Show simple item record

dc.contributor.authorContreras M.A
dc.contributor.authorSerrano-Rivero Y
dc.contributor.authorGonzález-Pose A
dc.contributor.authorSalazar-Uribe J
dc.contributor.authorRubio-Carrasquilla M
dc.contributor.authorSoares-Alves M
dc.contributor.authorParra N.C
dc.contributor.authorCamacho-Casanova F
dc.contributor.authorSánchez-Ramos O
dc.contributor.authorMoreno E.
dc.date.accessioned2023-10-24T19:24:00Z
dc.date.available2023-10-24T19:24:00Z
dc.date.created2023
dc.identifier.issn14203049
dc.identifier.urihttp://hdl.handle.net/11407/7902
dc.description.abstractNanobodies (Nbs) are single domain antibody fragments derived from heavy-chain antibodies found in members of the Camelidae family. They have become a relevant class of biomolecules for many different applications because of several important advantages such as their small size, high solubility and stability, and low production costs. On the other hand, synthetic Nb libraries are emerging as an attractive alternative to animal immunization for the selection of antigen-specific Nbs. Here, we present the design and construction of a new synthetic nanobody library using the phage display technology, following a structure-based approach in which the three hypervariable loops were subjected to position-specific randomization schemes. The constructed library has a clonal diversity of 108 and an amino acid variability that matches the codon distribution set by design at each randomized position. We have explored the capabilities of the new library by selecting nanobodies specific for three antigens: vascular endothelial growth factor (VEGF), tumor necrosis factor (TNF) and the glycoprotein complex (GnGc) of Andes virus. To test the potential of the library to yield a variety of antigen-specific Nbs, we introduced a biopanning strategy consisting of a single selection round using stringent conditions. Using this approach, we obtained several binders for each of the target antigens. The constructed library represents a promising nanobody source for different applications. © 2023 by the authors.eng
dc.language.isoeng
dc.publisherMDPI
dc.relation.isversionofhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85159311205&doi=10.3390%2fmolecules28093708&partnerID=40&md5=c0ff280c23421835560e4aa5146af1dc
dc.sourceMolecules
dc.sourceMoleculeseng
dc.subjectAndes viruseng
dc.subjectBiopanningeng
dc.subjectCDR randomizationeng
dc.subjectNanobodyeng
dc.subjectPhage displayeng
dc.subjectSynthetic libraryeng
dc.subjectTumor necrosis factoreng
dc.subjectVascular endothelial growth factoreng
dc.titleDesign and Construction of a Synthetic Nanobody Library: Testing Its Potential with a Single Selection Round Strategyeng
dc.typeArticle
dc.rights.accessrightsinfo:eu-repo/semantics/restrictedAccess
dc.publisher.programCiencias Básicasspa
dc.type.spaArtículo
dc.identifier.doi10.3390/molecules28093708
dc.relation.citationvolume28
dc.relation.citationissue9
dc.publisher.facultyFacultad de Ciencias Básicasspa
dc.affiliationContreras, M.A., Pharmacology Department, School of Biological Sciences, University of Concepcion, Concepcion, 4070386, Chile
dc.affiliationSerrano-Rivero, Y., Faculty of Basic Sciences, University of Medellin, Medellin, 050026, Colombia
dc.affiliationGonzález-Pose, A., Faculty of Basic Sciences, University of Medellin, Medellin, 050026, Colombia
dc.affiliationSalazar-Uribe, J., Faculty of Basic Sciences, University of Medellin, Medellin, 050026, Colombia
dc.affiliationRubio-Carrasquilla, M., Faculty of Basic Sciences, University of Medellin, Medellin, 050026, Colombia
dc.affiliationSoares-Alves, M., Pharmacology Department, School of Biological Sciences, University of Concepcion, Concepcion, 4070386, Chile
dc.affiliationParra, N.C., Pharmacology Department, School of Biological Sciences, University of Concepcion, Concepcion, 4070386, Chile
