Development of a novel circular mRNA vaccine of six protein combinations against Staphylococcus aureus

References

• Abbas, A. K., Trotta, E. D. R. S., Marson, A., & Bluestone, J. A. (2018). Revisiting IL-2: Biology and therapeutic prospects. Science Immunology, 25, 3. https://doi.org/10.1126/sciimmunol.aat1482
   Google Scholar
• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Alfeo, M. J., Pagotto, A., Barbieri, G., Foster, T. J., Vanhoorelbeke, K., De Filippis, V., Speziale, P., & Pietrocola, G. (2021). Staphylococcus aureus iron-regulated surface determinant B (IsdB) protein interacts with von Willebrand factor and promotes adherence to endothelial cells. Scientific Reports, 11(1), 22799. https://doi.org/10.1038/s41598-021-02065-w
   PubMed Web of Science ®Google Scholar
• Antimicrobial Resistance. (2022). Global burden of bacterial antimicrobial resistance in 2019: A systematic analysis. The Lancet, 399(10325), 629–655. https://doi.org/10.1016/S0140-6736(21)02724-0
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Bahl, K., Senn, J. J., Yuzhakov, O., Bulychev, A., Brito, L. A., Hassett, K. J., Laska, M. E., Smith, M., Almarsson, Ö., Thompson, J., Ribeiro, A. M., Watson, M., Zaks, T., & Ciaramella, G. (2017). Preclinical and clinical demonstration of immunogenicity by mRNA vaccines against H10N8 and H7N9 influenza viruses. Molecular Therapy, 25(6), 1316–1327. https://doi.org/10.1016/j.ymthe.2017.03.035
   PubMed Web of Science ®Google Scholar
• Begier, E., Seiden, D. J., Patton, M., Zito, E., Severs, J., Cooper, D., Eiden, J., Gruber, W. C., Jansen, K. U., Anderson, A. S., & Gurtman, A. (2017). SA4Ag, a 4-antigen Staphylococcus aureus vaccine, rapidly induces high levels of bacteria-killing antibodies. Vaccine, 35(8), 1132–1139. https://doi.org/10.1016/j.vaccine.2017.01.024
   PubMed Web of Science ®Google Scholar
• 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
   Web of Science ®Google Scholar
• Bui, H. H., Sidney, J., Dinh, K., Southwood, S., Newman, M. J., & Sette, A. (2006). Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics, 7(1), 153. https://doi.org/10.1186/1471-2105-7-153
   PubMed Web of Science ®Google Scholar
• Cabrera, R., Fernández-Barat, L., Motos, A., López-Aladid, R., Vázquez, N., Panigada, M., Álvarez-Lerma, F., López, Y., Muñoz, L., Castro, P., Vila, J., & Torres, A. (2020). Molecular characterization of methicillin-resistant Staphylococcus aureus clinical strains from the endotracheal tubes of patients with nosocomial pneumonia. Antimicrobial Resistance and Infection Control, 9(1), 43. https://doi.org/10.1186/s13756-020-0679-z
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Chambers, H. F., & Deleo, F. R. (2009). Waves of resistance: Staphylococcus aureus in the antibiotic era. Nature Reviews. Microbiology, 7(9), 629–641. https://doi.org/10.1038/nrmicro2200
   PubMed Web of Science ®Google Scholar
• Chauhan, V., Rungta, T., Rawat, M., Goyal, K., Gupta, Y., & Singh, M. P. (2021). Excavating SARS-coronavirus 2 genome for epitope-based subunit vaccine synthesis using immunoinformatics approach. Journal of Cellular Physiology, 236(2), 1131–1147. https://doi.org/10.1002/jcp.29923
   PubMed Web of Science ®Google Scholar
• Chen, C., Li, Z., Huang, H., Suzek, B. E., Wu, C. H., & UniProt, C. (2013). A fast peptide match service for UniProt knowledgebase. Bioinformatics (Oxford, England), 29(21), 2808–2809. https://doi.org/10.1093/bioinformatics/btt484
   PubMed Web of Science ®Google Scholar
• Cohen, I., Coban, M., Shahar, A., Sankaran, B., Hockla, A., Lacham, S., Caulfield, T. R., Radisky, E. S., & Papo, N. (2019). Disulfide engineering of human Kunitz-type serine protease inhibitors enhances proteolytic stability and target affinity toward mesotrypsin. The Journal of Biological Chemistry, 294(13), 5105–5120. https://doi.org/10.1074/jbc.RA118.007292
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Craig, D. B., & Dombkowski, A. A. (2013). Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins. BMC Bioinformatics, 14, 346. https://doi.org/10.1186/1471-2105-14-346
