{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T23:59:05Z","timestamp":1770335945991,"version":"3.49.0"},"reference-count":59,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2024,10,23]],"date-time":"2024-10-23T00:00:00Z","timestamp":1729641600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002383","name":"King Saud University","doi-asserted-by":"publisher","award":["RSPD2024R632"],"award-info":[{"award-number":["RSPD2024R632"]}],"id":[{"id":"10.13039\/501100002383","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Bioengineering"],"abstract":"<jats:p>Despite the seriousness of the disease carried by ticks, little is known about the Bourbon virus. Only three US states have recorded human cases of Bourbon virus (BRBV) infection; in all cases, a tick bite was connected with the onset of the illness. The Bourbon virus (BRBV) belongs to the Orthomyxoviridae family and Thogotovirus genus, originating in the states of the US, i.e., Kansas, Oklahoma and Missouri. The growing rates of BRBV infections in various parts of the US highlight the necessity for a thorough analysis of the virus\u2019s transmission mechanisms, vector types and reservoir hosts. Currently, there are no vaccines or efficient antiviral therapies to stop these infections. It is imperative to produce a vaccination that is both affordable and thermodynamically stable to reduce the likelihood of future pandemics. Various computational techniques and reverse vaccinology methodologies were employed to identify specific B- and T-cell epitopes. After thorough examination, the linker proteins connected the B- and T-cell epitopes, resulting in this painstakingly constructed vaccine candidate. Furthermore, 3D modeling directed the vaccine construct toward molecular docking to determine its binding affinity and interaction with TLR-4. Human beta-defensin was used as an adjuvant and linked to the N-terminus to boost immunogenicity. Furthermore, the C-IMMSIM simulation resulted in high immunogenic activities, with activation of high interferon, interleukins and immunoglobulin. The results of the in silico cloning process for E. coli indicated that the vaccine construct will try its utmost to express itself in the host, with a codon adaptation CAI value of 0.94. A net binding free energy of \u2212677.7 kcal\/mol obtained during docking showed that the vaccine has a high binding affinity for immunological receptors. Further validation was achieved via molecular dynamic simulations, inferring the confirmational changes during certain time intervals, but the vaccine remained intact to the binding site for a 100 ns interval. The thermostability determined using an RMSF score predicted certain changes in the mechanistic insights of the loop region with carbon alpha deviations, but no major changes were observed during the simulations. Thus, the results obtained highlight a major concern for researchers to further validate the vaccine\u2019s efficacy using in vitro and in vivo approaches.<\/jats:p>","DOI":"10.3390\/bioengineering11111056","type":"journal-article","created":{"date-parts":[[2024,10,23]],"date-time":"2024-10-23T09:07:04Z","timestamp":1729674424000},"page":"1056","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Reverse Vaccinology Integrated with Biophysics Techniques for Designing a Peptide-Based Subunit Vaccine for Bourbon Virus"],"prefix":"10.3390","volume":"11","author":[{"given":"Taghreed N.","family":"Almanaa","sequence":"first","affiliation":[{"name":"Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,10,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"22336","DOI":"10.1007\/s11356-020-08896-w","article-title":"Climatic Changes and Their Role in Emergence and Re-Emergence of Diseases","volume":"27","author":"Kamel","year":"2020","journal-title":"Environ. Sci. Pollut. Res. Int."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"496","DOI":"10.15585\/mmwr.mm6717e1","article-title":"Vital Signs: Trends in Reported Vectorborne Disease Cases\u2014United States and Territories, 2004\u20132016","volume":"67","author":"Rosenberg","year":"2018","journal-title":"MMWR Morb. Mortal. Wkly. Rep."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.disamonth.2018.01.007","article-title":"Tick Borne Illness-Lyme Disease","volume":"64","author":"Bush","year":"2018","journal-title":"Dis. Mon."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1099\/jmm.0.001206","article-title":"Emerging Tick-Borne Pathogens of Public Health Importance: A Mini-Review","volume":"69","author":"Rochlin","year":"2020","journal-title":"J. Med. Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1752","DOI":"10.3201\/eid2509.181902","article-title":"Bourbon Virus in Wild and Domestic Animals, Missouri, USA, 2012\u20132013","volume":"25","author":"Jackson","year":"2019","journal-title":"Emerg. Infect. Dis."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"760","DOI":"10.3201\/eid2105.150150","article-title":"Novel Thogotovirus Associated with Febrile Illness and Death, United States, 2014","volume":"21","author":"Kosoy","year":"2015","journal-title":"Emerg. Infect. Dis."