{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T18:52:24Z","timestamp":1790621544907,"version":"4.1.0"},"reference-count":103,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2024,5,17]],"date-time":"2024-05-17T00:00:00Z","timestamp":1715904000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"King Saud University","award":["RSP2024R494"],"award-info":[{"award-number":["RSP2024R494"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Bioengineering"],"abstract":"<jats:p>Bartonella henselae is a Gram-negative bacterium causing a variety of clinical symptoms, ranging from cat-scratch disease to severe systemic infections, and it is primarily transmitted by infected fleas. Its status as an emerging zoonotic pathogen and its capacity to persist within host erythrocytes and endothelial cells emphasize its clinical significance. Despite progress in understanding its pathogenesis, limited knowledge exists about the virulence factors and regulatory mechanisms specific to the B. henselae strain Houston-1. Exploring these aspects is crucial for targeted therapeutic strategies against this versatile pathogen. Using reverse-vaccinology-based subtractive proteomics, this research aimed to identify the most antigenic proteins for formulating a multi-epitope vaccine against the B. henselae strain Houston-1. One crucial virulent and antigenic protein, the PAS domain-containing sensor histidine kinase protein, was identified. Subsequently, the identification of B-cell and T-cell epitopes for the specified protein was carried out and the evaluated epitopes were checked for their antigenicity, allergenicity, solubility, MHC binding capability, and toxicity. The filtered epitopes were merged using linkers and an adjuvant to create a multi-epitope vaccine construct. The structure was then refined, with 92.3% of amino acids falling within the allowed regions. Docking of the human receptor (TLR4) with the vaccine construct was performed and demonstrated a binding energy of \u22121047.2 Kcal\/mol with more interactions. Molecular dynamic simulations confirmed the stability of this docked complex, emphasizing the conformation and interactions between the molecules. Further experimental validation is necessary to evaluate its effectiveness against B. henselae.<\/jats:p>","DOI":"10.3390\/bioengineering11050505","type":"journal-article","created":{"date-parts":[[2024,5,17]],"date-time":"2024-05-17T09:10:22Z","timestamp":1715937022000},"page":"505","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Subtractive Proteomics and Reverse-Vaccinology Approaches for Novel Drug Target Identification and Chimeric Vaccine Development against Bartonella henselae Strain Houston-1"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3257-5960","authenticated-orcid":false,"given":"Sudais","family":"Rahman","sequence":"first","affiliation":[{"name":"Department of Zoology, Abdul Wali Khan University, Mardan 23200, Khyber Pakhtunkhwa, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chien-Chun","family":"Chiou","sequence":"additional","affiliation":[{"name":"Department of Dermatology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 600, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6782-8713","authenticated-orcid":false,"given":"Shabir","family":"Ahmad","sequence":"additional","affiliation":[{"name":"Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas (UNICAMP), Campinas 13084-862, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5672-5719","authenticated-orcid":false,"given":"Zia Ul","family":"Islam","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Abdul Wali Khan University, Mardan 23200, Khyber Pakhtunkhwa, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1756-924X","authenticated-orcid":false,"given":"Tetsuya","family":"Tanaka","sequence":"additional","affiliation":[{"name":"Laboratory of Infectious Diseases, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8863-3870","authenticated-orcid":false,"given":"Abdulaziz","family":"Alouffi","sequence":"additional","affiliation":[{"name":"King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9599-0884","authenticated-orcid":false,"given":"Chien-Chin","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Pathology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 600, Taiwan"},{"name":"Department of Cosmetic Science, Chia Nan University of Pharmacy and Science, Tainan 717, Taiwan"},{"name":"Ph.D. Program in Translational Medicine, Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan"},{"name":"Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9746-4765","authenticated-orcid":false,"given":"Mashal M.","family":"Almutairi","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6411-6625","authenticated-orcid":false,"given":"Abid","family":"Ali","sequence":"additional","affiliation":[{"name":"Department of Zoology, Abdul Wali Khan University, Mardan 23200, Khyber Pakhtunkhwa, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,5,17]]},"reference":[{"key":"ref_1","first-page":"63","article-title":"Cat scratch disease","volume":"2","author":"Zhang","year":"2015","journal-title":"Radiol. Infect. Dis."