   PubMed Web of Science ®Google Scholar
• Dalla Serra, M., Coraiola, M., Viero, G., Comai, M., Potrich, C., Ferreras, M., Baba-Moussa, L., Colin, D. A., Menestrina, G., Bhakdi, S., & Prévost, G. (2005). Staphylococcus aureus bicomponent gamma-hemolysins, HlgA, HlgB, and HlgC, can form mixed pores containing all components. Journal of Chemical Information and Modelling, 45(6), 1539–1545. https://doi.org/10.1021/ci050175y
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: AnN⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Dey, J., Mahapatra, S. R., Lata, S., Patro, S., Misra, N., & Suar, M. (2022). Exploring Klebsiella pneumoniae capsule polysaccharide proteins to design multiepitope subunit vaccine to fight against pneumonia. Expert Review of Vaccines, 21(4), 569–587. https://doi.org/10.1080/14760584.2022.2021882
   PubMed Web of Science ®Google Scholar
• Dey, J., Mahapatra, S. R., Patnaik, S., Lata, S., Kushwaha, G. S., Panda, R. K., Misra, N., & Suar, M. (2022). Molecular characterization and designing of a novel multiepitope vaccine construct against Pseudomonas aeruginosa. International Journal of Peptide Research and Therapeutics, 28(2), 49. https://doi.org/10.1007/s10989-021-10356-z
   PubMed Web of Science ®Google Scholar
• Dey, J., Mahapatra, S. R., Raj, T. K., Kaur, T., Jain, P., Tiwari, A., Patro, S., Misra, N., & Suar, M. (2022). Designing a novel multi-epitope vaccine to evoke a robust immune response against pathogenic multidrug-resistant Enterococcus faecium bacterium. Gut Pathogens, 14(1), 21. https://doi.org/10.1186/s13099-022-00495-z
   PubMed Web of Science ®Google Scholar
• Dey, J., Mahapatra, S. R., Singh, P., Patro, S., Kushwaha, G. S., Misra, N., & Suar, M. (2021). B and T cell epitope-based peptides predicted from clumping factor protein of Staphylococcus aureus as vaccine targets. Microbial Pathogenesis, 160, 105171. https://doi.org/10.1016/j.micpath.2021.105171
   PubMed Web of Science ®Google Scholar
• Dhanda, S. K., Gupta, S., Vir, P., & Raghava, G. P. (2013). Prediction of IL4 inducing peptides. Clinical & Developmental Immunology, 2013, 263952. https://doi.org/10.1155/2013/263952
   PubMedGoogle Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Dimitrov, I., Bangov, I., Flower, D. R., & Doytchinova, I. (2014). AllerTOP v.2–a server for in silico prediction of allergens. Journal of Molecular Modelling, 20(6), 2278. https://doi.org/10.1007/s00894-014-2278-5
   PubMed Web of Science ®Google Scholar
• Dombkowski, A. A., Sultana, K. Z., & Craig, D. B. (2014). Protein disulfide engineering. FEBS Letters, 588(2), 206–212. https://doi.org/10.1016/j.febslet.2013.11.024
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Edwards, A. M., Potts, J. R., Josefsson, E., & Massey, R. C. (2010). Staphylococcus aureus host cell invasion and virulence in sepsis is facilitated by the multiple repeats within FnBPA. PLoS Pathogens, 6(6), e1000964. https://doi.org/10.1371/journal.ppat.1000964
   PubMed Web of Science ®Google Scholar
• Ford, E., & Ares, M. Jr. (1994). Synthesis of circular RNA in bacteria and yeast using RNA cyclase ribozymes derived from a group I intron of phage T4. Proceedings of the National Academy of Sciences of the United States of America, 91(8), 3117–3121. https://doi.org/10.1073/pnas.91.8.3117
   PubMed Web of Science ®Google Scholar
• Francois, B., Mercier, E., Gonzalez, C., Asehnoune, K., Nseir, S., Fiancette, M., Desachy, A., Plantefève, G., Meziani, F., de Lame, P.-A., & Laterre, P.-F. (2018). Safety and tolerability of a single administration of AR-301, a human monoclonal antibody, in ICU patients with severe pneumonia caused by Staphylococcus aureus: first-in-human trial. Intensive Care Medicine, 44(11), 1787–1796. https://doi.org/10.1007/s00134-018-5229-2
   PubMed Web of Science ®Google Scholar
• Frenck, R. W., Creech, C. B., Sheldon, E. A., Seiden, D. J., Kankam, M. K., Baber, J., Zito, E., Hubler, R., Eiden, J., Severs, J. M., Sebastian, S., Nanra, J., Jansen, K. U., Gruber, W. C., Anderson, A. S., & Girgenti, D. (2017). Safety, tolerability, and immunogenicity of a 4-antigen Staphylococcus aureus vaccine (SA4Ag): Results from a first-in-human randomised, placebo-controlled phase 1/2 study. Vaccine, 35(2), 375–384. https://doi.org/10.1016/j.vaccine.2016.11.010