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2017","DOI":"10.3201\/eid2312.170532","article-title":"Bourbon Virus in Field-Collected Ticks, Missouri, USA","volume":"23","author":"Savage","year":"2017","journal-title":"Emerg. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3201\/eid2901.212295","article-title":"Comprehensive Review of Emergence and Virology of Tickborne Bourbon Virus in the United States","volume":"29","author":"Roe","year":"2023","journal-title":"Emerg. Infect. Dis."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Garba, A., Riley, J., Lahmers, K.K., and Eastwood, G. (2024). Widespread Circulation of Tick-Borne Viruses in Virginia-Evidence of Exposure to Heartland, Bourbon, and Powassan Viruses in Wildlife and Livestock. Microorganisms, 12.","DOI":"10.3390\/microorganisms12050899"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Shah, T., Li, Q., Wang, B., Baloch, Z., and Xia, X. (2023). Geographical Distribution and Pathogenesis of Ticks and Tick-Borne Viral Diseases. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1185829"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.3201\/eid2507.181062","article-title":"Essential Role of Interferon Response in Containing Human Pathogenic Bourbon Virus","volume":"25","author":"Fuchs","year":"2019","journal-title":"Emerg. Infect. Dis."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.jsb.2019.08.005","article-title":"Postfusion Structure of Human-Infecting Bourbon Virus Envelope Glycoprotein","volume":"208","author":"Bai","year":"2019","journal-title":"J. Struct. Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1613","DOI":"10.1093\/jme\/tjy103","article-title":"Surveillance for Heartland and Bourbon Viruses in Eastern Kansas, June 2016","volume":"55","author":"Savage","year":"2018","journal-title":"J. Med. Entomol."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Cumbie, A.N., Trimble, R.N., and Eastwood, G. (2022). Pathogen Spillover to an Invasive Tick Species: First Detection of Bourbon Virus in Haemaphysalis Longicornis in the United States. Pathogens, 11.","DOI":"10.3390\/pathogens11040454"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1007\/s12026-022-09284-x","article-title":"Reverse Vaccinology Approach to Design a Multi-Epitope Vaccine Construct Based on the Mycobacterium Tuberculosis Biomarker PE_PGRS17","volume":"70","author":"Moodley","year":"2022","journal-title":"Immunol. Res."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Patronov, A., and Doytchinova, I. (2021). T-Cell Epitope Vaccine Design by Immunoinformatics. Open Biol., 3.","DOI":"10.1098\/rsob.120139"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Parihar, A., Malviya, S., and Khan, R. (2022). Immunoinformatics and Reverse Vaccinomic Approaches for Effective Design. Computational Approaches for Novel Therapeutic and Diagnostic Designing to Mitigate SARS-CoV-2 Infection, Academic Press.","DOI":"10.1016\/B978-0-323-91172-6.00004-2"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Ong, E., Wong, M.U., Huffman, A., and He, Y. (2020). COVID-19 Coronavirus Vaccine Design Using Reverse Vaccinology and Machine Learning. bioRxiv, 11.","DOI":"10.3389\/fimmu.2020.01581"},{"key":"ref_19","first-page":"608","article-title":"Centers for Disease Control (CDC) Use of Serogroup B Meningococcal Vaccines in Persons Aged \u226510 Years at Increased Risk for Serogroup B Meningococcal Disease: Recommendations of the Advisory Committee on Immunization Practices, 2015","volume":"64","author":"Folaranmi","year":"2015","journal-title":"MMWR Morb. Mortal. Wkly. Rep."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1128\/CVI.00030-08","article-title":"Recombinant Group B Streptococcus Alpha-Like Protein 3 Is an Effective Immunogen and Carrier Protein","volume":"15","author":"Yang","year":"2008","journal-title":"Clin. Vaccine Immunol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1016\/j.immuni.2010.09.017","article-title":"Reverse Vaccinology: Developing Vaccines in the Era of Genomics","volume":"33","author":"Sette","year":"2010","journal-title":"Immunity"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.3892\/ol.2010.193","article-title":"Prediction and Analysis of HLA-A2\/A24-Restricted Cytotoxic T-Lymphocyte Epitopes of the Tumor Antigen MAGE-n Using the Artificial Neural Networks Method on NetCTL1.2 Server","volume":"1","author":"Zhang","year":"2010","journal-title":"Oncol. Lett."