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.vetmic.2010.09.033","article-title":"A comparative study of the interaction of Bartonella henselae strains with human endothelial cells","volume":"149","author":"Chang","year":"2011","journal-title":"Vet. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1128\/JCM.40.3.1023-1030.2002","article-title":"Genomic variation of Bartonella henselae strains detected in lymph nodes of patients with cat scratch disease","volume":"40","author":"Zeaiter","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1186\/s13071-016-1547-9","article-title":"Vasculitis, cerebral infarction and persistent Bartonella henselae infection in a child","volume":"9","author":"Balakrishnan","year":"2016","journal-title":"Parasites Vectors"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1089\/vbz.2010.0106","article-title":"Bartonella henselae and the potential for arthropod vector-borne transmission","volume":"11","author":"Mosbacher","year":"2011","journal-title":"Vector-Borne Zoonotic Dis."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"446","DOI":"10.3947\/ic.2013.45.4.446","article-title":"First case of Bartonella henselae bacteremia in Korea","volume":"45","author":"Im","year":"2013","journal-title":"Infect. Chemother."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1179573519832014","DOI":"10.1177\/1179573519832014","article-title":"Bartonella henselae Bloodstream Infection in a Boy With Pediatric Acute-Onset Neuropsychiatric Syndrome","volume":"11","author":"Breitschwerdt","year":"2019","journal-title":"J. Cent. Nerv. Syst. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Ali, A., Ahmad, S., Wadood, A., Rehman, A.U., Zahid, H., Qayash Khan, M., Nawab, J., Rahman, Z.U., and Alouffi, A.S. (2020). Modeling novel putative drugs and vaccine candidates against tick-borne pathogens: A subtractive proteomics approach. Vet. Sci., 7.","DOI":"10.3390\/vetsci7030129"},{"key":"ref_9","first-page":"262","article-title":"Subtractive proteomics for identification of drug targets in bacterial pathogens: A review","volume":"9","author":"Maurya","year":"2020","journal-title":"Int. J. Eng. Res. Technol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Ali, A., Ahmad, S., de Albuquerque, P.M.M., Kamil, A., Alshammari, F.A., Alouffi, A., and da Silva Vaz, I. (2021). Prediction of novel drug targets and vaccine candidates against human lice (Insecta), Acari (Arachnida), and their associated pathogens. Vaccines, 10.","DOI":"10.3390\/vaccines10010008"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Shahid, F., Ashfaq, U.A., Saeed, S., Munir, S., Almatroudi, A., and Khurshid, M. (2020). In silico subtractive proteomics approach for identification of potential drug targets in Staphylococcus saprophyticus. Int. J. Environ. Res. Public Health, 17.","DOI":"10.3390\/ijerph17103644"},{"key":"ref_12","unstructured":"Raju, S., and Rao, V.U.M. (2010). Current development strategies for vaccines and the role of reverse vaccinology. Asian J. Pharm. Res. Health Care, 339\u2013346."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1554","DOI":"10.1074\/mcp.M000022-MCP201","article-title":"Proteome analysis of the surface of Trichomonas vaginalis reveals novel proteins and strain-dependent differential expression","volume":"9","author":"Lustig","year":"2010","journal-title":"Mol. Cell. Proteom."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"3374","DOI":"10.1016\/j.ygeno.2020.06.022","article-title":"Identification of novel vaccine candidate against Salmonella enterica serovar Typhi by reverse vaccinology method and evaluation of its immunization","volume":"112","author":"Esmailnia","year":"2020","journal-title":"Genomics"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"104293","DOI":"10.1016\/j.micpath.2020.104293","article-title":"Identification and qualitative characterization of new therapeutic targets in Stenotrophomonas maltophilia through in silico proteome exploration","volume":"149","author":"Chakrabarty","year":"2020","journal-title":"Microb. Pathog."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1038\/s41421-021-00370-2","article-title":"CoVac501, a self-adjuvanting peptide vaccine conjugated with TLR7 agonists, against SARS-CoV-2 induces protective immunity","volume":"8","author":"Long","year":"2022","journal-title":"Cell Discov."