   PubMed Web of Science ®Google Scholar
• Geriak, M., Haddad, F., Rizvi, K., Rose, W., Kullar, R., LaPlante, K., Yu, M., Vasina, L., Ouellette, K., Zervos, M., Nizet, V., & Sakoulas, G. (2019). Clinical data on daptomycin plus ceftaroline versus standard of care monotherapy in the treatment of methicillin-resistant Staphylococcus aureus bacteremia. Antimicrobial Agents and Chemotherapy, 63(5), e02483-18. https://doi.org/10.1128/AAC.02483-18
   Web of Science ®Google Scholar
• Gianquinto, E., Moscetti, I., De Bei, O., Campanini, B., Marchetti, M., Luque, F. J., Cannistraro, S., Ronda, L., Bizzarri, A. R., Spyrakis, F., & Bettati, S. (2019). Interaction of human hemoglobin and semi-hemoglobins with the Staphylococcus aureus hemophore IsdB: A kinetic and mechanistic insight. Scientific Reports, 9(1), 18629. https://doi.org/10.1038/s41598-019-54970-w
   PubMedGoogle Scholar
• Graille, M., Stura, E. A., Corper, A. L., Sutton, B. J., Taussig, M. J., Charbonnier, J. B., & Silverman, G. J. (2000). Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: Structural basis for recognition of B-cell receptors and superantigen activity. Proceedings of the National Academy of Sciences of the United States of America, 97(10), 5399–5404. https://doi.org/10.1073/pnas.97.10.5399
   PubMed Web of Science ®Google Scholar
• Grote, A., Hiller, K., Scheer, M., Munch, R., Nortemann, 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
   PubMed Web of Science ®Google Scholar
• Guo, Y., Song, G., Sun, M., Wang, J., & Wang, Y. (2020). Prevalence and therapies of antibiotic-resistance in Staphylococcus aureus. Frontiers in Cellular and Infection Microbiology, 10, 107. https://doi.org/10.3389/fcimb.2020.00107
   PubMed Web of Science ®Google Scholar
• Gupta, S., Kapoor, P., Chaudhary, K., Gautam, A., Kumar, R., Open Source Drug Discovery, C., & Raghava, G. P. (2013). In silico approach for predicting toxicity of peptides and proteins. PLoS One, 8(9), e73957. https://doi.org/10.1371/journal.pone.0073957
   PubMed Web of Science ®Google Scholar
• Hallgren, J., Tsirigos, K. D., Pedersen, M. D., Almagro Armenteros, J. J., Marcatili, P., Nielsen, H., Krogh, A., & Winther, O. (2022). DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. https://doi.org/10.1101/2022.04.08.487609
   Google Scholar
• Hess, B. (2008). P-LINCS: A parallel linear constraint solver for molecular simulation. Journal of Chemical Theory and Computation, 4(1), 116–122. https://doi.org/10.1021/ct700200b
   PubMed Web of Science ®Google Scholar
• Hussain, S., Joo, J., Kang, J., Kim, B., Braun, G. B., She, Z.-G., Kim, D., Mann, A. P., Mölder, T., Teesalu, T., Carnazza, S., Guglielmino, S., Sailor, M. J., & Ruoslahti, E. (2018). Antibiotic-loaded nanoparticles targeted to the site of infection enhance antibacterial efficacy. Nature Biomedical Engineering, 2(2), 95–103. https://doi.org/10.1038/s41551-017-0187-5
   PubMed Web of Science ®Google Scholar
• Hussain, M., Kohler, C., & Becker, K. (2022). Enolase of Staphylococcus lugdunensis is a surface-exposed moonlighting protein that binds to extracellular matrix and the plasminogen/plasmin system. Frontiers in Microbiology, 13, 837297. https://doi.org/10.3389/fmicb.2022.837297
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Jun, S. Y., Jang, I. J., Yoon, S., Jang, K., Yu, K.-S., Cho, J. Y., Seong, M.-W., Jung, G. M., Yoon, S. J., & Kang, S. H. (2017). Pharmacokinetics and tolerance of the phage endolysin-based candidate drug SAL200 after a single intravenous administration among healthy volunteers. Antimicrobial Agents and Chemotherapy, 61(6), e02629-16. https://doi.org/10.1128/AAC.02629-16
   PubMed Web of Science ®Google Scholar
• Junttila, I. S. (2018). Tuning the cytokine responses: An update on interleukin (IL)-4 and IL-13 receptor complexes. Frontiers in Immunology, 9, 888. https://doi.org/10.3389/fimmu.2018.00888
