{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T05:16:15Z","timestamp":1787030175305,"version":"build-2736575974"},"reference-count":41,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2021,6,18]],"date-time":"2021-06-18T00:00:00Z","timestamp":1623974400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Vaccines"],"abstract":"<jats:p>Moraxella catarrhalis (M. catarrhalis) is a Gram-negative bacterium that can cause serious respiratory tract infections and middle ear infections in children and adults. M. catarrhalis has demonstrated an increasing rate of antibiotic resistance in the last few years, thus development of an effective vaccine is a major health priority. We report here a novel designed multitope vaccine based on the mapped epitopes of the vaccine candidates filtered out of the whole proteome of M. catarrhalis. After analysis of 1615 proteins using a reverse vaccinology approach, only two proteins (outer membrane protein assembly factor BamA and LPS assembly protein LptD) were nominated as potential vaccine candidates. These proteins were found to be essential, outer membrane, virulent and non-human homologs with appropriate molecular weight and high antigenicity score. For each protein, cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL) and B cell lymphocyte (BCL) epitopes were predicted and confirmed to be highly antigenic and cover conserved regions of the proteins. The mapped epitopes constituted the base of the designed multitope vaccine where suitable linkers were added to conjugate them. Additionally, beta defensin adjuvant and pan-HLA DR-binding epitope (PADRE) peptide were also incorporated into the construct to improve the stimulated immune response. The constructed multitope vaccine was analyzed for its physicochemical, structural and immunological characteristics and it was found to be antigenic, soluble, stable, non-allergenic and have a high affinity to its target receptor. Although the in silico analysis of the current study revealed that the designed multitope vaccine has the ability to trigger a specific immune response against M. catarrhalis, additional translational research is required to confirm the effectiveness of the designed vaccine.<\/jats:p>","DOI":"10.3390\/vaccines9060669","type":"journal-article","created":{"date-parts":[[2021,6,20]],"date-time":"2021-06-20T21:50:15Z","timestamp":1624225815000},"page":"669","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":67,"title":["In Silico Prediction of a Multitope Vaccine against Moraxella catarrhalis: Reverse Vaccinology and Immunoinformatics"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3030-1659","authenticated-orcid":false,"given":"Mohamed A.","family":"Soltan","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nada","family":"Elbassiouny","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2188-8566","authenticated-orcid":false,"given":"Helmy","family":"Gamal","sequence":"additional","affiliation":[{"name":"Biochemistry Division, Chemistry Department, Faculty of Science, Mansoura University, Mansura 35516, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2546-8035","authenticated-orcid":false,"given":"Eslam B.","family":"Elkaeed","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Ad Diriyah, Riyadh 13713, Saudi Arabia"},{"name":"Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5633-9562","authenticated-orcid":false,"given":"Refaat A.","family":"Eid","sequence":"additional","affiliation":[{"name":"Department of Pathology, College of Medicine, King Khalid University, Abha 62529, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5280-7736","authenticated-orcid":false,"given":"Muhammad Alaa","family":"Eldeen","sequence":"additional","affiliation":[{"name":"Cell Biology, Histology & Genetics Division, Zoology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8173-6073","authenticated-orcid":false,"given":"Ahmed A.","family":"Al-Karmalawy","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,6,18]]},"reference":[{"key":"ref_1","first-page":"w13694","article-title":"Molecular pathogenesis of infections caused by Moraxella catarrhalis in children","volume":"142","author":"Bernhard","year":"2012","journal-title":"Swiss Med. Wkly."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Singh, B., Alvarado-Kristensson, M., Johansson, M., Hallgren, O., Westergren-Thorsson, G., M\u00f6rgelin, M., and Riesbeck, K. (2016). The Respiratory Pathogen Moraxella catarrhalis Targets Collagen for Maximal Adherence to Host Tissues. mBio, 7.","DOI":"10.1128\/mBio.00066-16"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1111\/2049-632X.12129","article-title":"Residence ofStreptococcus pneumoniaeandMoraxella catarrhaliswithin polymicrobial biofilm promotes antibiotic resistance and bacterial persistencein vivo","volume":"70","author":"Perez","year":"2014","journal-title":"Pathog. Dis."