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: Accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/2629691","article-title":"NCBI BLASTP on high-performance reconfigurable computing systems","volume":"7","author":"Mahram","year":"2015","journal-title":"ACM Trans. Reconfigurable Technol. Syst."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"D677","DOI":"10.1093\/nar\/gkaa917","article-title":"DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools","volume":"49","author":"Luo","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"D457","DOI":"10.1093\/nar\/gkv1070","article-title":"KEGG as a reference resource for gene and protein annotation","volume":"4","author":"Kanehisa","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"W182","DOI":"10.1093\/nar\/gkm321","article-title":"KAAS: An automatic genome annotation and pathway reconstruction server","volume":"35","author":"Moriya","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1002\/prot.21018","article-title":"Prediction of protein subcellular localization","volume":"64","author":"Yu","year":"2006","journal-title":"Proteins Struct. Funct. Genet."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1038\/nrd.2018.4","article-title":"2017 FDA drug approvals","volume":"17","author":"Mullard","year":"2018","journal-title":"Nat. Rev. Drug Discov."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1016\/j.cgh.2013.03.038","article-title":"Analysis of the human gut microbiome and association with disease","volume":"11","author":"Wu","year":"2013","journal-title":"Clin. Gastroenterol. Hepatol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2936","DOI":"10.1093\/bioinformatics\/btq551","article-title":"High-throughput prediction of protein antigenicity using protein microarray data","volume":"26","author":"Magnan","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"D808","DOI":"10.1093\/nar\/gks1094","article-title":"STRING v9. 1: Protein-protein interaction networks, with increased coverage and integration","volume":"41","author":"Franceschini","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Larsen, M.V., Lundegaard, C., Lamberth, K., Buus, S., Lund, O., and Nielsen, M. (2007). Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinform., 8.","DOI":"10.1186\/1471-2105-8-424"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1146\/annurev-immunol-082119-124838","article-title":"T cell epitope predictions","volume":"38","author":"Peters","year":"2020","journal-title":"Annu. Rev. Immunol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1111\/jphp.12810","article-title":"Immunogenicity assessment during the development of protein therapeutics","volume":"70","author":"Rosenberg","year":"2018","journal-title":"J. Pharm. Pharmacol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1522","DOI":"10.1093\/bioinformatics\/btx820","article-title":"An automated benchmarking platform for MHC class II binding prediction methods","volume":"34","author":"Andreatta","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1111\/j.1365-2567.2010.03268.x","article-title":"MHC class II epitope predictive algorithms","volume":"130","author":"Nielsen","year":"2010","journal-title":"Immunology"},{"key":"ref_32","first-page":"838035","article-title":"Trans-species polymorphism in immune genes: General pattern or MHC-restricted phenomenon?","volume":"2015","author":"Vinkler","year":"2015","journal-title":"J. Immunol. Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1272","DOI":"10.1016\/j.cell.2017.09.050","article-title":"MHC-I genotype restricts the oncogenic mutational landscape","volume":"171","author":"Marty","year":"2017","journal-title":"Cell"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"6760830","DOI":"10.1155\/2016\/6760830","article-title":"An introduction to B-cell epitope mapping and in silico epitope prediction","volume":"2016","author":"Potocnakova","year":"2016","journal-title":"J. Immunol. Res."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1016\/0014-5793(90)80535-Q","article-title":"A semi-empirical method for prediction of antigenic determinants on protein antigens","volume":"276","author":"Kolaskar","year":"1990","journal-title":"FEBS Lett."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1128\/jvi.55.3.836-839.1985","article-title":"Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide","volume":"55","author":"Emini","year":"1985","journal-title":"J. Virol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1007\/BF01195768","article-title":"Prediction of chain flexibility in proteins","volume":"72","author":"Karplus","year":"1985","journal-title":"Naturwissenschaften"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1146\/annurev.bi.47.070178.001343","article-title":"Empirical predictions of protein conformation","volume":"47","author":"Chou","year":"1978","journal-title":"Annu. Rev. Biochem."