   PubMed Web of Science ®Google Scholar
• Kak, G., Raza, M., & Tiwari, B. K. (2018). Interferon-gamma (IFN-gamma): Exploring its implications in infectious diseases. Biomolecular Concepts, 9(1), 64–79. https://doi.org/10.1515/bmc-2018-0007
   PubMedGoogle Scholar
• Khan, S., Shaker, B., Ahmad, S., Abbasi, S. W., Arshad, M., Haleem, A., Ismail, S., Zaib, A., & Sajjad, W. (2021). Towards a novel peptide vaccine for Middle East respiratory syndrome coronavirus and its possible use against pandemic COVID-19. Journal of Molecular Liquids, 324, 114706. https://doi.org/10.1016/j.molliq.2020.114706
   PubMed Web of Science ®Google Scholar
• Khodadadi, M., Ghaffarifar, F., Dalimi, A., & Ahmadpour, E. (2021). Immunogenicity of in-silico designed multi-epitope DNA vaccine encoding SAG1, SAG3 and SAG5 of Toxoplasma gondii adjuvanted with CpG-ODN against acute toxoplasmosis in BALB/c mice. Acta Tropica, 216, 105836. https://doi.org/10.1016/j.actatropica.2021.105836
   PubMed Web of Science ®Google Scholar
• Kim, S. C., Sekhon, S. S., Shin, W. R., Ahn, G., Cho, B. K., Ahn, J. Y., & Kim, Y. H. (2022). Modifications of mRNA vaccine structural elements for improving mRNA stability and translation efficiency. Molecular & Cellular Toxicology, 18(1), 1–8. https://doi.org/10.1007/s13273-021-00171-4
   PubMed Web of Science ®Google Scholar
• Ko, J., Park, H., Heo, L., & Seok, C. (2012). GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Research, 40(Web Server issue), W294–297. https://doi.org/10.1093/nar/gks493
   PubMed Web of Science ®Google Scholar
• Kohlgraf, K. G., Pingel, L. C., Dietrich, D. E., & Brogden, K. A. (2010). Defensins as anti-inflammatory compounds and mucosal adjuvants. Future Microbiology, 5(1), 99–113. https://doi.org/10.2217/fmb.09.104
   PubMed Web of Science ®Google Scholar
• Kou, Y., Xu, Y., Zhao, Z., Liu, J., Wu, Y., You, Q., Wang, L., Gao, F., Cai, L., & Jiang, C. (2017). Tissue plasminogen activator (tPA) signal sequence enhances immunogenicity of MVA-based vaccine against tuberculosis. Immunology Letters, 190, 51–57. https://doi.org/10.1016/j.imlet.2017.07.007
   PubMed Web of Science ®Google Scholar
• Krautler, N. J., Suan, D., Butt, D., Bourne, K., Hermes, J. R., Chan, T. D., Sundling, C., Kaplan, W., Schofield, P., Jackson, J., Basten, A., Christ, D., & Brink, R. (2017). Differentiation of germinal centre B cells into plasma cells is initiated by high-affinity antigen and completed by Tfh cells. The Journal of Experimental Medicine, 214(5), 1259–1267. https://doi.org/10.1084/jem.20161533
   PubMed Web of Science ®Google Scholar
• Kreiter, S., Selmi, A., Diken, M., Sebastian, M., Osterloh, P., Schild, H., Huber, C., Türeci, O., & Sahin, U. (2008). Increased antigen presentation efficiency by coupling antigens to MHC class I trafficking signals. Journal of Immunology (Baltimore, Md. : 1950), 180(1), 309–318. https://doi.org/10.4049/jimmunol.180.1.309
   PubMed Web of Science ®Google Scholar
• Kurcinski, M., Jamroz, M., Blaszczyk, M., Kolinski, A., & Kmiecik, S. (2015). CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site. Nucleic Acids Research, 43(W1), W419–424. https://doi.org/10.1093/nar/gkv456
   PubMed Web of Science ®Google Scholar
• Lamiable, A., Thevenet, P., Rey, J., Vavrusa, M., Derreumaux, P., & Tuffery, P. (2016). PEP-FOLD3: Faster de novo structure prediction for linear peptides in solution and in complex. Nucleic Acids Research, 44(W1), W449–454. https://doi.org/10.1093/nar/gkw329
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., Rullmannn, J. A., MacArthur, M. W., Kaptein, R., & Thornton, J. M. (1996). AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. Journal of Biomolecular NMR, 8(4), 477–486. https://doi.org/10.1007/BF00228148
   PubMed Web of Science ®Google Scholar
• Li, G., Huang, Z., Zhang, C., Dong, B.-J., Guo, R.-H., Yue, H.-W., Yan, L.-T., & Xing, X.-H. (2016). Construction of a linker library with widely controllable flexibility for fusion protein design. Applied Microbiology and Biotechnology, 100(1), 215–225. https://doi.org/10.1007/s00253-015-6985-3
