An immunoinformatic approach towards development of a potent and effective multi-epitope vaccine against monkeypox virus (MPXV)

References

• Abdelmageed, M. I., Abdelmoneim, A. H., Mustafa, M. I., Elfadol, N. M., Murshed, N. S., Shantier, S. W., & Makhawi, A. M. (2020). Design of a multiepitope-based peptide vaccine against the E protein of human COVID-19: An immunoinformatics approach. BioMed Research International, 2020, 1–12. https://doi.org/10.1155/2020/2683286
   Web of Science ®Google Scholar
• Abdi, S. A. H., Ali, A., Sayed, S. F., Abutahir, Ali, A., & Alam, P. (2022). Multi-epitope-based vaccine candidate for monkeypox: An in silico approach. Vaccines, 10(9), 1564. https://doi.org/10.3390/vaccines10091564
   PubMed Web of Science ®Google Scholar
• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindah, E. (2015). Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Aiman, S., Alhamhoom, Y., Ali, F., Rahman, N., Rastrelli, L., Khan, A., Farooq, Q., Ul, A., Ahmed, A., Khan, A., & Li, C. (2022). Multi-epitope chimeric vaccine design against emerging Monkeypox virus via reverse vaccinology techniques - A bioinformatics and immunoinformatics approach. Frontiers in Immunology, 13, 985450. https://doi.org/10.3389/fimmu.2022.985450
   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
• Bowie, J. U., Lüthy, R., & Eisenberg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science (New York, N.Y.), 253(5016), 164–170. https://doi.org/10.1126/science.1853201
   PubMed Web of Science ®Google Scholar
• Bui, H.-H., Sidney, J., Li, W., Fusseder, N., & Sette, A. (2007). Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics, 8(1), 361. https://doi.org/10.1186/1471-2105-8-361
   PubMed Web of Science ®Google Scholar
• Bunge, E. M., Hoet, B., Chen, L., Lienert, F., Weidenthaler, H., Baer, L. R., & Steffen, R. (2022). The changing epidemiology of human monkeypox—A potential threat? A systematic review. PLOS Neglected Tropical Diseases, 16(2), e0010141. https://doi.org/10.1371/journal.pntd.0010141
   PubMed Web of Science ®Google Scholar
• Chauhan, V., Rungta, T., Goyal, K., & Singh, M. P. (2019). Designing a multi-epitope based vaccine to combat Kaposi Sarcoma utilizing immunoinformatics approach. Scientific Reports, 9(1), 1–15. https://doi.org/10.1038/s41598-019-39299-8
   PubMed Web of Science ®Google Scholar
• Chen, H., Wu, B., Zhang, T., Jia, J., Lu, J., Chen, Z., Ni, Z., & Tan, T. (2017). Effect of linker length and flexibility on the Clostridium thermocellum esterase displayed on bacillus subtilis spores. Applied Biochemistry and Biotechnology, 182(1), 168–180. https://doi.org/10.1007/s12010-016-2318-y
   PubMed Web of Science ®Google Scholar
• Chou, P. Y., & Fasman, G. D. (1978). Prediction of the secondary structure of proteins from their amino acid sequence. Advances in Enzymology and Related Areas of Molecular Biology, 47, 45–148. https://doi.org/10.1002/9780470122921.ch2
   PubMedGoogle Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Coulocheri, S. A., Pigis, D. G., Papavassiliou, K. A., & Papavassiliou, A. G. (2007). Hydrogen bonds in protein–DNA complexes: Where geometry meets plasticity. Biochimie, 89(11), 1291–1303. https://doi.org/10.1016/j.biochi.2007.07.020
   PubMed Web of Science ®Google Scholar
• Daura, X., Gademann, K., Jaun, B., Seebach, D., Van Gunsteren, W. F., & Mark, A. E. (1999). Peptide folding: When simulation meets experiment. Angewandte Chemie - International Edition, 38(1–2), 236–240. https://doi.org/10.1002/(sici)1521-3773(19990115)38:1/2<236::aid-anie236>3.0.co;2-m
   Google Scholar
• Dehury, B., Raina, V., Misra, N., & Suar, M. (2021). Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: A molecular dynamics simulations study. Journal of Biomolecular Structure & Dynamics, 39(18), 7231–7245. https://doi.org/10.1080/07391102.2020.1802348
   PubMed Web of Science ®Google Scholar
• Dehury, B., Tang, N., Blundell, T. L., & Kepp, K. P. (2019). Structure and dynamics of γ-secretase with presenilin 2 compared to presenilin 1. RSC Advances, 9(36), 20901–20916. https://doi.org/10.1039/C9RA02623A
   PubMed Web of Science ®Google Scholar
• Dermime, S., Gilham, D. E., Shaw, D. M., Davidson, E. J., Meziane, E.-K., Armstrong, A., Hawkins, R. E., & Stern, P. L. (2004). Vaccine and antibody-directed T cell tumour immunotherapy. Biochimica et Biophysica Acta, 1704(1), 11–35.
