title: Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins.
abstract: Antibodies are powerful tools in life sciences research, as well as in diagnostic and therapeutic applications, because of their ability to bind given molecules with high affinity and specificity. Using current methods, however, it is laborious and sometimes difficult to generate antibodies to target specific epitopes within a protein, in particular if these epitopes are not effective antigens. Here we present a method to rationally design antibodies to enable them to bind virtually any chosen disordered epitope in a protein. The procedure consists in the sequence-based design of one or more complementary peptides targeting a selected disordered epitope and the subsequent grafting of such peptides on an antibody scaffold. We illustrate the method by designing six single-domain antibodies to bind different epitopes within three disease-related intrinsically disordered proteins and peptides (α-synuclein, Aβ42, and IAPP). Our results show that all these designed antibodies bind their targets with good affinity and specificity. As an example of an application, we show that one of these antibodies inhibits the aggregation of α-synuclein at substoichiometric concentrations and that binding occurs at the selected epitope. Taken together, these results indicate that the design strategy that we propose makes it possible to obtain antibodies targeting given epitopes in disordered proteins or protein regions.
authors.affiliation: Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.
authors.forename: Pietro
authors.initials: P
authors.lastname: Sormanni
authors.affiliation: Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.
authors.forename: Francesco A
authors.initials: FA
authors.lastname: Aprile
authors.affiliation: Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom mv245@cam.ac.uk.
authors.forename: Michele
authors.initials: M
authors.lastname: Vendruscolo
mesh_terms: D000595:Amino Acid Sequence; D016229:Amyloid beta-Peptides / Q000737:chemistry; D000906:Antibodies / Q000737:chemistry*; D000918:Antibody Specificity / Q000276:immunology; D015153:Blotting, Western; D004591:Electrophoresis, Polyacrylamide Gel; D004797:Enzyme-Linked Immunosorbent Assay; D000939:Epitopes / Q000276:immunology*; D005453:Fluorescence; D006801:Humans; D064267:Intrinsically Disordered Proteins / Q000737:chemistry*; D058228:Islet Amyloid Polypeptide / Q000737:chemistry; D008969:Molecular Sequence Data; D050505:Mutant Proteins / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D066329:Protein Aggregates; D011485:Protein Binding; D015202:Protein Engineering / Q000379:methods*; D017433:Protein Structure, Secondary; D061905:Single-Domain Antibodies; D051844:alpha-Synuclein / Q000737:chemistry
chemical_list: D016229:Amyloid beta-Peptides; D000906:Antibodies; D000939:Epitopes; D064267:Intrinsically Disordered Proteins; D058228:Islet Amyloid Polypeptide; D050505:Mutant Proteins; D010455:Peptides; D066329:Protein Aggregates; D061905:Single-Domain Antibodies; D051844:alpha-Synuclein
keywords: complementary peptides; protein aggregation; protein design