   PubMed Web of Science ®Google Scholar
• Li, W., Joshi, M. D., Singhania, S., Ramsey, K. H., & Murthy, A. K. (2014). Peptide vaccine: Progress and challenges. Vaccines, 2(3), 515–536. https://doi.org/10.3390/vaccines2030515
   PubMedGoogle Scholar
• Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins, 78(8), 1950–1958. https://doi.org/10.1002/prot.22711
   PubMed Web of Science ®Google Scholar
• Liu, X., Zhang, Y., Zhou, S., Dain, L., Mei, L., & Zhu, G. (2022). Circular RNA: An emerging frontier in RNA therapeutic targets, RNA therapeutics, and mRNA vaccines. Journal of Controlled Release, 348, 84–94. https://doi.org/10.1016/j.jconrel.2022.05.043
   PubMed Web of Science ®Google Scholar
• Livingston, B., Crimi, C., Newman, M., Higashimoto, Y., Appella, E., Sidney, J., & Sette, A. (2002). A rational strategy to design multiepitope immunogens based on multiple Th lymphocyte epitopes. Journal of Immunology (Baltimore, Md.: 1950), 168(11), 5499–5506. https://doi.org/10.4049/jimmunol.168.11.5499
   PubMed Web of Science ®Google Scholar
• Lopez-Blanco, J. R., Aliaga, J. I., Quintana-Orti, E. S., & Chacon, P. (2014). iMODS: Internal coordinates normal mode analysis server. Nucleic Acids Research, 42(Web Server issue), W271–276. https://doi.org/10.1093/nar/gku339
   PubMed Web of Science ®Google Scholar
• Madeira, F., Pearce, M., Tivey, A. R. N., Basutkar, P., Lee, J., Edbali, O., … Lopez, R. (2022). Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Research, 50(W1), W276–9. https://doi.org/10.1093/nar/gkac240
   Web of Science ®Google Scholar
• Mahapatra, S. R., Dey, J., Jaiswal, A., Roy, R., Misra, N., & Suar, M. (2022). Immunoinformatics-guided designing of epitope-based subunit vaccine from Pilus assembly protein of Acinetobacter baumannii bacteria. Journal of Immunological Methods, 508, 113325. https://doi.org/10.1016/j.jim.2022.113325
   PubMed Web of Science ®Google Scholar
• Mahapatra, S. R., Dey, J., Kushwaha, G. S., Puhan, P., Mohakud, N. K., Panda, S. K., Lata, S., Misra, N., & Suar, M. (2021). Immunoinformatic approach employing modelling and simulation to design a novel vaccine construct targeting MDR efflux pumps to confer wide protection against typhoidal Salmonella serovars. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2021.1964600
   Web of Science ®Google Scholar
• Mahapatra, S. R., Dey, J., Raj, T. K., Kumar, V., Ghosh, M., Verma, K. K., Kaur, T., Kesawat, M. S., Misra, N., & Suar, M. (2022). The potential of plant-derived secondary metabolites as novel drug candidates against Klebsiella pneumoniae: Molecular docking and simulation investigation. South African Journal of Botany, 149, 789–797. https://doi.org/10.1016/j.sajb.2022.04.043
   PubMed Web of Science ®Google Scholar
• Mele, T., & Madrenas, J. (2010). TLR2 signalling: At the crossroads of commensalism, invasive infections and toxic shock syndrome by Staphylococcus aureus. The International Journal of Biochemistry & Cell Biology, 42(7), 1066–1071. https://doi.org/10.1016/j.biocel.2010.03.021
   PubMed Web of Science ®Google Scholar
• Meyer, F., Girardot, R., Piemont, Y., Prevost, G., & Colin, D. A. (2009). Analysis of the specificity of panton-valentine leucocidin and gamma-hemolysin F component binding. Infection and Immunity, 77(1), 266–273. https://doi.org/10.1128/IAI.00402-08
   PubMed Web of Science ®Google Scholar
• Miller, L. S., Fowler, V. G., Shukla, S. K., Rose, W. E., & Proctor, R. A. (2020). Development of a vaccine against Staphylococcus aureus invasive infections: Evidence based on human immunity, genetics and bacterial evasion mechanisms. FEMS Microbiology Reviews, 44(1), 123–153. https://doi.org/10.1093/femsre/fuz030
   PubMed Web of Science ®Google Scholar
• Nain, Z., Abdulla, F., Rahman, M. M., Karim, M. M., Khan, M. S. A., Sayed, S. B., Mahmud, S., Rahman, S. M. R., Sheam, M. M., Haque, Z., & Adhikari, U. K. (2020). Proteome-wide screening for designing a multi-epitope vaccine against emerging pathogen Elizabethkingia anophelis using immunoinformatic approaches. Journal of Biomolecular Structure & Dynamics, 38(16), 4850–4867. https://doi.org/10.1080/07391102.2019.1692072