   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), 1–19. https://doi.org/10.1007/s10989-021-10356-z
   PubMed Web of Science ®Google Scholar
• Di Giulio, D. B., & Eckburg, P. B. (2004). Human monkeypox: An emerging zoonosis. The Lancet. Infectious Diseases, 4(1), 15–25. https://doi.org/10.1016/S1473-3099(03)00856-9
   PubMed Web of Science ®Google Scholar
• Dikhit, M. R., Vijayamahantesh, Kumar, A., Amit, A., Dehury, B., Nathsharma, Y. P., Ansari, M. Y., Ali, V., Topno, R. K., Das, V. N. R., Pandey, K., Sahoo, G. C., Bimal, S., & Das, P. (2018). Mining the proteome of Leishmania donovani for the development of novel MHC class I restricted epitope for the control of visceral leishmaniasis. Journal of Cellular Biochemistry, 119(1), 378–391. https://doi.org/10.1002/jcb.26190
   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 Modeling, 20(6), 2278. https://doi.org/10.1007/s00894-014-2278-5
   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), 7. https://doi.org/10.1186/1471-2105-8-4
   PubMedGoogle Scholar
• Fadaka, A. O., Sibuyi, N. R. S., Martin, D. R., Goboza, M., Klein, A., Madiehe, A. M., & Meyer, M. (2021). Immunoinformatics design of a novel epitope-based vaccine candidate against dengue virus. Scientific Reports, 11(1), 19707. https://doi.org/10.1038/s41598-021-99227-7
   PubMed Web of Science ®Google Scholar
• Fine, P. E. M., 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
   PubMed Web of Science ®Google Scholar
• Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server; The proteomics protocols handbook (Vol. 112, pp. 531–552). Humana Press.
   Google Scholar
• Girometti, N., Byrne, R., Bracchi, M., Heskin, J., McOwan, A., Tittle, V., Gedela, K., Scott, C., Patel, S., Gohil, J., Nugent, D., Suchak, T., Dickinson, M., Feeney, M., Mora-Peris, B., Stegmann, K., Plaha, K., Davies, G., Moore, L. S. P., … Whitlock, G. (2022). Demographic and clinical characteristics of confirmed human monkeypox virus cases in individuals attending a sexual health centre in London, UK: An observational analysis. The Lancet. Infectious Diseases, 22(9), 1321–1328. https://doi.org/10.1016/S1473-3099(22)00411-X
   PubMed Web of Science ®Google Scholar
• 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), W526–W531. https://doi.org/10.1093/nar/gki376
   PubMed Web of Science ®Google Scholar
• Gupta, S., Kapoor, P., Chaudhary, K., Gautam, A., Kumar, R., & Raghava, G. P. S., Open Source Drug Discovery Consortium. (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
• He, R., Yang, X., Liu, C., Chen, X., Wang, L., Xiao, M., Ye, J., Wu, Y., & Ye, L. (2018). Efficient control of chronic LCMV infection by a CD4 T cell epitope-based heterologous prime-boost vaccination in a murine model. Cellular & Molecular Immunology, 15(9), 815–826. https://doi.org/10.1038/cmi.2017.3
   PubMed Web of Science ®Google Scholar
• Hebditch, M., Carballo-Amador, M. A., Charonis, S., Curtis, R., & Warwicker, J. (2017). Protein–Sol: A web tool for predicting protein solubility from sequence. Bioinformatics (Oxford, England), 33(19), 3098–3100. https://doi.org/10.1093/bioinformatics/btx345