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1517\/14728222.2015.1081686","article-title":"Vaccine targets againstMoraxella catarrhalis","volume":"20","author":"Ren","year":"2016","journal-title":"Expert Opin. Ther. Targets"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.1086\/382508","article-title":"Intranasal Vaccination with Recombinant P6 Protein and Adamantylamide Dipeptide as Mucosal Adjuvant Confers Efficient Protection against Otitis Media and Lung Infection by Nontypeable Haemophilus influenzae","volume":"189","author":"Bertot","year":"2004","journal-title":"J. Infect. Dis."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"5603","DOI":"10.1016\/j.vaccine.2011.06.019","article-title":"Temporal development of the humoral immune response to surface antigens of Moraxella catarrhalis in young infants","volume":"29","author":"Verhaegh","year":"2011","journal-title":"Vaccine"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"99","DOI":"10.7774\/cevr.2015.4.1.99","article-title":"In silicoanalysis for identifying potential vaccine candidates againstStaphylococcus aureus","volume":"4","author":"Delfani","year":"2015","journal-title":"Clin. Exp. Vaccine Res."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1080\/17460441.2018.1413088","article-title":"The use of databases, data mining and immunoinformatics in vaccinology: Where are we?","volume":"13","author":"Hegde","year":"2018","journal-title":"Expert Opin. Drug Discov."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Capelli, R., Peri, C., Villa, R., Nithichanon, A., Conchillo-Sol\u00e9, O., Yero, D., Gagni, P., Chiari, M., Lertmemongkolchai, G., and Cretich, M. (2018). BPSL1626: Reverse and Structural Vaccinology Reveal a Novel Candidate for Vaccine Design Against Burkholderia pseudomallei. Antibodies, 7.","DOI":"10.3390\/antib7030026"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Carvalho, T.F., Haddad, J.P.A., Paix\u00e3o, T.A., and Santos, R.L. (2016). Meta-Analysis and Advancement of Brucellosis Vaccinology. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0166582"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.3389\/fmicb.2019.01236","article-title":"Geptop 2.0: An Updated, More Precise, and Faster Geptop Server for Identification of Prokaryotic Essential Genes","volume":"10","author":"Wen","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_12","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_13","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/S1672-0229(06)60015-6","article-title":"VICMpred: An SVM-based method for the prediction of functional proteins of Gram-negative bacteria using amino acid patterns and composition","volume":"4","author":"Saha","year":"2006","journal-title":"Genom. Proteom. Bioinforma"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden markov model: Application to complete genomes11Edited by F. Cohen","volume":"305","author":"Krogh","year":"2001","journal-title":"J. Mol. Biol."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Walker, J.M. (2005). Protein Identification and Analysis Tools on the ExPASy Server. The Proteomics Protocols Handbook, Humana Press.","DOI":"10.1385\/1592598900"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Doytchinova, I.A., and Flower, D.R. (2007). VaxiJen: A server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinform., 8.","DOI":"10.1186\/1471-2105-8-4"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"E2046","DOI":"10.1073\/pnas.1305227110","article-title":"Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells","volume":"110","author":"Weiskopf","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1007\/s00251-011-0513-0","article-title":"Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes","volume":"63","author":"Greenbaum","year":"2011","journal-title":"Immunogenetics"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.meegid.2016.12.010","article-title":"Immunoinformatics analysis and in silico designing of a novel multi-epitope peptide vaccine against Staphylococcus aureus","volume":"48","author":"Hajighahramani","year":"2017","journal-title":"Infect. Genet. Evol."},{"key":"ref_20","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_21","doi-asserted-by":"crossref","first-page":"W384","DOI":"10.1093\/nar\/gkt458","article-title":"GalaxyRefine: Protein structure refinement driven by side-chain repacking","volume":"41","author":"Heo","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.micpath.2019.02.023","article-title":"Reverse vaccinology approach to design a novel multi-epitope subunit vaccine against avian influenza A (H7N9) virus","volume":"130","author":"Hasan","year":"2019","journal-title":"Microb. Pathog."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"W407","DOI":"10.1093\/nar\/gkm290","article-title":"ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins","volume":"35","author":"Wiederstein","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_24","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_25","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-018-26689-7","article-title":"Subtractive proteomics to identify novel drug targets and reverse vaccinology for the development of chimeric vaccine against Acinetobacter baumannii","volume":"8","author":"Solanki","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_26","first-page":"79","article-title":"The role of TLR2 ininfection and immunity","volume":"3","author":"Massari","year":"2012","journal-title":"Front. Immunol."