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/s43018-021-00197-6","article-title":"A Machine Learning Model for Ranking Candidate HLA Class I Neoantigens Based on Known Neoepitopes from Multiple Human Tumor Types","volume":"2","author":"Gartner","year":"2021","journal-title":"Nat. Cancer"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Charoenkwan, P., Nantasenamat, C., Hasan, M.M., and Shoombuatong, W. (2020). iTTCA-Hybrid: Improved and Robust Identification of Tumor T Cell Antigens by Utilizing Hybrid Feature Representation. Anal. Biochem., 599.","DOI":"10.1016\/j.ab.2020.113747"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Prawiningrum, A.F., Paramita, R.I., and Panigoro, S.S. (2022). Immunoinformatics Approach for Epitope-Based Vaccine Design: Key Steps for Breast Cancer Vaccine. Diagnostics, 12.","DOI":"10.3390\/diagnostics12122981"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"124725","DOI":"10.1016\/j.molliq.2024.124725","article-title":"Multiepitope Subunit Vaccine against Colorado Tick Fever Virus by Using Reverse Vaccinology Approach","volume":"402","author":"Ayaz","year":"2024","journal-title":"J. Mol. Liq."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Alsubaiyel, A.M., and Bukhari, S.I. (2023). Computational Exploration and Design of a Multi-Epitopes Vaccine Construct against Chlamydia psittaci. J. Biomol. Struct. Dyn., 1\u201317.","DOI":"10.1080\/07391102.2023.2268173"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.pep.2014.10.007","article-title":"Design and Construction of a Chimeric Multi-Epitope Gene as an Epitope-Vaccine Strategy against ALV-J","volume":"106","author":"Xu","year":"2015","journal-title":"Protein Expr. Purif."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/j.synbio.2024.03.010","article-title":"Discovering Peptides and Computational Investigations of a Multiepitope Vaccine Target Mycobacterium Tuberculosis","volume":"9","author":"Nguyen","year":"2024","journal-title":"Synth. Syst. Biotechnol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Yu, C., Wu, Q., Xin, J., Yu, Q., Ma, Z., Xue, M., Xu, Q., and Zheng, C. (2024). Designing a Smallpox B-Cell and T-Cell Multi-Epitope Subunit Vaccine Using a Comprehensive Immunoinformatics Approach. Microbiol. Spectr., 12.","DOI":"10.1128\/spectrum.00465-24"},{"key":"ref_31","unstructured":"ProtParam, E. (2024, August 26). ExPASy-ProtParam Tool. Available online: https:\/\/web.expasy.org\/protparam\/."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"W526","DOI":"10.1093\/nar\/gkh468","article-title":"Protein Structure Prediction and Analysis Using the Robetta Server","volume":"32","author":"Kim","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"3641","DOI":"10.1080\/07391102.2023.2214228","article-title":"Immunoinformatic Based Designing of Potential Immunogenic Novel mRNA and Peptide-Based Prophylactic Vaccines against H5N1 and H7N9 Avian Influenza Viruses","volume":"42","author":"Ghafoor","year":"2024","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2369","DOI":"10.51470\/jez.2023.26.2.2369","article-title":"In silico analysis of lipase gene from Bacillus subtilis to predict the binding potential with industrial important compounds","volume":"26","author":"Chaudhary","year":"2023","journal-title":"J. Exp. Zool. India"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Sura, K., Rohilla, H., Kumar, D., Jakhar, R., Ahlawat, V., Kaushik, D., Dangi, M., and Chhillar, A.K. (2023). Exploring Structural Antigens of Yellow Fever Virus to Design Multi-Epitope Subunit Vaccine Candidate by Utilizing an Immuno-Informatics Approach. J. Genet. Eng. Biotechnol., 21.","DOI":"10.1186\/s43141-023-00621-7"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"162","DOI":"10.2174\/1872208317666230523105759","article-title":"In Silico Design and Evaluation of a Novel Therapeutic Agent Against the Spike Protein as a Novel Treatment Strategy for COVID-19 Treatment","volume":"18","author":"Sarmadi","year":"2024","journal-title":"Recent. Pat. Biotechnol."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Alam, M.M., Saikat, A.S.M., and Uddin, M.E. (2023). Bioinformatics Approaches for Structural and Functional Annotation of an Uncharacterized Protein of Helicobacter Pylori. Eng. Proc., 37.","DOI":"10.3390\/ECP2023-14671"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1016\/j.bioorg.2018.03.022","article-title":"Synthesis, in Vitro \u03b1-Glucosidase Inhibitory Potential and Molecular Docking Study of Thiadiazole Analogs","volume":"78","author":"Javid","year":"2018","journal-title":"Bioorg Chem."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"159","DOI":"10.4103\/1735-5362.367795","article-title":"A Comparative Study of the Arazyme-Based Fusion Proteins with Various Ligands for More Effective Targeting Cancer Therapy: An in-Silico Analysis","volume":"18","author":"Mehrab","year":"2023","journal-title":"Res. Pharm. Sci."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"10","DOI":"10.22271\/23487941.2023.v10.i2a.665","article-title":"Molecular Dynamics Studies on the Arginine Kinase Protein of Aedes Sollicitans: Against the Natural Chemical Compound, Gedunin","volume":"10","author":"Nijanthi","year":"2023","journal-title":"Int. J. Mosq. Res."