   PubMed Web of Science ®Google Scholar
• Hollingsworth, S. A., & Dror, R. O. (2018). Molecular dynamics simulation for all. Neuron, 99(6), 1129–1143. https://doi.org/10.1016/j.neuron.2018.08.011
   PubMed Web of Science ®Google Scholar
• Honorato, R. V., Koukos, P. I., Jiménez-García, B., Tsaregorodtsev, A., Verlato, M., Giachetti, A., Rosato, A., & Bonvin, A. M. J. J. (2021). Structural biology in the clouds: The WeNMR-EOSC ecosystem. Frontiers in Molecular Biosciences, 8(July), 729513–729517. https://doi.org/10.3389/fmolb.2021.729513
   PubMedGoogle Scholar
• Hoof, I., Peters, B., Sidney, J., Pedersen, L. E., Sette, A., Lund, O., Buus, S., & Nielsen, M. (2009). NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics, 61(1), 1–13. https://doi.org/10.1007/s00251-008-0341-z
   PubMed Web of Science ®Google Scholar
• Hubbard, R. E., & Kamran Haider, M. (2010). Hydrogen bonds in proteins: Role and strength. ELS, February, 1-7. https://doi.org/10.1002/9780470015902.a0003011.pub2
   Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–33-38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Islam, S. I., Mou, M. J., & Sanjida, S. (2022). Application of reverse vaccinology to design a multi-epitope subunit vaccine against a new strain of Aeromonas veronii. Journal, Genetic Engineering & Biotechnology, 20(1), 118. https://doi.org/10.1186/s43141-022-00391-8
   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
• Jezek, Z., Grab, B., Szczeniowski, M., Paluku, K. M., & Mutombo, M. (1988). Clinico-epidemiological features of monkeypox patients with an animal or human source of infection. Bulletin of the World Health Organization, 66(4), 459–464.
   PubMed Web of Science ®Google Scholar
• Jiang, P., Cai, Y., Chen, J., Ye, X., Mao, S., Zhu, S., Xue, X., Chen, S., & Zhang, L. (2017). Evaluation of tandem Chlamydia trachomatis MOMP multi-epitopes vaccine in BALB/c mice model. Vaccine, 35(23), 3096–3103. https://doi.org/10.1016/j.vaccine.2017.04.031
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 118(45), 11225–11236. https://doi.org/10.1021/ja9621760
   Web of Science ®Google Scholar
• Kanampalliwar, A. M., Soni, R., Girdhar, A., & Tiwari, A. (2013). Reverse vaccinology: Basics and applications. Journal of Vaccines and Vaccination, 4(6), 2–7. https://doi.org/10.4172/2157-7560.1000194
   Google Scholar
• Kar, T., Narsaria, U., Basak, S., Deb, D., Castiglione, F., Mueller, D. M., & Srivastava, A. P. (2020). A candidate multi-epitope vaccine against SARS-CoV-2. Scientific Reports, 10(1), 1–24. https://doi.org/10.1038/s41598-020-67749-1
   PubMed Web of Science ®Google Scholar
• Karplus, M., & McCammon, J. A. (2002). Molecular dynamics simulations of biomolecules. Nature Structural Biology, 9(9), 646–652. https://doi.org/10.1038/nsb0902-646
   PubMedGoogle Scholar
• Karplus, P. A., & Schulz, G. E. (1985). Prediction of chain flexibility in proteins synthesis of acetylcholine receptors in Xenopus oocytes induced by poly (A) + -mRNA from locust nervous tissue. 72, 212–213. https://doi.org/10.1007/BF01195768
   Google Scholar