},{"key":"ref_27","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_28","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.biopha.2016.06.010","article-title":"High-throughput virtual screening and quantum mechanics approach to develop imipramine analogues as leads against trypanothione reductase of leishmania","volume":"83","author":"Pandey","year":"2016","journal-title":"Biomed. Pharmacother."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Awan, F.M., Obaid, A., Ikram, A., and Janjua, H.A. (2017). Mutation-Structure-Function Relationship Based Integrated Strategy Reveals the Potential Impact of Deleterious Missense Mutations in Autophagy Related Proteins on Hepatocellular Carcinoma (HCC): A Comprehensive Informatics Approach. Int. J. Mol. Sci., 18.","DOI":"10.3390\/ijms18010139"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"W271","DOI":"10.1093\/nar\/gku339","article-title":"iMODS: Internal coordinates normal mode analysis server","volume":"42","author":"Aliaga","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"W526","DOI":"10.1093\/nar\/gki376","article-title":"JCat: A novel tool to adapt codon usage of a target gene to its potential expression host","volume":"33","author":"Grote","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"837","DOI":"10.2217\/pgs.09.25","article-title":"Application of pharmacogenomics to vaccines","volume":"10","author":"Poland","year":"2009","journal-title":"Pharmacogenomics"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"3096","DOI":"10.1016\/j.vaccine.2017.04.031","article-title":"Evaluation of tandem Chlamydia trachomatis MOMP multi-epitopes vaccine in BALB\/c mice model","volume":"35","author":"Jiang","year":"2017","journal-title":"Vaccine"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1089\/omi.2019.0183","article-title":"Design of Staphylococcus aureus New Vaccine Candidates with B and T Cell Epitope Mapping, Reverse Vaccinology, and Immunoinformatics","volume":"24","author":"Soltan","year":"2020","journal-title":"OMICS A J. Integr. Biol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"15","DOI":"10.7774\/cevr.2020.9.1.15","article-title":"Reverse vaccinology approach for the identification and characterization of outer membrane proteins of Shigella flexneri as potential cellular- and antibody-dependent vaccine candidates","volume":"9","author":"Leow","year":"2020","journal-title":"Clin. Exp. Vaccine Res."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12859-017-1540-0","article-title":"VacSol: A high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology","volume":"18","author":"Rizwan","year":"2017","journal-title":"BMC Bioinform."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/S1286-4579(02)01545-9","article-title":"Outer membrane proteins: Key players for bacterial adaptation in host niches","volume":"4","author":"Lin","year":"2002","journal-title":"Microbes Infect."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/nrmicro.2016.25","article-title":"Lipopolysaccharide transport and assembly at the outer mem-brane: The PEZ model","volume":"14","author":"Okuda","year":"2016","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-019-55613-w","article-title":"Designing a multi-epitopic vaccine against the enterotoxigenic Bacteroides fragilis based on immunoinformatics approach","volume":"9","author":"Majid","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1938","DOI":"10.1093\/infdis\/jiw062","article-title":"Immunoinformatics Identifies a Lactoferrin Binding Protein A Peptide as a Promising Vaccine With a Global Protective Prospective AgainstMoraxella catarrhalis","volume":"213","author":"Yassin","year":"2016","journal-title":"J. Infect. Dis."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Ghaffari-Nazari, H., Tavakkol-Afshari, J., Jaafari, M.R., Tahaghoghi-Hajghorbani, S., Masoumi, E., and Jalali, S.A. (2015). Improving Multi-Epitope Long Peptide Vaccine Potency by Using a Strategy that Enhances CD4+ T Help in BALB\/c Mice. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0142563"}],"container-title":["Vaccines"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-393X\/9\/6\/669\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T06:18:26Z","timestamp":1760163506000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-393X\/9\/6\/669"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,6,18]]},"references-count":41,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2021,6]]}},"alternative-id":["vaccines9060669"],"URL":"https:\/\/doi.org\/10.3390\/vaccines9060669","relation":{},"ISSN":["2076-393X"],"issn-type":[{"value":"2076-393X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,6,18]]}}}