   PubMed Web of Science ®Google Scholar
• Narang, P. K., Dey, J., Mahapatra, S. R., Ghosh, M., Misra, N., Suar, M., Kumar, V., & Raina, V. (2021a). Functional annotation and sequence-structure characterization of a hypothetical protein putatively involved in carotenoid biosynthesis in microalgae. South African Journal of Botany, 141, 219–226. https://doi.org/10.1016/j.sajb.2021.04.014
   Web of Science ®Google Scholar
• Narang, P. K., Dey, J., Mahapatra, S. R., Roy, R., Kushwaha, G. S., Misra, N., Suar, M., & Raina, V. (2021b). Genome-based identification and comparative analysis of enzymes for carotenoid biosynthesis in microalgae. World Journal of Microbiology & Biotechnology, 38(1), 8. https://doi.org/10.1007/s11274-021-03188-y
   PubMed Web of Science ®Google Scholar
• Olson, R., Nariya, H., Yokota, K., Kamio, Y., & Gouaux, E. (1999). Crystal structure of staphylococcal LukF delineates conformational changes accompanying formation of a transmembrane channel. Nature Structural Biology, 6(2), 134–140. https://doi.org/10.1038/5821
   PubMedGoogle Scholar
• 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
   Web of Science ®Google Scholar
• Paul, S., Sidney, J., Sette, A., & Peters, B. (2016). TepiTool: A pipeline for computational prediction of T cell epitope candidates. Current Protocols in Immunology, 114, 18.19.1–18.19.24. https://doi.org/10.1002/cpim.12
   PubMedGoogle Scholar
• Peck, M., Rothenberg, M. E., Deng, R., Lewin-Koh, N., She, G., Kamath, A. V., Carrasco-Triguero, M., Saad, O., Castro, A., Teufel, L., Dickerson, D. S., Leonardelli, M., & Tavel, J. A. (2019). A Phase 1, randomized, single-ascending-dose study to investigate the safety, tolerability, and pharmacokinetics of DSTA4637S, an anti-Staphylococcus aureus thiomab antibody-antibiotic conjugate, in healthy volunteers. Antimicrobial Agents and Chemotherapy, 63(6), e02588-18. https://doi.org/10.1128/AAC.02588-18
   PubMed Web of Science ®Google Scholar
• 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. The New England Journal of Medicine, 383(27), 2603–2615. https://doi.org/10.1056/NEJMoa2034577
   PubMed Web of Science ®Google Scholar
• Pollard, A. J., Perrett, K. P., & Beverley, P. C. (2009). Maintaining protection against invasive bacteria with protein-polysaccharide conjugate vaccines. Nature Reviews. Immunology, 9(3), 213–220. https://doi.org/10.1038/nri2494
   PubMed Web of Science ®Google Scholar
• Ponomarenko, J., Bui, H. H., Li, W., Fusseder, N., Bourne, P. E., Sette, A., & Peters, B. (2008). ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics, 9, 514. https://doi.org/10.1186/1471-2105-9-514
   PubMed Web of Science ®Google Scholar
• Puttaraju, M., & Been, M. D. (1992). Group I permuted intron-exon (PIE) sequences self-splice to produce circular exons. Nucleic Acids Research, 20(20), 5357–5364. https://doi.org/10.1093/nar/20.20.5357
   PubMed Web of Science ®Google Scholar
• Qu, L., Yi, Z., Shen, Y., Lin, L., Chen, F., Xu, Y., Wu, Z., Tang, H., Zhang, X., Tian, F., Wang, C., Xiao, X., Dong, X., Guo, L., Lu, S., Yang, C., Tang, C., Yang, Y., Yu, W., … Wei, W. (2022). Circular RNA vaccines against SARS-CoV-2 and emerging variants. Cell, 185(10), 1728–1744.e16. https://doi.org/10.1016/j.cell.2022.03.044
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Reynisson, B., Barra, C., Kaabinejadian, S., Hildebrand, W. H., Peters, B., & Nielsen, M. (2020). Improved prediction of MHC II antigen presentation through integration and motif deconvolution of mass spectrometry MHC eluted ligand data. Journal of Proteome Research, 19(6), 2304–2315. https://doi.org/10.1021/acs.jproteome.9b00874
   PubMed Web of Science ®Google Scholar
• Richner, J. M., Himansu, S., Dowd, K. A., Butler, S. L., Salazar, V., Fox, J. M., Julander, J. G., Tang, W. W., Shresta, S., Pierson, T. C., Ciaramella, G., & Diamond, M. S. (2017). Modified mRNA vaccines protect against zika virus infection. Cell, 168(6), 1114–1125.e10. e1110. https://doi.org/10.1016/j.cell.2017.02.017
