{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T19:44:09Z","timestamp":1769197449643,"version":"3.49.0"},"reference-count":36,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2023,3,17]],"date-time":"2023-03-17T00:00:00Z","timestamp":1679011200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Javna agencija za raziskovalno dejavnost Republike Slovenije","award":["ARRS\/P3-0428"],"award-info":[{"award-number":["ARRS\/P3-0428"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>Vaccination against dengue virus is challenged by the fact that a generic immune response can induce antibody-dependent-enhancement (ADE) in secondary infections. Only some antibodies targeting a quaternary epitope formed by the dimerization of the virus protein E possess sufficient neutralizing capacity. Therefore, the immunization with anti-idiotypic antibodies of neutralizing antibodies might represent a safe vaccination strategy. Starting from a large pre-immune library, we succeeded in isolating a wide set of anti-idiotypic nanobodies characterized by selective and strong binding to the paratope of the neutralizing antibody 1C10. However, the mice immunized with such constructs did not produce effective antibodies, despite at least some of them eliciting an immune response selective for the nanobody variable regions. The results suggest that complex conformational epitopes might be difficult to be recreated by anti-idiotypic structures. The selection process of the anti-idiotypic candidates might be optimized by applying epitope mapping and modeling approaches aimed at identifying the key residues that is necessary to bind to trigger selective immune response.<\/jats:p>","DOI":"10.3390\/biom13030551","type":"journal-article","created":{"date-parts":[[2023,3,20]],"date-time":"2023-03-20T04:33:31Z","timestamp":1679286811000},"page":"551","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Nanobodies Selectively Binding to the Idiotype of a Dengue Virus Neutralizing Antibody Do Not Necessarily Mimic the Viral Epitope"],"prefix":"10.3390","volume":"13","author":[{"given":"Monica","family":"Poggianella","sequence":"first","affiliation":[{"name":"Molecular Immunology Laboratory, International Centre for Genetic Engineering and Biotechnolgy, Padriciano 99, 34149 Trieste, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Bernedo","sequence":"additional","affiliation":[{"name":"Laboratory for Environmental and Life Sciences, University of Nova Gorica, 5000 Nova Gorica, Slovenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandra","family":"Oloketuyi","sequence":"additional","affiliation":[{"name":"Laboratory for Environmental and Life Sciences, University of Nova Gorica, 5000 Nova Gorica, Slovenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7729-819X","authenticated-orcid":false,"given":"Ario","family":"de Marco","sequence":"additional","affiliation":[{"name":"Laboratory for Environmental and Life Sciences, University of Nova Gorica, 5000 Nova Gorica, Slovenia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,3,17]]},"reference":[{"key":"ref_1","first-page":"159","article-title":"Idiotypes as immunogens: Facing the challenge of inducing strong therapeutic immune responses against the variable region of immunoglobulins","volume":"2","author":"Burrone","year":"2012","journal-title":"Front. Oncol."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"D\u00fcbel, S., and Reichert, J.M. (2014). Handbook of Therapeutic Antibodies, Wiley-VCH Verlag GmbH & Co. KGaA. [2nd ed.].","DOI":"10.1002\/9783527682423"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/375291a0","article-title":"The envelope glycoprotein from tick-borne encephalitis virus at 2 \u00c5 resolution","volume":"375","author":"Rey","year":"1995","journal-title":"Nature"},{"key":"ref_4","unstructured":"Knipe, D.M., and Howley, P.M. (2007). Fields Virology, Lippincott-Raven Publishers. [5th ed.]."