• Kaur, R., Arora, N., Rawat, S. S., Keshri, A. K., Singh, N., Show, S. K., Kumar, P., Mishra, A., & Prasad, A. (2021). Immunoinformatics driven construction of multi-epitope vaccine candidate against Ascaris lumbricoides using its entire immunogenic epitopes. Expert Review of Vaccines, 20(12), 1637–1649. https://doi.org/10.1080/14760584.2021.1974298
   PubMed Web of Science ®Google Scholar
• Khan, S., Khan, A., Rehman, A. U., Ahmad, I., Ullah, S., Khan, A. A., Ali, S. S., Afridi, S. G., & Wei, D.-Q. (2019). Immunoinformatics and structural vaccinology driven prediction of multi-epitope vaccine against Mayaro virus and validation through in-silico expression. Infection, Genetics and Evolution, 73, 390–400. https://doi.org/10.1016/j.meegid.2019.06.006
   PubMed Web of Science ®Google Scholar
• Kim, D. E., Chivian, D., & Baker, D. (2004). Protein structure prediction and analysis using the Robetta Server. 32, 526–531. https://doi.org/10.1093/nar/gkh468
   Google Scholar
• Kim, H. M., Park, B. S., Kim, J. I., Kim, S. E., Lee, J., Oh, S. C., Enkhbayar, P., Matsushima, N., Lee, H., Yoo, O. J., & Lee, J. O. (2007). Crystal structure of the TLR4-MD-2 complex with bound endotoxin antagonist Eritoran. Cell, 130(5), 906–917. https://doi.org/10.1016/j.cell.2007.08.002
   PubMed Web of Science ®Google Scholar
• Kolaskar, A. S., & Tongaonkar, P. C. (1990). A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Letters, 276(1-2), 172–174. https://doi.org/10.1016/0014-5793(90)80535-Q
   PubMed Web of Science ®Google Scholar
• Kozakov, D., Hall, D. R., Xia, B., Porter, K. A., Padhorny, D., Yueh, C., Beglov, D., & Vajda, S. (2017). The ClusPro web server for protein-protein docking. Nature Protocols, 12(2), 255–278. https://doi.org/10.1038/nprot.2016.169
   PubMed Web of Science ®Google Scholar
• Kumar, A., Kumar, P., Saumya, K. U., Kapuganti, S. K., Bhardwaj, T., & Giri, R. (2020). Exploring the SARS-CoV-2 structural proteins for multi-epitope vaccine development: An in-silico approach. Expert Review of Vaccines, 19(9), 887–898. https://doi.org/10.1080/14760584.2020.1813576
   PubMed Web of Science ®Google Scholar
• Ladnyj, I. D., 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.
   PubMed Web of Science ®Google Scholar
• 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
   Web of Science ®Google Scholar
• Laskowski, R. A., Rullmann, J. A. C., 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, H., Zhang, H., Ding, K., Wang, X.-H., Sun, G.-Y., Liu, Z.-X., & Luo, Y. (2022). The evolving epidemiology of monkeypox virus. Cytokine & Growth Factor Reviews, 68(September), 1–12. https://doi.org/10.1016/j.cytogfr.2022.10.002
   PubMedGoogle Scholar
• Li, Y., Olson, V. A., Laue, T., Laker, M. T., & Damon, I. K. (2006). Detection of monkeypox virus with real-time PCR assays. Journal of Clinical Virology, 36(3), 194–203. https://doi.org/10.1016/j.jcv.2006.03.012
   PubMed Web of Science ®Google Scholar
• Li, Y., Zhao, H., Wilkins, K., Hughes, C., & Damon, I. K. (2010). Real-time PCR assays for the specific detection of monkeypox virus West African and Congo Basin strain DNA. Journal of Virological Methods, 169(1), 223–227.