   PubMed Web of Science ®Google Scholar
• Rigi, G., Ghaedmohammadi, S., & Ahmadian, G. (2019). A comprehensive review on staphylococcal protein A (SpA): Its production and applications. Biotechnology and Applied Biochemistry, 66(3), 454–464. https://doi.org/10.1002/bab.1742
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Sakr, A., Bregeon, F., Mege, J. L., Rolain, J. M., & Blin, O. (2018). Staphylococcus aureus nasal colonization: An update on mechanisms, epidemiology, risk factors, and subsequent infections. Frontiers in Microbiology, 9, 2419. https://doi.org/10.3389/fmicb.2018.02419
   PubMed Web of Science ®Google Scholar
• Sapay, N., Guermeur, Y., & Deleage, G. (2006). Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier. BMC Bioinformatics, 7, 255. https://doi.org/10.1186/1471-2105-7-255
   PubMed Web of Science ®Google Scholar
• Schmidt, C. S., White, C. J., Ibrahim, A. S., Filler, S. G., Fu, Y., Yeaman, M. R., Edwards, J. E., & Hennessey, J. P. Jr. (2012). NDV-3, a recombinant alum-adjuvanted vaccine for Candida and Staphylococcus aureus, is safe and immunogenic in healthy adults. Vaccine, 30(52), 7594–7600. https://doi.org/10.1016/j.vaccine.2012.10.038
   PubMed Web of Science ®Google Scholar
• Shang, W., Hu, Q., Yuan, W., Cheng, H., Yang, J., Hu, Z., Yuan, J., Zhang, X., Peng, H., Yang, Y., Hu, X., Li, M., Zhu, J., & Rao, X. (2016). Comparative fitness and determinants for the characteristic drug resistance of ST239-MRSA-III-t030 and ST239-MRSA-III-t037 strains isolated in China. Microbial Drug Resistance (Larchmont, N.Y.), 22(3), 185–192. https://doi.org/10.1089/mdr.2015.0226
   PubMed Web of Science ®Google Scholar
• Sharma, N., Patiyal, S., Dhall, A., Pande, A., Arora, C., & Raghava, G. P. S. (2021). AlgPred 2.0: An improved method for predicting allergenic proteins and mapping of IgE epitopes. Brief Bioinform, 22(4), bbaa294. https://doi.org/10.1093/bib/bbaa294
   Web of Science ®Google Scholar
• Sinha, B., François, P. P., Nüsse, O., Foti, M., Hartford, O. M., Vaudaux, P., Foster, T. J., Lew, D. P., Herrmann, M., & Krause, K. H. (1999). Fibronectin-binding protein acts as Staphylococcus aureus invasin via fibronectin bridging to integrin alpha5beta1. Cellular Microbiology, 1(2), 101–117. https://doi.org/10.1046/j.1462-5822.1999.00011.x
   PubMed Web of Science ®Google Scholar
• Szabo, G. T., Mahiny, A. J., & Vlatkovic, I. (2022). COVID-19 mRNA vaccines: Platforms and current developments. Molecular Therapy, 30(5), 1850–1868. https://doi.org/10.1016/j.ymthe.2022.02.016
   PubMed Web of Science ®Google Scholar
• Tahir Ul Qamar, M., Ahmad, S., Fatima, I., Ahmad, F., Shahid, F., Naz, A., Abbasi, S. W., Khan, A., Mirza, M. U., Ashfaq, U. A., & Chen, L.-L. (2021). Designing multi-epitope vaccine against Staphylococcus aureus by employing subtractive proteomics, reverse vaccinology and immuno-informatics approaches. Computers in Biology and Medicine, 132, 104389. https://doi.org/10.1016/j.compbiomed.2021.104389
   PubMed Web of Science ®Google Scholar
• Tarrahimofrad, H., Rahimnahal, S., Zamani, J., Jahangirian, E., & Aminzadeh, S. (2021). Designing a multi-epitope vaccine to provoke the robust immune response against influenza A H7N9. Scientific Reports, 11(1), 24485. https://doi.org/10.1038/s41598-021-03932-2
   PubMed Web of Science ®Google Scholar
• Teufel, F., Almagro Armenteros, J. J., Johansen, A. R., Gíslason, M. H., Pihl, S. I., Tsirigos, K. D., Winther, O., Brunak, S., von Heijne, G., & Nielsen, H. (2022). SignalP 6.0 predicts all five types of signal peptides using protein language models. Nature Biotechnology, 40(7), 1023–1025. https://doi.org/10.1038/s41587-021-01156-3
   PubMed Web of Science ®Google Scholar
• Thess, A., Grund, S., Mui, B. L., Hope, M. J., Baumhof, P., Fotin-Mleczek, M., & Schlake, T. (2015). Sequence-engineered mRNA without chemical nucleoside modifications enables an effective protein therapy in large animals. Molecular Therapy, 23(9), 1456–1464. https://doi.org/10.1038/mt.2015.103
   PubMed Web of Science ®Google Scholar