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/j.virol.2011.01.030","article-title":"Amino acid changes within the E protein hinge region that affect dengue virus type 2 infectivity and fusion","volume":"413","author":"Butrapet","year":"2020","journal-title":"Virology"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/nrmicro1067","article-title":"A structural perspective of the flavivirus life cycle","volume":"3","author":"Mukhopadhyay","year":"2005","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/nsb990","article-title":"Visualization of membrane protein domains by cryo-electron microscopy of dengue virus","volume":"10","author":"Zhang","year":"2003","journal-title":"Nat. Struct. Biol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/ni.3058","article-title":"A new class of highly potent, broadly neutralizing antibodies isolated from viremic patients infected with dengue virus","volume":"16","author":"Dejnirattisai","year":"2015","journal-title":"Nat. Immunol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1038\/nature18938","article-title":"Structural basis of potent Zika-dengue virus antibody cross-neutralization","volume":"536","author":"Dejnirattisai","year":"2016","journal-title":"Nature"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/nature14130","article-title":"Recognition determinants of broadly neutralizing human antibodies against dengue viruses","volume":"520","author":"Rouvinski","year":"2015","journal-title":"Nature"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1038\/s41598-017-01097-5","article-title":"Temperature-dependent folding allows stable dimerization of secretory and virus-associated E proteins of Dengue and Zika viruses in mammalian cells","volume":"7","author":"Marchese","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Poggianella, M., Slon Campos, J.L., Chan, K.R., Tan, H.C., Bestagno, M., Ooi, E.E., and Burrone, O.R. (2015). Dengue E protein domain III-based DNA immunisation induces strong antibody responses to all four viral serotypes. PLoS Negl. Trop. Dis., 9.","DOI":"10.1371\/journal.pntd.0003947"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Slon Campos, J.L., Poggianella, M., Marchese, S., Mossenta, M., Rana, J., Arnoldi, F., Bestagno, M., and Burrone, O.R. (2017). DNA-immunisation with dengue virus E protein domains I\/II, but not domain III, enhances Zika, West Nile and Yellow Fever virus infection. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0181734"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2649","DOI":"10.3390\/v2122649","article-title":"The complexity of antibody-dependent enhancement of dengue virus infection","volume":"2","author":"Guzman","year":"2010","journal-title":"Viruses"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1093\/protein\/gzp002","article-title":"Immunological applications of single domain llama recombinant antibodies isolated from a na\u00efve library","volume":"22","author":"Monegal","year":"2009","journal-title":"Protein Eng. Des. Sel."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Predonzani, A., Arnoldi, F., L\u00f3pez-Requena, A., and Burrone, O.R. (2008). In vivo site-specific biotinylation of proteins within the secretory pathway using a single vector system. BMC Biotechnol., 8.","DOI":"10.1186\/1472-6750-8-41"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e01415-20","DOI":"10.1128\/JVI.01415-20","article-title":"Zika Virus-Like particles bearing a covalent dimer of envelope protein protect mice from lethal challenge","volume":"95","author":"Tandavanitj","year":"2020","journal-title":"J. Virol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"15411","DOI":"10.1038\/ncomms15411","article-title":"Covalently linked dengue virus envelope glycoprotein dimers reduce exposure of the immunodominant fusion loop epitope","volume":"8","author":"Rouvinski","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1093\/protein\/gzy017","article-title":"Analysis of nanobody paratopes reveals greater diversity than classical antibodies","volume":"31","author":"Mitchell","year":"2018","journal-title":"Protein Eng. Des. Sel."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1016\/j.dci.2011.06.016","article-title":"Single heavy chain antibodies with VH hallmarks are positively selected during panning of llama (Lama glama) na\u00efve libraries","volume":"36","author":"Monegal","year":"2012","journal-title":"Dev. Comp. Immunol."