dc.affiliationCamacho-Casanova, F., Pharmacology Department, School of Biological Sciences, University of Concepcion, Concepcion, 4070386, Chile
dc.affiliationSánchez-Ramos, O., Pharmacology Department, School of Biological Sciences, University of Concepcion, Concepcion, 4070386, Chile
dc.affiliationMoreno, E., Faculty of Basic Sciences, University of Medellin, Medellin, 050026, Colombia
dc.relation.referencesHamers-Casterman, C., Atarhouch, T., Muyldermans, S., Robinson, G., Hammers, C., Songa, E.B., Bendahman, N., Hammers, R., Naturally Occurring Antibodies Devoid of Light Chains (1993) Nature, 363, pp. 446-448. , 8502296
dc.relation.referencesValdés-Tresanco, M.S., Valdés-Tresanco, M.E., Molina-Abad, E., Moreno, E., NbThermo: A New Thermostability Database for Nanobodies (2023) Database, p. baad021. , 37042467
dc.relation.referencesHassanzadeh-Ghassabeh, G., Devoogdt, N., De Pauw, P., Vincke, C., Muyldermans, S., Nanobodies and Their Potential Applications (2013) Nanomedicine, 8, pp. 1013-1026. , 23730699
dc.relation.referencesMorrison, C., Nanobody Approval Gives Domain Antibodies a Boost (2019) Nat. Rev. Drug. Discov, 18, pp. 485-487
dc.relation.referencesKeam, S.J., Ozoralizumab: First Approval (2023) Drugs, 83, pp. 87-92
dc.relation.referencesMuyldermans, S., A Guide to: Generation and Design of Nanobodies (2021) FEBS. J, 288, pp. 2084-2102
dc.relation.referencesValdés-Tresanco, M.S., Molina-Zapata, A., Pose, A.G., Moreno, E., Structural Insights into the Design of Synthetic Nanobody Libraries (2022) Molecules, 27
dc.relation.referencesMoutel, S., Bery, N., Bernard, V., Keller, L., Lemesre, E., de Marco, A., Ligat, L., Olichon, A., NaLi-H1: A Universal Synthetic Library of Humanized Nanobodies Providing Highly Functional Antibodies and Intrabodies (2016) Elife, 5, p. e16228
dc.relation.referencesMcMahon, C., Baier, A.S., Pascolutti, R., Wegrecki, M., Zheng, S., Ong, J.X., Erlandson, S.C., Ring, A.M., Yeast Surface Display Platform for Rapid Discovery of Conformationally Selective Nanobodies (2018) Nat. Struct. Mol. Biol, 25, pp. 289-296
dc.relation.referencesZimmermann, I., Egloff, P., Hutter, C.A., Arnold, F.M., Stohler, P., Bocquet, N., Hug, M.N., Hetemann, L., Synthetic Single Domain Antibodies for the Conformational Trapping of Membrane Proteins (2018) Elife, 7, p. e34317
dc.relation.referencesSevy, A.M., Chen, M.-T., Castor, M., Sylvia, T., Krishnamurthy, H., Ishchenko, A., Hsieh, C.-M., Structure- and Sequence-Based Design of Synthetic Single-Domain Antibody Libraries (2020) Protein. Eng. Des. Selection, 33, p. gzaa028
dc.relation.referencesZimmermann, I., Egloff, P., Hutter, C.A.J., Kuhn, B.T., Bräuer, P., Newstead, S., Dawson, R.J.P., Seeger, M.A., Generation of Synthetic Nanobodies against Delicate Proteins (2020) Nat. Protoc, 15, pp. 1707-1741
dc.relation.referencesZhao, Y., Wang, Y., Su, W., Li, S., Construction of Synthetic Nanobody Library in Mammalian Cells by DsDNA-Based Strategies (2021) Chem. BioChem, 22, pp. 2957-2965
dc.relation.referencesChen, X., Gentili, M., Hacohen, N., Regev, A., A Cell-Free Nanobody Engineering Platform Rapidly Generates SARS-CoV-2 Neutralizing Nanobodies (2021) Nat. Commun, 12, p. 5506
dc.relation.referencesMoreno, E., Valdés-Tresanco, M.S., Molina-Zapata, A., Sánchez-Ramos, O., Structure-Based Design and Construction of a Synthetic Phage Display Nanobody Library (2022) BMC. Res. Notes, 15
dc.relation.referencesDe Genst, E., Silence, K., Decanniere, K., Conrath, K., Loris, R., Kinne, J., Muyldermans, S., Wyns, L., Molecular Basis for the Preferential Cleft Recognition by Dromedary Heavy-Chain Antibodies (2006) Proc. Natl. Acad. Sci. USA, 103, pp. 4586-4591
dc.relation.referencesUchański, T., Pardon, E., Steyaert, J., Nanobodies to Study Protein Conformational States (2020) Curr. Opin. Struct. Biol, 60, pp. 117-123
