10.7150/ijbs.59233
Polack, F. P., Thomas, S. J., Kitchin, N., Absalon, J., Gurtman, A., Lockhart, S., Perez, J. L., Pérez Marc, G., Moreira, E. D., Zerbini, C., Bailey, R., Swanson, K. A., Roychoudhury, S., Koury, K., Li, P., Kalina, W. V., Cooper, D., Frenck, R. W., Hammitt, L. L., … Gruber, W. C. (2020). Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine. New England Journal of Medicine, 383(27), 2603–2615. https://doi.org/10.1056/nejmoa2034577
Rodríguez-Chávez, S., Reyes-Zamora, M. C., Castro-Almarales, R. L., Vega-Valdés, J. C., Díaz-Barroso, Y., Rodríguez-Barrientos, D., & Izquierdo-Alfonso, N. (2023). Safety of SOBERANAS® vaccines in children of workers of a BioCubaFarma institution. VacciMonitor, 32. https://doi.org/10.1056/NEJMoa2116298
Saadh, M. J., & Jaber, S. A. (2022). Efficacy of COVID-19 vaccines. Microbial Pathogenesis, 171. https://doi.org/10.1016/j.micpath.2022.105729
Saddik, B., Elbarazi, I., Temsah, M. H., Saheb Sharif-Askari, F., Kheder, W., Hussein, A., Najim, H., Bendardaf, R., Hamid, Q., & Halwani, R. (2021). Psychological Distress and Anxiety Levels Among Health Care Workers at the Height of the COVID-19 Pandemic in the United Arab Emirates. International Journal of Public Health, 66. https://doi.org/10.3389/ijph.2021.1604369
Sadoff, J., Gray, G., Vandebosch, A., Cárdenas, V., Shukarev, G., Grinsztejn, B., Goepfert, P. A., Truyers, C., Fennema, H., Spiessens, B., Offergeld, K., Scheper, G., Taylor, K. L., Robb, M. L., Treanor, J., Barouch, D. H., Stoddard, J., Ryser, M. F., Marovich, M. A., … Douoguih, M. (2021). Safety and Efficacy of Single-Dose Ad26.COV2.S Vaccine against Covid-19. New England Journal of Medicine, 384(23), 2187–2201. https://doi.org/10.1056/nejmoa2101544
Sahin, U., Muik, A., Derhovanessian, E., Vogler, I., Kranz, L. M., Vormehr, M., Baum, A., Pascal, K., Quandt, J., Maurus, D., Brachtendorf, S., Lörks, V., Sikorski, J., Hilker, R., Becker, D., Eller, A. K., Grützner, J., Boesler, C., Rosenbaum, C., … Türeci, Ö. (2020). COVID-19 vaccine BNT162b1 elicits human antibody and TH1 T cell responses. Nature, 586(7830), 594–599. https://doi.org/10.1038/s41586-020-2814-7
Starostina, E. V., Sharabrin, S. V., Antropov, D. N., Stepanov, G. A., Shevelev, G. Y., Lemza, A. E., Rudometov, A. P., Borgoyakova, M. B., Rudometova, N. B., Marchenko, V. Y., Danilchenko, N. V., Chikaev, A. N., Bazhan, S. I., Ilyichev, A. A., & Karpenko, L. I. (2021). Construction and immunogenicity of modified mrna-vaccine variants encoding influenza virus antigens. Vaccines, 9(5). https://doi.org/10.3390/vaccines9050452
Tanriover, M. D., Doğanay, H. L., Akova, M., Güner, H. R., Azap, A., Akhan, S., Köse, Ş., Erdinç, F. Ş., Akalın, E. H., Tabak, Ö. F., Pullukçu, H., Batum, Ö., Şimşek Yavuz, S., Turhan, Ö., Yıldırmak, M. T., Köksal, İ., Taşova, Y., Korten, V., Yılmaz, G., … Aksu, K. (2021). Efficacy and safety of an inactivated whole-virion SARS-CoV-2 vaccine (CoronaVac): interim results of a double-blind, randomised, placebo-controlled, phase 3 trial in Turkey. The Lancet, 398(10296), 213–222. https://doi.org/10.1016/S0140-6736(21)01429-X
Thomas, S. J., Moreira, E. D., Kitchin, N., Absalon, J., Gurtman, A., Lockhart, S., Perez, J. L., Pérez Marc, G., Polack, F. P., Zerbini, C., Bailey, R., Swanson, K. A., Xu, X., Roychoudhury, S., Koury, K., Bouguermouh, S., Kalina, W. V., Cooper, D., Frenck, R. W., … Jansen, K. U. (2021). Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine through 6 Months. New England Journal of Medicine, 385(19), 1761–1773. https://doi.org/10.1056/nejmoa2110345
Udwadia, Z. F., Singh, P., Barkate, H., Patil, S., Rangwala, S., Pendse, A., Kadam, J., Wu, W., Caracta, C. F., & Tandon, M. (2021). Efficacy and safety of favipiravir, an oral RNA-dependent RNA polymerase inhibitor, in mild-to-moderate COVID-19: A randomized, comparative, open-label, multicenter, phase 3 clinical trial. International Journal of Infectious Diseases, 103, 62–71. https://doi.org/10.1016/j.ijid.2020.11.142
Verbeke, R., Lentacker, I., De Smedt, S. C., & Dewitte, H. (2021). The dawn of mRNA vaccines: The COVID-19 case. Journal of Controlled Release, 333, 511–520. https://doi.org/10.1016/j.jconrel.2021.03.043
Vogel, A. B., Kanevsky, I., Che, Y., Swanson, K. A., Muik, A., Vormehr, M., Kranz, L. M., Walzer, K. C., Hein, S., Güler, A., Loschko, J., Maddur, M. S., Ota-Setlik, A., Tompkins, K., Cole, J., Lui, B. G., Ziegenhals, T., Plaschke, A., Eisel, D., … Sahin, U. (2021). BNT162b vaccines protect rhesus macaques from SARS-CoV-2. Nature, 592(7853), 283–289. https://doi.org/10.1038/s41586-021-03275-y
Voysey, M., Clemens, S. A. C., Madhi, S. A., Weckx, L. Y., Folegatti, P. M., Aley, P. K., Angus, B., Baillie, V. L., Barnabas, S. L., Bhorat, Q. E., Bibi, S., Briner, C., Cicconi, P., Collins, A. M., Colin-Jones, R., Cutland, C. L., Darton, T. C., Dheda, K., Duncan, C. J. A., … Pollard, A. J. (2021). Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK. The Lancet, 397(10269), 99–111. https://doi.org/10.1016/S0140-6736(20)32661-1
World Health Organization. (2020, March 11). WHO Director-General’s opening remarks at the media briefing on COVID-19 - 11 March 2020. World Health Organization. https://www.who.int/director-general/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19---11-march-2020
World Health Organization. (2021). Coronavirus disease (COVID-19) pandemic. World Health Organization. https://www.who.int/emergencies/diseases/novel-coronavirus-2019
Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C. L., Abiona, O., Graham, B. S., & McLellan, J. S. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science, 367(6483), 1260–1263.
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