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1016\/j.drudis.2020.03.006","article-title":"Epitope-based vaccine design: A comprehensive overview of bioinformatics approaches","volume":"25","author":"Parvizpour","year":"2020","journal-title":"Drug Discov. Today"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Santhoshkumar, R., and Yusuf, A. (2020). In silico structural modeling and analysis of physicochemical properties of curcumin synthase (CURS1, CURS2, and CURS3) proteins of Curcuma longa. J. Genet. Eng. Biotechnol., 18.","DOI":"10.1186\/s43141-020-00041-x"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"398","DOI":"10.2174\/1573409915666190318121838","article-title":"VaxiJen dataset of bacterial immunogens: An update","volume":"15","author":"Zaharieva","year":"2019","journal-title":"Curr. Comput. Aided Drug Des."},{"key":"ref_42","first-page":"35","article-title":"In silico assessment of plant L-asparaginase and estimating its allergenicity in comparison to bacteria asparaginase","volume":"19","author":"Yazdi","year":"2020","journal-title":"Issues Hematol. \/Oncol. Immunopathol. Pediatr."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Almofti, Y.A., Abd-Elrahman, K.A., and Eltilib, E.E. (2021). Vaccinomic approach for novel multi epitopes vaccine against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). BMC Immunol., 22.","DOI":"10.1186\/s12865-021-00412-0"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1002\/pro.3289","article-title":"PDBsum: Structural summaries of PDB entries","volume":"27","author":"Laskowski","year":"2018","journal-title":"Protein Sci."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"W72","DOI":"10.1093\/nar\/gki396","article-title":"SCRATCH: A protein structure and structural feature prediction server","volume":"33","author":"Cheng","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S.E., Wilkins, M.R., Appel, R.D., and Bairoch, A. (2005). Protein Identification and Analysis Tools on the ExPASy Server, Humana Press.","DOI":"10.1385\/1-59259-890-0:571"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Craig, D.B., and Dombkowski, A.A. (2013). Disulfide by Design 2.0: A web-based tool for disulfide engineering in proteins. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-346"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.biotechadv.2004.09.002","article-title":"Formation of disulfide bonds in proteins and peptides","volume":"23","author":"Bulaj","year":"2005","journal-title":"Biotechnol. Adv."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/nprot.2016.169","article-title":"The ClusPro web server for protein\u2013protein docking","volume":"12","author":"Kozakov","year":"2017","journal-title":"Nat. Protoc."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1002\/pro.3943","article-title":"UCSF ChimeraX: Structure visualization for researchers, educators, and developers","volume":"30","author":"Pettersen","year":"2021","journal-title":"Protein Sci."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"da Fonseca, A.M., Caluaco, B.J., Madureira, J.M.C., Cabongo, S.Q., Gaieta, E.M., Djata, F., Colares, R.P., Neto, M.M., Fernandes, C.F.C., and Marinho, G.S. (2023). Screening of potential inhibitors targeting the main protease structure of SARS-CoV-2 via molecular docking, and approach with molecular dynamics, RMSD, RMSF, H-bond, SASA and MMGBSA. Mol. Biotechnol.","DOI":"10.1007\/s12033-023-00831-x"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"406","DOI":"10.2174\/1574893611666160815102521","article-title":"Using a machine-learning approach to predict discontinuous antibody-specific B-cell epitopes","volume":"12","author":"Lin","year":"2017","journal-title":"Curr. Bioinform."},{"key":"ref_55","unstructured":"Del Tordello, E., Rappuoli, R., and Delany, I. (2017). Human Vaccines, Academic Press."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1016\/j.ijbiomac.2015.03.027","article-title":"Comparison of predicted extinction coefficients of monoclonal antibodies with experimental values as measured by the Edelhoch method","volume":"77","author":"Maity","year":"2015","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_57","first-page":"31","article-title":"The expression level of a recombinant lipase predicted in silico by different codon optimization algorithms","volume":"137","author":"Bello","year":"2019","journal-title":"World Sci. News"},{"key":"ref_58","first-page":"117","article-title":"Mutation Detection of Multidrug-Resistant Tuberculosis by RT-PCR Method as the Diagnostic Tool of MDR-TB","volume":"10","author":"Novianti","year":"2023","journal-title":"J. Bioteknol. Biosains Indones."