dc.relation.referencesShi, Z., Li, X., Wang, L., Sun, Z., Zhang, H., Chen, X., Cui, Q., Zhang, X., Structural Basis of Nanobodies Neutralizing SARS-CoV-2 Variants (2022) Structure, 30, pp. 707-720.e5
dc.relation.referencesConrath, K.E., Lauwereys, M., Galleni, M., Matagne, A., Frère, J.-M., Kinne, J., Wyns, L., Muyldermans, S., β-Lactamase Inhibitors Derived from Single-Domain Antibody Fragments Elicited in the Camelidae (2001) Antimicrob. Agents. Chemother, 45, pp. 2807-2812
dc.relation.referencesDumoulin, M., Conrath, K., Van Meirhaeghe, A., Meersman, F., Heremans, K., Frenken, L.G.J., Muyldermans, S., Matagne, A., Single-Domain Antibody Fragments with High Conformational Stability (2002) Protein. Sci, 11, pp. 500-515
dc.relation.referencesSaerens, D., Pellis, M., Loris, R., Pardon, E., Dumoulin, M., Matagne, A., Wyns, L., Conrath, K., Identification of a Universal VHH Framework to Graft Non-Canonical Antigen-Binding Loops of Camel Single-Domain Antibodies (2005) J. Mol. Biol, 352, pp. 597-607. , 16095608
dc.relation.referencesWei, G., Meng, W., Guo, H., Pan, W., Liu, J., Peng, T., Chen, L., Chen, C.-Y., Potent Neutralization of Influenza A Virus by a Single-Domain Antibody Blocking M2 Ion Channel Protein (2011) PLoS ONE, 6. , 22164266
dc.relation.referencesYan, J., Li, G., Hu, Y., Ou, W., Wan, Y., Construction of a Synthetic Phage-Displayed Nanobody Library with CDR3 Regions Randomized by Trinucleotide Cassettes for Diagnostic Applications (2014) J. Transl. Med, 12, p. 343. , 25496223
dc.relation.referencesChi, X., Liu, X., Wang, C., Zhang, X., Li, X., Hou, J., Ren, L., Yang, W., Humanized Single Domain Antibodies Neutralize SARS-CoV-2 by Targeting the Spike Receptor Binding Domain (2020) Nat. Commun, 11, p. 4528
dc.relation.referencesVincke, C., Loris, R., Saerens, D., Martinez-Rodriguez, S., Muyldermans, S., Conrath, K., General Strategy to Humanize a Camelid Single-Domain Antibody and Identification of a Universal Humanized Nanobody Scaffold (2009) J. Biol. Chem, 284, pp. 3273-3284
dc.relation.referencesCornish-Bowden, A., Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences: Rcommendations 1984 (1985) Nucleic Acids Res, 13, pp. 3021-3030
dc.relation.referencesHoogenboom, H.R., Griffiths, A.D., Johnson, K.S., Chiswell, D.J., Hudson, P., Winter, G., Multi-Subunit Proteins on the Surface of Filamentous Phage: Methodologies for Displaying Antibody (Fab) Heavy and Light Chains (1991) Nucleic Acids Res, 19, pp. 4133-4137
dc.relation.referencesvan Loo, G., Bertrand, M.J.M., Death by TNF: A Road to Inflammation (2022) Nat. Rev. Immunol, 15, pp. 1-15
dc.relation.referencesLeone, G.M., Mangano, K., Petralia, M.C., Nicoletti, F., Fagone, P., Past, Present and (Foreseeable) Future of Biological Anti-TNF Alpha Therapy (2023) J. Clin. Med, 12
dc.relation.referencesGhalehbandi, S., Yuzugulen, J., Pranjol, M.Z.I., Pourgholami, M.H., The Role of VEGF in Cancer-Induced Angiogenesis and Research Progress of Drugs Targeting VEGF (2023) Eur. J. Pharmacol, p. 175586
dc.relation.referencesArezumand, R., Alibakhshi, A., Ranjbari, J., Ramazani, A., Muyldermans, S., Nanobodies As Novel Agents for Targeting Angiogenesis in Solid Cancers (2017) Front. Immunol, 8, p. 1746
dc.relation.referencesDennis, M.S., Zhang, M., Meng, Y.G., Kadkhodayan, M., Kirchhofer, D., Combs, D., Damico, L.A., Albumin Binding as a General Strategy for Improving the Pharmacokinetics of Proteins (2002) J. Biolo. Chem, 277, pp. 35035-35043
dc.relation.referencesJonsson, A., Dogan, J., Herne, N., Abrahmsen, L., Nygren, P.-A., Engineering of a Femtomolar Affinity Binding Protein to Human Serum Albumin (2008) Protein Eng. Des. Sel, 21, pp. 515-527
dc.relation.referencesJohansson, M.U., Frick, I.-M., Nilsson, H., Kraulis, P.J., Hober, S., Jonasson, P., Linhult, M., Björck, L., Structure, Specificity, and Mode of Interaction for Bacterial Albumin-Binding Modules (2002) J. Biol. Chem, 277, pp. 8114-8120