   PubMed Web of Science ®Google Scholar
• Lu, I. N., Farinelle, S., Sausy, A., & Muller, C. P. (2017). Identification of a CD4 T-cell epitope in the hemagglutinin stalk domain of pandemic H1N1 influenza virus and its antigen-driven TCR usage signature in BALB/c mice. Cellular & Molecular Immunology, 14(6), 511–520. https://doi.org/10.1038/cmi.2016.20
   PubMed Web of Science ®Google Scholar
• Lüthy, R., Bowie, J. U., & Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature, 356(6364), 83–85. https://doi.org/10.1038/356083a0
   PubMed Web of Science ®Google Scholar
• Ma, J., Qiu, J., Wang, S., Ji, Q., Xu, D., Wang, H., Wu, Z., & Liu, Q. (2021). A novel design of multi-epitope vaccine against Helicobacter pylori by immunoinformatics approach. International Journal of Peptide Research and Therapeutics, 27(2), 1027–1042. https://doi.org/10.1007/s10989-020-10148-x
   PubMed Web of Science ®Google Scholar
• Mandel-Gutfreund, Y., Schueler, O., & Margalit, H. (1995). Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles. Journal of Molecular Biology, 253(2), 370–382. https://doi.org/10.1006/jmbi.1995.0559
   PubMed Web of Science ®Google Scholar
• Maurer-Stroh, S., Krutz, N. L., Kern, P. S., Gunalan, V., Nguyen, M. N., Limviphuvadh, V., Eisenhaber, F., & Gerberick, G. F. (2019). AllerCatPro-prediction of protein allergenicity potential from the protein sequence. Bioinformatics (Oxford, England), 35(17), 3020–3027. https://doi.org/10.1093/bioinformatics/btz029
   PubMed Web of Science ®Google Scholar
• Maximova, T., Moffatt, R., Ma, B., Nussinov, R., & Shehu, A. (2016). Principles and overview of sampling methods for modeling macromolecular structure and dynamics. PLoS Computational Biology, 12(4), e1004619. https://doi.org/10.1371/journal.pcbi.1004619
   PubMed Web of Science ®Google Scholar
• Mazurkov, O. Y., Kabanov, A. S., Shishkina, L. N., Sergeev, A. A., Skarnovich, M. O., Bormotov, N. I., Skarnovich, M. A., Ovchinnikova, A. S., Titova, K. A., Galahova, D. O., Bulychev, L. E., Sergeev, A. A., Taranov, O. S., Selivanov, B. A., Tikhonov, A. Y., Zavjalov, E. L., Agafonov, A. P., & Sergeev, A. N. (2016). New effective chemically synthesized anti-smallpox compound NIOCH-14. The Journal of General Virology, 97(5), 1229–1239. https://doi.org/10.1099/jgv.0.000422
   PubMedGoogle Scholar
• Meloen, R. H., Langeveld, J. P. M., Schaaper, W. M. M., & Slootstra, J. W. (2001). Synthetic peptide vaccines: Unexpected fulfillment of discarded hope? Biologicals, 29(3–4), 233–236.
   PubMed Web of Science ®Google Scholar
• Mohanty, E., Dehury, B., Satapathy, A. K., & Dwibedi, B. (2018). Design and testing of a highly conserved human rotavirus VP8* immunogenic peptide with potential for vaccine development. Journal of Biotechnology, 281, 48–60. https://doi.org/10.1016/j.jbiotec.2018.06.306
   PubMed Web of Science ®Google Scholar
• Moutaftsi, M., Peters, B., Pasquetto, V., Tscharke, D. C., Sidney, J., Bui, H.-H., Grey, H., & Sette, A. (2006). A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus. Nature Biotechnology, 24(7), 817–819. https://doi.org/10.1038/nbt1215
   PubMed Web of Science ®Google Scholar
• Mustafa, M. I., Shantier, S. W., Abdelmageed, M. I., & Makhawi, A. M. (2021). Epitope-based peptide vaccine against Bombali Ebolavirus viral protein 40: An immunoinformatics combined with molecular docking studies. Informatics in Medicine Unlocked, 25, 100694. https://doi.org/10.1016/j.imu.2021.100694
