Mapping the Energetic Epitope of an Antibody/Interleukin-23 Interaction with Hydrogen/Deuterium Exchange, Fast Photochemical Oxidation of Proteins Mass Spectrometry, and Alanine Shave Mutagenesis

Anal Chem. 2017 Feb 21;89(4):2250-2258. doi: 10.1021/acs.analchem.6b03058. Epub 2017 Feb 9.

Abstract

Epitope mapping the specific residues of an antibody/antigen interaction can be used to support mechanistic interpretation, antibody optimization, and epitope novelty assessment. Thus, there is a strong need for mapping methods, particularly integrative ones. Here, we report the identification of an energetic epitope by determining the interfacial hot-spot that dominates the binding affinity for an anti-interleukin-23 (anti-IL-23) antibody by using the complementary approaches of hydrogen/deuterium exchange mass spectrometry (HDX-MS), fast photochemical oxidation of proteins (FPOP), alanine shave mutagenesis, and binding analytics. Five peptide regions on IL-23 with reduced backbone amide solvent accessibility upon antibody binding were identified by HDX-MS, and five different peptides over the same three regions were identified by FPOP. In addition, FPOP analysis at the residue level reveals potentially key interacting residues. Mutants with 3-5 residues changed to alanine have no measurable differences from wild-type IL-23 except for binding of and signaling blockade by the 7B7 anti-IL-23 antibody. The M5 IL-23 mutant differs from wild-type by five alanine substitutions and represents the dominant energetic epitope of 7B7. M5 shows a dramatic decrease in binding to BMS-986010 (which contains the 7B7 Fab, where Fab is fragment antigen-binding region of an antibody), yet it maintains functional activity, binding to p40 and p19 specific reagents, and maintains biophysical properties similar to wild-type IL-23 (monomeric state, thermal stability, and secondary structural features).

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Alanine / metabolism*
  • Antibodies, Monoclonal / metabolism*
  • Antigen-Antibody Reactions
  • Cloning, Molecular
  • Deuterium Exchange Measurement
  • Epitope Mapping / methods*
  • Epitopes / metabolism*
  • Immunoglobulin Fab Fragments / metabolism
  • Interleukin-23 / metabolism*
  • Mass Spectrometry
  • Models, Molecular
  • Mutagenesis
  • Oxidation-Reduction
  • Protein Binding

Substances

  • Antibodies, Monoclonal
  • Epitopes
  • Immunoglobulin Fab Fragments
  • Interleukin-23
  • Alanine