dc.relation.referencesEble, J.A., Titration ELISA as a Method to Determine the Dissociation Constant of Receptor Ligand Interaction (2018) J. Vis. Exp, 15, p. 57334
dc.relation.referencesLakzaei, M., Rasaee, M.J., Fazaeli, A.A., Aminian, M., A Comparison of Three Strategies for Biopanning of Phage-scFv Library against Diphtheria Toxin (2019) J. Cell. Physiol, 234, pp. 9486-9494
dc.relation.referencesJaroszewicz, W., Morcinek-Orłowska, J., Pierzynowska, K., Gaffke, L., Węgrzyn, G., Phage Display and Other Peptide Display Technologies (2022) FEMS Microbiol. Rev, 46, p. fuab052
dc.relation.referencesScarrone, M., González-Techera, A., Alvez-Rosado, R., Delfin-Riela, T., Modernell, Á., González-Sapienza, G., Lassabe, G., Development of Anti-Human IgM Nanobodies as Universal Reagents for General Immunodiagnostics (2021) New Biotechnol, 64, pp. 9-16
dc.relation.referencesRoshan, R., Naderi, S., Behdani, M., Cohan, R.A., Ghaderi, H., Shokrgozar, M.A., Golkar, M., Kazemi-Lomedasht, F., Isolation and Characterization of Nanobodies against Epithelial Cell Adhesion Molecule as Novel Theranostic Agents for Cancer Therapy (2021) Mol. Immunol, 129, pp. 70-77
dc.relation.referencesKazemi-Lomedasht, F., Behdani, M., Bagheri, K.P., Habibi-Anbouhi, M., Abolhassani, M., Arezumand, R., Shahbazzadeh, D., Mirzahoseini, H., Inhibition of Angiogenesis in Human Endothelial Cell Using VEGF Specific Nanobody (2015) Mol. Immunol, 65, pp. 58-67
dc.relation.referencesWu, M., Tu, Z., Huang, F., He, Q., Fu, J., Li, Y., Panning Anti-LPS Nanobody as a Capture Target to Enrich Vibrio Fluvialis (2019) Biochem. Biophys. Res. Commun, 512, pp. 531-536. , 30905409
dc.relation.referencesLunder, M., Bratkovič, T., Urleb, U., Kreft, S., Štrukelj, B., Ultrasound in Phage Display: A New Approach to Nonspecific Elution (2008) Biotechniques, 44, pp. 893-900. , 18533899
dc.relation.referencesHumphrey, W., Dalke, A., Schulten, K., VMD: Visual Molecular Dynamics (1996) J. Mol. Graph, 14, pp. 33-38. , 8744570
dc.relation.referencesTonikian, R., Zhang, Y., Boone, C., Sidhu, S.S., Identifying Specificity Profiles for Peptide Recognition Modules from Phage-Displayed Peptide Libraries (2007) Nat. Protoc, 2, pp. 1368-1386
dc.relation.referencesChen, G., Sidhu, S.S., Design and Generation of Synthetic Antibody Libraries for Phage Display (2014) Monoclonal Antibodies: Methods and Protocols, pp. 113-131. , Ossipow V., Fischer N., (eds), Humana Press, Totowa, NJ, USA
dc.relation.referencesContreras, M.A., Macaya, L., Neira, P., Camacho, F., González, A., Acosta, J., Montesino, R., Sánchez, O., New Insights on the Interaction Mechanism of RhTNFα with Its Antagonists Adalimumab and Etanercept (2020) Biochem. J, 477, pp. 3299-3311
dc.relation.referencesParra, N.C., Mansilla, R., Aedo, G., Vispo, N.S., González-Horta, E.E., González-Chavarría, I., Castillo, C., Sánchez, O., Expression and Characterization of Human Vascular Endothelial Growth Factor Produced in SiHa Cells Transduced with Adenoviral Vector (2019) Protein J, 38, pp. 693-703
dc.relation.referencesBeltrán-Ortiz, C.E., Starck-Mendez, M.F., Fernández, Y., Farnós, O., González, E.E., Rivas, C.I., Camacho, F., Sánchez, O., Expression and Purification of the Surface Proteins from Andes Virus (2017) Protein. Expr. Purif, 139, pp. 63-70
dc.relation.referencesBaek, H., Suk, K., Kim, Y., Cha, S., An Improved Helper Phage System for Efficient Isolation of Specific Antibody Molecules in Phage Display (2002) Nucleic. Acids. Res, 30, p. e18
dc.type.versioninfo:eu-repo/semantics/publishedVersion
dc.identifier.reponamereponame:Repositorio Institucional Universidad de Medellín
dc.identifier.repourlrepourl:https://repository.udem.edu.co/
dc.identifier.instnameinstname:Universidad de Medellín


Files in this item

FilesSizeFormatView

There are no files associated with this item.

This item appears in the following Collection(s)

Show simple item record