   Google Scholar
• Nguyen, M. N., Krutz, N. L., Limviphuvadh, V., Lopata, A. L., Gerberick, G. F., & Maurer-Stroh, S. (2022). AllerCatPro 2.0: A web server for predicting protein allergenicity potential. Nucleic Acids Research, 50(W1), W36–W43. https://doi.org/10.1093/nar/gkac446
   PubMed Web of Science ®Google Scholar
• Rao, A. K., Petersen, B. W., Whitehill, F., Razeq, J. H., Isaacs, S. N., Merchlinsky, M. J., Campos-Outcalt, D., Morgan, R. L., Damon, I., Sánchez, P. J., & Bell, B. P. (2022). Use of JYNNEOS (smallpox and monkeypox vaccine, live, nonreplicating) for preexposure vaccination of persons at risk for occupational exposure to orthopoxviruses: Recommendations of the advisory committee on immunization practices—United States, 2022. MMWR. Morbidity and Mortality Weekly Report, 71(22), 734–742. https://doi.org/10.15585/mmwr.mm7122e1
   PubMed Web of Science ®Google Scholar
• Release, P. (2022). Multi-country monkeypox outbreak: Situation update (10 June 2022). June, 1–9. https://www.who.int/emergencies/disease-outbreak-news/item/2022-DON392
   Google Scholar
• Sahoo, C. R., Paidesetty, S. K., Sarathbabu, S., Dehury, B., Senthil Kumar, N., & Padhy, R. N. (2022). Molecular dynamics simulation, synthesis and topoisomerase inhibitory actions of vanillin derivatives: A systematic computational structural integument. Journal of Biomolecular Structure and Dynamics, 40(22), 11653–11663. https://doi.org/10.1080/07391102.2021.1961867
   PubMed Web of Science ®Google Scholar
• Saijo, M., Ami, Y., Suzaki, Y., Nagata, N., Iwata, N., Hasegawa, H., Ogata, M., Fukushi, S., Mizutani, T., Iizuka, I., Sakai, K., Sata, T., Kurata, T., Kurane, I., & Morikawa, S. (2008). Diagnosis and assessment of monkeypox virus (MPXV) infection by quantitative PCR assay: Differentiation of Congo Basin and West African MPXV strains. Japanese Journal of Infectious Diseases, 61(2), 140–142.
   PubMed Web of Science ®Google Scholar
• Sayers, E. W., Bolton, E. E., Brister, J. R., Canese, K., Chan, J., Comeau, D. C., Connor, R., Funk, K., Kelly, C., Kim, S., Madej, T., Marchler-Bauer, A., Lanczycki, C., Lathrop, S., Lu, Z., Thibaud-Nissen, F., Murphy, T., Phan, L., Skripchenko, Y., … Sherry, S. T. (2022). Database resources of the national center for biotechnology information. Nucleic Acids Research, 50(D1), D20–D26. https://doi.org/10.1093/nar/gkab1112
   PubMed Web of Science ®Google Scholar
• Shankar, U., Jain, N., Mishra, S. K., Sk, M. F., Kar, P., & Kumar, A. (2022). Mining of Ebola virus genome for the construction of multi-epitope vaccine to combat its infection. Journal of Biomolecular Structure & Dynamics, 40(11), 4815–4831. https://doi.org/10.1080/07391102.2021.1874529
   PubMed Web of Science ®Google Scholar
• Shantier, S. W., Mustafa, M. I., Abdelmoneim, A. H., Fadl, H. A., Elbager, S. G., & Makhawi, A. M. (2022). Novel multi epitope-based vaccine against monkeypox virus: Vaccinomic approach. Scientific Reports, 12(1), 15983. https://doi.org/10.1038/s41598-022-20397-z
   PubMed Web of Science ®Google Scholar
• Sklenovská, N., & Van Ranst, M. (2018). Emergence of monkeypox as the most important orthopoxvirus infection in humans. Frontiers in Public Health, 6(September), 241–212. https://doi.org/10.3389/fpubh.2018.00241
   PubMedGoogle Scholar
• Thompson, M. R., Kaminski, J. J., Kurt-Jones, E. A., & Fitzgerald, K. A. (2011). Pattern recognition receptors and the innate immune response to viral infection. Viruses, 3(6), 920–940. https://doi.org/10.3390/v3060920