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Pourseif, M.M., Parvizpour, S., Jafari, B., Dehghani, J., Naghili, B., and Omidi, Y. (2021). A domain-based vaccine construct against SARS-CoV-2, the causative agent of COVID-19 pandemic: Development of self-amplifying mRNA and peptide vaccines. BioImpacts BI, 11.","DOI":"10.21203\/rs.3.rs-32539\/v1"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"12777","DOI":"10.1080\/07391102.2023.2175256","article-title":"A study on the design of an in silico self-amplifying mRNA vaccine against Nipah virus using immunoinformatics","volume":"41","author":"Rangacharya","year":"2023","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"225","DOI":"10.3233\/ISB-2009-0399","article-title":"In silico identification of candidate drug and vaccine targets from various pathways in Neisseria gonorrhoeae","volume":"9","author":"Barh","year":"2009","journal-title":"Silico Biol."},{"key":"ref_62","first-page":"355","article-title":"A novel genomics approach for the identification of drug targets in pathogens, with special reference to Pseudomonas aeruginosa","volume":"4","author":"Sakharkar","year":"2004","journal-title":"Silico Biol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1007\/s00294-009-0254-x","article-title":"Identification of genes differentially expressed in vivo by Metarhizium anisopliae in the hemolymph of Locusta migratoria using suppression-subtractive hybridization","volume":"55","author":"Zhang","year":"2009","journal-title":"Curr. Genet."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"657","DOI":"10.15252\/embr.201338283","article-title":"Metabolomic strategies for the identification of new enzyme functions and metabolic pathways","volume":"15","author":"Prosser","year":"2014","journal-title":"EMBO Rep."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1561","DOI":"10.1080\/14760584.2021.1987222","article-title":"Vaccinomics: A future avenue for vaccine development against emerging pathogens","volume":"20","author":"Contreras","year":"2021","journal-title":"Expert Rev. Vaccines"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1093\/bioinformatics\/btq249","article-title":"PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes","volume":"26","author":"Yu","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Alturki, N.A., Mashraqi, M.M., Jalal, K., Khan, K., Basharat, Z., and Alzamami, A. (2022). Therapeutic target identification and inhibitor screening against riboflavin synthase of colorectal cancer associated fusobacterium nucleatum. Cancers, 14.","DOI":"10.3390\/cancers14246260"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","article-title":"VFDB 2022: A general classification scheme for bacterial virulence factors","volume":"50","author":"Liu","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"6086","DOI":"10.1021\/acs.chemrev.8b00608","article-title":"Characterization of lipid\u2013protein interactions and lipid-mediated modulation of membrane protein function through molecular simulation","volume":"119","author":"Muller","year":"2019","journal-title":"Chem. Rev."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Chakraborty, S., and Kenney, L.J. (2018). A new role of OmpR in acid and osmotic stress in Salmonella and E. coli. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.02656"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/S1534-5807(03)00191-6","article-title":"The asymmetric spatial distribution of bacterial signal transduction proteins coordinates cell cycle events","volume":"5","author":"Lam","year":"2003","journal-title":"Dev. Cell"},{"key":"ref_72","unstructured":"Bedrunka, P. (2017). The Role of the Second Messenger Cyclic di-GMP in Bacillus subtilis, Philipps-Universit\u00e4t Marburg."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1016\/j.bj.2020.01.002","article-title":"Immunoinformatics prediction of potential B-cell and T-cell epitopes as effective vaccine candidates for eliciting immunogenic responses against Epstein\u2013Barr virus","volume":"44","author":"Olotu","year":"2021","journal-title":"Biomed. J."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1016\/j.bj.2021.05.001","article-title":"Integrative immunoinformatics paradigm for predicting potential B-cell and T-cell epitopes as viable candidates for subunit vaccine design against COVID-19 virulence","volume":"44","author":"Sarma","year":"2021","journal-title":"Biomed. J."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1111\/cbdd.13357","article-title":"Selection-based design of in silico dengue epitope ensemble vaccines","volume":"93","author":"Murphy","year":"2019","journal-title":"Chem. Biol. Drug Des."