Identification of a novel anti-EGFR nanobody by phage display and its distinct paratope and epitope via homology modeling and molecular docking

• Published in: Molecular immunology 2020-12, Vol.128, p.165-174
• Main Authors: Xi, Xi, Sun, Weihan, Su, Hang, Zhang, Xitian, Sun, Fei
• Format: Article
• Language: English
• Subjects: Animals; Antibodies, Monoclonal - immunology; Antibodies, Monoclonal, Humanized - immunology; Bacteriophages - immunology; Binding Sites, Antibody - immunology; Camelus - immunology; Cell Line; Cell Surface Display Techniques - methods; EGFR; Epitope; Epitopes - immunology; ErbB Receptors - immunology; Homology modeling; Humans; Molecular docking; Molecular Docking Simulation - methods; Molecular Dynamics Simulation; Nanobody; Single-Domain Antibodies - immunology
• ISSN: 0161-5890; 1872-9142
• DOI: 10.1016/j.molimm.2020.10.014

•Domain III of EGFR was successfully expressed as the immunogen and had high affinity with anti-EGFR antibody H11.•A novel anti-EGFR nanobody (Nb AS32611) was screened through phage display and epitope binning.•The structure of AS32611 was built through homology modeling.•The epitope and paratope of AS32611 were predicted by molecular docking to provide the structural basis for multi-epitope therapy. Since EGFR is an important and effective target for tumor therapy in the clinic. Several monoclonal antibodies and nanobodies were proved to target domain III of EGFR. Regarding the increased attention on nanobodies, the present study aimed to generate nanobodies specifically against domain III. After camel immunization, a gene repertoire of sdAb fragments with a diversity of 3×109 clones was produced. Following the construction of two sdAb phage display libraries, the successful epitope binning was carried out to identify the nanobody with the designated epitope. Modelling of the identified nanobody and molecular docking studies illustrated the paratope and epitope. Docking analysis revealed that the paratope focused on CDR2 loop of the identified nanobody. The identified nanobody potently cover part of the epitope of Matuzumab and Nb 9G8, which indicated that it blocked EGFR by preventing dimerization of the receptors.