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Beikzadeh, B. (2023). Immunoinformatics Design of Multi-Epitope Vaccine Using OmpA, OmpD and Enterotoxin against Non-Typhoidal Salmonellosis. BMC Bioinform., 24.","DOI":"10.1186\/s12859-023-05183-6"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Mazumder, L., Shahab, M., Islam, S., Begum, M., Oliveira, J.I.N., Begum, S., and Akter, S. (2023). An Immunoinformatics Approach to Epitope-Based Vaccine Design against PspA in Streptococcus Pneumoniae. J. Genet. Eng. Biotechnol., 21.","DOI":"10.1186\/s43141-023-00506-9"},{"key":"ref_43","unstructured":"Case, D.A., Betz, R.M., Cerutti, D.S., Cheatham, T., Darden, T., Duke, R.E., Giese, T.J., Gohlke, H., G\u00f6tz, A.W., and Homeyer, N. (2016). Amber 16, University of California, San Francisco, University of California."},{"key":"ref_44","first-page":"29","article-title":"The FF14SB Force Field","volume":"14","author":"Case","year":"2014","journal-title":"Amber"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"223","DOI":"10.4208\/cicp.210711.121011s","article-title":"Examining Electrostatic Influences on Base-Flipping: A Comparison of TIP3P and GB Solvent Models","volume":"13","author":"Brice","year":"2013","journal-title":"Commun. Comput. Phys."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.1063\/1.448118","article-title":"Molecular Dynamics with Coupling to an External Bath","volume":"81","author":"Berendsen","year":"1984","journal-title":"J. Chem. Phys."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"3084","DOI":"10.1021\/ct400341p","article-title":"PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data","volume":"9","author":"Roe","year":"2013","journal-title":"J. Chem. Theory Comput."},{"key":"ref_48","unstructured":"(2023, December 31). 385 PDFs|Review Articles in XMGRACE. Available online: https:\/\/www.researchgate.net\/topic\/Xmgrace\/publications."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"3314","DOI":"10.1021\/ct300418h","article-title":"MMPBSA.Py: An Efficient Program for End-State Free Energy Calculations","volume":"8","author":"Miller","year":"2012","journal-title":"J. Chem. Theory Comput."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1186\/s13071-019-3468-x","article-title":"Counterattacking the Tick Bite: Towards a Rational Design of Anti-Tick Vaccines Targeting Pathogen Transmission","volume":"12","author":"Rego","year":"2019","journal-title":"Parasites Vectors"},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Windhaber, S., Xin, Q., and Lozach, P.-Y. (2021). Orthobunyaviruses: From Virus Binding to Penetration into Mammalian Host Cells. Viruses, 13.","DOI":"10.3390\/v13050872"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-4419-7185-2_1","article-title":"The Value of Vaccination","volume":"697","author":"Bloom","year":"2011","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1111\/j.1365-2567.2011.03517.x","article-title":"T-Cell-Inducing Vaccines\u2014What\u2019s the Future","volume":"135","author":"Gilbert","year":"2012","journal-title":"Immunology"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"825","DOI":"10.4269\/ajtmh.2009.08-0625","article-title":"Dengue Plaque Reduction Neutralization Test (PRNT) in Primary and Secondary Dengue Virus Infections: How Alterations in Assay Conditions Impact Performance","volume":"81","author":"Thomas","year":"2009","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1038\/nri3254","article-title":"Cross-Presentation by Dendritic Cells","volume":"12","author":"Joffre","year":"2012","journal-title":"Nat. Rev. Immunol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"8509","DOI":"10.1002\/jcp.27782","article-title":"CD8+ Cytotoxic T Lymphocytes in Cancer Immunotherapy: A Review","volume":"234","author":"Farhood","year":"2019","journal-title":"J. Cell Physiol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1111\/j.1600-065X.2009.00773.x","article-title":"Molecular Mechanisms of T-Cell Receptor and Costimulatory Molecule Ligation\/Blockade in Autoimmune Disease Therapy","volume":"229","author":"Podojil","year":"2009","journal-title":"Immunol. Rev."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1126\/science.274.5284.94","article-title":"Phenotypic Analysis of Antigen-Specific T Lymphocytes","volume":"274","author":"Altman","year":"1996","journal-title":"Science"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1153","DOI":"10.1016\/j.cell.2015.10.047","article-title":"Htr2a-Expressing Cells in the Central Amygdala Control the Hierarchy between Innate and Learned Fear","volume":"163","author":"Isosaka","year":"2015","journal-title":"Cell"}],"container-title":["Bioengineering"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-5354\/11\/11\/1056\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T16:18:38Z","timestamp":1760113118000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-5354\/11\/11\/1056"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,10,23]]},"references-count":59,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2024,11]]}},"alternative-id":["bioengineering11111056"],"URL":"https:\/\/doi.org\/10.3390\/bioengineering11111056","relation":{},"ISSN":["2306-5354"],"issn-type":[{"value":"2306-5354","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,10,23]]}}}