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1038\/s41541-019-0148-y","article-title":"Identification of antigens presented by MHC for vaccines against tuberculosis","volume":"5","author":"Bettencourt","year":"2020","journal-title":"NPJ Vaccines"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"5995","DOI":"10.1016\/j.vaccine.2017.05.092","article-title":"Novel CTL epitopes identified through a Y. pestis proteome-wide analysis in the search for vaccine candidates against plague","volume":"35","author":"Zvi","year":"2017","journal-title":"Vaccine"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"98","DOI":"10.7324\/JAPS.2019.90114","article-title":"Study of B cell epitope conserved region of the Zika virus envelope glycoprotein to develop multi-strain vaccine","volume":"9","author":"Adianingsih","year":"2019","journal-title":"J. Appl. Pharm. Sci."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"3740","DOI":"10.1080\/07391102.2018.1526714","article-title":"Epitope-driven common subunit vaccine design against H. pylori strains","volume":"37","author":"Pasala","year":"2019","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"18","DOI":"10.22159\/ijap.2024v16i1.49563","article-title":"Navigating the landscape of adjuvants for subunit vaccines: Recent advances and future perspectives","volume":"10","author":"Orosco","year":"2024","journal-title":"Int. J. Appl. Pharmaceut."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"105150","DOI":"10.1016\/j.micpath.2021.105150","article-title":"Prioritization of potential vaccine candidates and designing a multiepitope-based subunit vaccine against multidrug-resistant Salmonella Typhi str. CT18: A subtractive proteomics and immunoinformatics approach","volume":"159","author":"Chand","year":"2021","journal-title":"Microb. Pathog."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"4892","DOI":"10.1007\/s12010-022-03995-5","article-title":"Identification of antigenic properties of Acinetobacter baumannii proteins as novel putative vaccine candidates using reverse vaccinology approach","volume":"194","author":"Doosti","year":"2022","journal-title":"Appl. Biochem. Biotechnol."},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Rawal, K., Sinha, R., Nath, S.K., Preeti, P., Kumari, P., Gupta, S., Sharma, T., Strych, U., Hotez, P., and Bottazzi, M.E. (2022). Vaxi-DL: A web-based deep learning server to identify potential vaccine candidates. Comput. Biol. Med., 145.","DOI":"10.1016\/j.compbiomed.2022.105401"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"3871","DOI":"10.1039\/D2FO02825E","article-title":"Allergenicity evaluation of five types of commercial food-derived oligopeptide products","volume":"14","author":"Xiong","year":"2023","journal-title":"Food Funct."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"151","DOI":"10.2478\/s11756-019-00324-w","article-title":"In silico analysis of codon usage and rare codon clusters in the halophilic bacteria L-asparaginase","volume":"75","author":"Mortazavi","year":"2020","journal-title":"Biologia"},{"key":"ref_86","doi-asserted-by":"crossref","unstructured":"Suleman, M., Ul Qamar, M.T., Rasool, S., Rasool, A., Albutti, A., Alsowayeh, N., Alwashmi, A.S., Aljasir, M.A., and Ahmad, S. (2021). Immunoinformatics and immunogenetics-based design of immunogenic peptides vaccine against the emerging tick-borne encephalitis virus (Tbev) and its validation through in silico cloning and immune simulation. Vaccines, 9.","DOI":"10.3390\/vaccines9111210"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"159","DOI":"10.2174\/1570163815666180227162157","article-title":"A systematic review on popularity, application and characteristics of protein secondary structure prediction tools","volume":"16","author":"Sakhteman","year":"2019","journal-title":"Curr. Drug Discov. Technol."},{"key":"ref_88","doi-asserted-by":"crossref","unstructured":"Jayaram, B., Dhingra, P., Mishra, A., Kaushik, R., Mukherjee, G., Singh, A., and Shekhar, S. (2014). Bhageerath-H: A homology\/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins. BMC Bioinform., 15.","DOI":"10.1186\/1471-2105-15-S16-S7"},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Cheng, P., Xue, Y., Wang, J., Jia, Z., Wang, L., and Gong, W. (2022). Evaluation of the consistence between the results of immunoinformatics predictions and real-world animal experiments of a new tuberculosis vaccine MP3RT. Front. Cell. Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.1047306"},{"key":"ref_90","doi-asserted-by":"crossref","unstructured":"Motamedi, H., Ari, M.M., Shahlaei, M., Moradi, S., Farhadikia, P., Alvandi, A., and Abiri, R. (2023). Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach. BMC Bioinform., 24.","DOI":"10.1186\/s12859-023-05197-0"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/j.ijbiomac.2020.02.297","article-title":"Receptor-ligand based molecular interaction to discover adjuvant for immune cell TLRs to develop next-generation vaccine","volume":"152","author":"Gupta","year":"2020","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"Biswas, S., Mahmud, S., Mita, M.A., Afrose, S., Hasan, M.R., Sultana Shimu, M.S., Saleh, M.A., Mostafa-Hedeab, G., Alqarni, M., and Obaidullah, A.J. (2022). Molecular docking and dynamics studies to explore effective inhibitory peptides against the spike receptor binding domain of SARS-CoV-2. Front. Mol. Biosci., 8.","DOI":"10.3389\/fmolb.2021.791642"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1186\/s12967-022-03590-6","article-title":"In silico designing of a novel epitope-based candidate vaccine against Streptococcus pneumoniae with introduction of a new domain of PepO as adjuvant","volume":"20","author":"Bahadori","year":"2022","journal-title":"J. Transl. Med."},{"key":"ref_94","doi-asserted-by":"crossref","unstructured":"Durrant, J.D., and McCammon, J.A. (2011). Molecular dynamics simulations and drug discovery. BMC Biol., 9.","DOI":"10.1186\/1741-7007-9-71"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1016\/j.molimm.2019.09.014","article-title":"B-cell epitopes: Discontinuity and conformational analysis","volume":"114","author":"Ferdous","year":"2019","journal-title":"Mol. Immunol."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"105290","DOI":"10.1016\/j.meegid.2022.105290","article-title":"Engineering a novel immunogenic chimera protein utilizing bacterial infections associated with atherosclerosis to induce a deviation in adaptive immune responses via Immunoinformatics approaches","volume":"102","author":"Saleki","year":"2022","journal-title":"Infect. Genet. Evol."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1093\/cid\/ciac796","article-title":"Booster vaccination against SARS-CoV-2 induces potent immune responses in people with human immunodeficiency virus","volume":"76","author":"Fidler","year":"2023","journal-title":"Clin. Infect. Dis."},{"key":"ref_98","doi-asserted-by":"crossref","unstructured":"Chatterjee, R., Sahoo, P., Mahapatra, S.R., Dey, J., Ghosh, M., Kushwaha, G.S., Misra, N., Suar, M., Raina, V., and Son, Y.O. (2021). Development of a conserved chimeric vaccine for induction of strong immune response against Staphylococcus aureus using immunoinformatics approaches. Vaccines, 9.","DOI":"10.3390\/vaccines9091038"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1007\/s40203-023-00140-w","article-title":"In silico design of a novel peptide-based vaccine against the ubiquitous apicomplexan Toxoplasma gondii using surface antigens","volume":"11","author":"Shams","year":"2023","journal-title":"Silico Pharmacol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"4859","DOI":"10.1016\/j.sjbs.2021.06.082","article-title":"Designing a highly immunogenic multi epitope based subunit vaccine against Bacillus cereus","volume":"28","author":"Rasheed","year":"2021","journal-title":"Saudi J. Biol. Sci."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"100394","DOI":"10.1016\/j.imu.2020.100394","article-title":"A SARS-CoV-2 vaccine candidate: In-silico cloning and validation","volume":"20","author":"Bhattacharya","year":"2020","journal-title":"Inform. Med. Unlocked"},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1093\/hmg\/ddac209","article-title":"Disease correction in mucopolysaccharidosis type IIIB mice by intraparenchymal or cisternal delivery of a capsid modified AAV8 codon-optimized NAGLU vector","volume":"32","author":"Rouse","year":"2023","journal-title":"Hum. Mol. Genet."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"W277","DOI":"10.1093\/nar\/gkp367","article-title":"CENTROIDFOLD: A web server for RNA secondary structure prediction","volume":"37","author":"Sato","year":"2009","journal-title":"Nucleic Acids Res."}],"container-title":["Bioengineering"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-5354\/11\/5\/505\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T14:44:03Z","timestamp":1760107443000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-5354\/11\/5\/505"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,17]]},"references-count":103,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2024,5]]}},"alternative-id":["bioengineering11050505"],"URL":"https:\/\/doi.org\/10.3390\/bioengineering11050505","relation":{},"ISSN":["2306-5354"],"issn-type":[{"value":"2306-5354","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,5,17]]}}}