Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping

Sci Rep. 2017 Jan 27:7:41306. doi: 10.1038/srep41306.

Abstract

Therapeutic and diagnostic applications of monoclonal antibodies often require careful selection of binders that recognize specific epitopes on the target molecule to exert a desired modulation of biological function. Here we present a proof-of-concept application for the rational design of an epitope-specific antibody binding with the target protein Keap1, by grafting pre-defined structural interaction patterns from the native binding partner protein, Nrf2, onto geometrically matched positions of a set of antibody scaffolds. The designed antibodies bind to Keap1 and block the Keap1-Nrf2 interaction in an epitope-specific way. One resulting antibody is further optimised to achieve low-nanomolar binding affinity by in silico redesign of the CDRH3 sequences. An X-ray co-crystal structure of one resulting design reveals that the actual binding orientation and interface with Keap1 is very close to the design model, despite an unexpected CDRH3 tilt and VH/VL interface deviation, which indicates that the modelling precision may be improved by taking into account simultaneous CDR loops conformation and VH/VL orientation optimisation upon antibody sequence change. Our study confirms that, given a pre-existing crystal structure of the target protein-protein interaction, hotspots grafting with CDR loop swapping is an attractive route to the rational design of an antibody targeting a pre-selected epitope.

MeSH terms

  • Amino Acid Sequence / genetics
  • Antibodies, Monoclonal / chemistry
  • Antibodies, Monoclonal / immunology*
  • Antibody Affinity / immunology
  • Complementarity Determining Regions / chemistry
  • Complementarity Determining Regions / immunology
  • Computer Simulation
  • Crystallography, X-Ray
  • Epitopes / chemistry*
  • Epitopes / immunology
  • Humans
  • Kelch-Like ECH-Associated Protein 1 / chemistry*
  • Kelch-Like ECH-Associated Protein 1 / genetics
  • Kelch-Like ECH-Associated Protein 1 / immunology
  • NF-E2-Related Factor 2 / chemistry*
  • NF-E2-Related Factor 2 / genetics
  • NF-E2-Related Factor 2 / immunology
  • Protein Binding / genetics
  • Protein Binding / immunology

Substances

  • Antibodies, Monoclonal
  • Complementarity Determining Regions
  • Epitopes
  • Kelch-Like ECH-Associated Protein 1
  • NF-E2-Related Factor 2
  • NFE2L2 protein, human