   PubMed Web of Science ®Google Scholar
• Thornhill, J. P., Barkati, S., Walmsley, S., Rockstroh, J., Antinori, A., Harrison, L. B., Palich, R., Nori, A., Reeves, I., Habibi, M. S., Apea, V., Boesecke, C., Vandekerckhove, L., Yakubovsky, M., Sendagorta, E., Blanco, J. L., Florence, E., Moschese, D., Maltez, F. M., … Orkin, C. M., SHARE-net Clinical Group. (2022). Monkeypox virus infection in humans across 16 countries—April–June 2022. The New England Journal of Medicine, 387(8), 679–691. https://doi.org/10.1056/nejmoa2207323
   PubMed Web of Science ®Google Scholar
• Tuffery, P., & Derreumaux, P. (2012). Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: Limitations of current computational approaches. Journal of the Royal Society, Interface, 9(66), 20–33. https://doi.org/10.1098/rsif.2011.0584
   PubMed Web of Science ®Google Scholar
• Ullah, A., Shahid, F. A., Haq, M. U., Tahir Ul Qamar, M., Irfan, M., Shaker, B., Ahmad, S., Alrumaihi, F., Allemailem, K. S., & Almatroudi, A. (2022). An integrative reverse vaccinology, immunoinformatic, docking and simulation approaches towards designing of multi-epitopes based vaccine against monkeypox virus. Journal of Biomolecular Structure and Dynamics, 1–14. https://doi.org/10.1080/07391102.2022.2125441
   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. (2016a). 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
   PubMed Web of Science ®Google Scholar
• Vartak, A., & Sucheck, S. J. (2016). Recent advances in subunit vaccine carriers. Vaccines, 4(2), 12–18. https://doi.org/10.3390/vaccines4020012
   Web of Science ®Google Scholar
• Vita, R., Mahajan, S., Overton, J. A., Dhanda, S. K., Martini, S., Cantrell, J. R., Wheeler, D. K., Sette, A., & Peters, B. (2019). The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Research, 47(D1), D339–D343. https://doi.org/10.1093/nar/gky1006
   PubMed Web of Science ®Google Scholar
• WHO. (2022). Monkeypox: Experts give virus variants new names. Monkeypox: Experts Give Virus Variants New Names, 16.
   Google Scholar
• Xu, D., Tsai, C.-J., & Nussinov, R. (1997). Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Engineering, 10(9), 999–1012. https://doi.org/10.1093/protein/10.9.999
   PubMedGoogle Scholar
• Yang, Z., Bogdan, P., & Nazarian, S. (2021). An in silico deep learning approach to multi-epitope vaccine design: A SARS-CoV-2 case study. Scientific Reports, 11(1), 3238. https://doi.org/10.1038/s41598-021-81749-9
   PubMed Web of Science ®Google Scholar
• Yinka-Ogunleye, A., Aruna, O., Dalhat, M., Ogoina, D., McCollum, A., Disu, Y., Mamadu, I., Akinpelu, A., Ahmad, A., Burga, J., Ndoreraho, A., Nkunzimana, E., Manneh, L., Mohammed, A., Adeoye, O., Tom-Aba, D., Silenou, B., Ipadeola, O., Saleh, M., … Satheshkumar, P. S. (2019). Outbreak of human monkeypox in Nigeria in 2017-18: A clinical and epidemiological report. The Lancet Infectious Diseases, 19(8), 872–879. https://doi.org/10.1016/S1473-3099(19)30294-4
   PubMed Web of Science ®Google Scholar
• Zhou, W.-Y., Shi, Y., Wu, C., Zhang, W.-J., Mao, X.-H., Guo, G., Li, H.-X., & Zou, Q.-M. (2009). Therapeutic efficacy of a multi-epitope vaccine against Helicobacter pylori infection in BALB/c mice model. Vaccine, 27(36), 5013–5019. https://doi.org/10.1016/j.vaccine.2009.05.009
   PubMed Web of Science ®Google Scholar