• Tomlinson, B. R., Malof, M. E., & Shaw, L. N. (2021). A global transcriptomic analysis of Staphylococcus aureus biofilm formation across diverse clonal lineages. Microbial Genomics, 7(7). https://doi.org/10.1099/mgen.0.000598
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• 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 Modelling of Biomolecular Complexes. Journal of Molecular Biology, 428(4), 720–725. https://doi.org/10.1016/j.jmb.2015.09.014
   PubMed Web of Science ®Google Scholar
• Waman, V. P., Sen, N., Varadi, M., Daina, A., Wodak, S. J., Zoete, V., Velankar, S., & Orengo, C. (2021). The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. Briefings in Bioinformatics, 22(2), 742–768. https://doi.org/10.1093/bib/bbaa362
   PubMed Web of Science ®Google Scholar
• Wang, X., Wang, C., Wu, M., Tian, T., Cheng, T., Zhang, X., & Zang, J. (2017). Enolase binds to RnpA in competition with PNPase in Staphylococcus aureus. FEBS Letters, 591(21), 3523–3535. https://doi.org/10.1002/1873-3468.12859
   PubMed Web of Science ®Google Scholar
• Wang, Y., Zhang, Z., Luo, J., Han, X., Wei, Y., & Wei, X. (2021). mRNA vaccine: A potential therapeutic strategy. Molecular Cancer, 20(1), 33. https://doi.org/10.1186/s12943-021-01311-z
   PubMed Web of Science ®Google Scholar
• Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303. https://doi.org/10.1093/nar/gky427
   PubMed Web of Science ®Google Scholar
• Wesselhoeft, R. A., Kowalski, P. S., & Anderson, D. G. (2018). Engineering circular RNA for potent and stable translation in eukaryotic cells. Nature Communications, 9(1), 2629. https://doi.org/10.1038/s41467-018-05096-6
   PubMed Web of Science ®Google Scholar
• Wesselhoeft, R. A., Kowalski, P. S., Parker-Hale, F. C., Huang, Y., Bisaria, N., & Anderson, D. G. (2019). RNA circularization diminishes immunogenicity and can extend translation duration in vivo. Molecular Cell, 74(3), 508–520.e4. e504. https://doi.org/10.1016/j.molcel.2019.02.015
   PubMed Web of Science ®Google Scholar
• Wilkins, M. R., Gasteiger, E., Bairoch, A., Sanchez, J. C., Williams, K. L., Appel, R. D., & Hochstrasser, D. F. (1999). Protein identification and analysis tools in the ExPASy server. Methods in Molecular Biology (Clifton, N.J.), 112, 531–552. https://doi.org/10.1385/1-59259-584-7:531
   PubMedGoogle Scholar
• Williams, R. E., Jevons, M. P., Shooter, R. A., Hunter, C. J., Girling, J. A., Griffiths, J. D., & Taylor, G. W. (1959). Nasal staphylococci and sepsis in hospital patients. British Medical Journal, 2(5153), 658–662. https://doi.org/10.1136/bmj.2.5153.658
   PubMedGoogle Scholar
• Xu, Z., Shi, L., Wang, Y., Zhang, J., Huang, L., Zhang, C., Liu, S., Zhao, P., Liu, H., Zhu, L., Tai, Y., Bai, C., Gao, T., Song, J., Xia, P., Dong, J., Zhao, J., & Wang, F.-S. (2020). Pathological findings of COVID-19 associated with acute respiratory distress syndrome. The Lancet. Respiratory Medicine, 8(4), 420–422. https://doi.org/10.1016/S2213-2600(20)30076-X
   PubMed Web of Science ®Google Scholar
• Xu, S., Yang, K., Li, R., & Zhang, L. (2020). mRNA vaccine era-mechanisms, drug platform and clinical prospection. International Journal of Molecular Sciences, 21(18), 6582. https://doi.org/10.3390/ijms21186582
   PubMed Web of Science ®Google Scholar
• Yoshitani, J., Kabata, T., Arakawa, H., Kato, Y., Nojima, T., Hayashi, K., Tokoro, M., Sugimoto, N., Kajino, Y., Inoue, D., Ueoka, K., Yamamuro, Y., & Tsuchiya, H. (2020). Combinational therapy with antibiotics and antibiotic-loaded adipose-derived stem cells reduce abscess formation in implant-related infection in rats. Scientific Reports, 10(1), 11182. https://doi.org/10.1038/s41598-020-68184-y
   PubMed Web of Science ®Google Scholar
• Zeng, H., Yang, F., Feng, Q., Zhang, J., Gu, J., Jing, H., Cai, C., Xu, L., Yang, X., Xia, X., Zeng, N., Fan, S., & Zou, Q. (2020). Rapid and broad immune efficacy of a recombinant five-antigen vaccine against Staphylococcus Aureus infection in animal models. Vaccines (Basel), 8(1), 134. https://doi.org/10.3390/vaccines8010134
   PubMed Web of Science ®Google Scholar