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Soler, M.A., Medagli, B., Wang, J., Oloketuyi, S., Bajc, G., Huang, H., Fortuna, S., and de Marco, A. (2021). Effect of humanizing mutations on the stability of the llama single-domain variable region. Biomolecules, 11.","DOI":"10.3390\/biom11020163"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Lei, J., Han, X., Tang, X., Wang, H., and Zhang, Q. (2020). Development of Anti-Idiotypic Nanobody-Phage Based Immuno-Loop-Mediated Isothermal Amplification Assay for Aflatoxins in Peanuts. Toxins, 12.","DOI":"10.3390\/toxins12090565"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.1016\/j.tibtech.2022.02.008","article-title":"A new chapter for anti-idiotypes in low molecular weight compound immunoassays","volume":"40","author":"Mills","year":"2022","journal-title":"Trends Biotechnol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1016\/j.talanta.2015.05.010","article-title":"Anti-idiotypic nanobody: A strategy for development of sensitive and green immunoassay for Fumonisin B1","volume":"143","author":"Shu","year":"2015","journal-title":"Talanta"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"9676","DOI":"10.1038\/s41598-017-10513-9","article-title":"Semi-synthetic vNAR libraries screened against therapeutic antibodies primarily deliver anti-idiotypic binders","volume":"7","author":"Rhiel","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1007\/978-1-4939-9853-1_11","article-title":"Selection and Characterization of Anti-idiotypic Shark Antibody Domains","volume":"2070","author":"Zielonka","year":"2020","journal-title":"Methods Mol. Biol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"261","DOI":"10.2144\/btn-2019-0089","article-title":"Affimers as anti-idiotypic affinity reagents for pharmacokinetic analysis of biotherapeutics","volume":"67","author":"Adamson","year":"2019","journal-title":"Biotechniques"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"4826","DOI":"10.1016\/j.vaccine.2009.05.067","article-title":"A llama single domain anti-idiotypic antibody mimicking HER2 as a vaccine: Immunogenicity and efficacy","volume":"27","author":"Ladjemi","year":"2009","journal-title":"Vaccine"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"7120","DOI":"10.4049\/jimmunol.178.11.7120","article-title":"Novel engineered trastuzumab conformational epitopes demonstrate in vitro and in vivo antitumor properties against HER-2\/neu","volume":"178","author":"Garrett","year":"2007","journal-title":"J. Immunol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"4656","DOI":"10.1074\/jbc.M411047200","article-title":"A novel peptide isolated from a phage display peptide library with trastuzumab can mimic antigen epitope of HER-2","volume":"280","author":"Jiang","year":"2005","journal-title":"J. Biol. Chem."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.jviromet.2015.06.003","article-title":"Development and characterization of mouse monoclonal antibodies against monomeric dengue virus non-structural glycoprotein 1 (NS1)","volume":"222","author":"Gelanew","year":"2015","journal-title":"J. Virol. Methods"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s12985-018-0925-7","article-title":"Development and characterization of serotype-specific monoclonal antibodies against the dengue virus-4 (DENV-4) non-structural protein (NS1)","volume":"15","author":"Gelanew","year":"2018","journal-title":"Virol. J."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"18086","DOI":"10.1038\/s41598-018-35923-1","article-title":"Selection and Characterization of Anti-Dengue NS1 Single Domain Antibodies","volume":"8","author":"Liu","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Leivo, J., Vehni\u00e4inen, M., and Lamminm\u00e4ki, U. (2020). Phage display selection of an anti-idiotype-antibody with broad-specificity to deoxynivalenol mycotoxins. Toxins, 13.","DOI":"10.3390\/toxins13010018"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.ijbiomac.2021.11.160","article-title":"Interference of p53:Twist1 interaction through competing nanobodies","volume":"194","author":"Mazzega","year":"2022","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"11669","DOI":"10.1021\/acs.analchem.1c00696","article-title":"Epitope mapping of polyclonal antibodies by hydrogen-deuterium exchange mass spectrometry (HDX-MS)","volume":"93","author":"Grauslund","year":"2021","journal-title":"Anal. Chem."}],"container-title":["Biomolecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2218-273X\/13\/3\/551\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T18:57:40Z","timestamp":1760122660000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2218-273X\/13\/3\/551"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,17]]},"references-count":36,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2023,3]]}},"alternative-id":["biom13030551"],"URL":"https:\/\/doi.org\/10.3390\/biom13030551","relation":{},"ISSN":["2218-273X"],"issn-type":[{"value":"2218-273X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,3,17]]}}}