A Rational Approach for Creating Peptides Mimicking Antibody Binding

Sci Rep. 2019 Jan 30;9(1):997. doi: 10.1038/s41598-018-37201-6.

Abstract

This study reports a novel method to design peptides that mimic antibody binding. Using the Knob-Socket model for protein-protein interaction, the interaction surface between Cetuximab and EGFR was mapped. EGFR binding peptides were designed based on geometry and the probability of the mapped knob-sockets pairs. Designed peptides were synthesized and then characterized for binding specificity, affinity, cytotoxicity of drug-peptide conjugate and inhibition of phosphorylation. In cell culture studies, designed peptides specifically bind and internalize to EGFR overexpressing cells with three to four-fold higher uptake compared to control cells that do not overexpress EGFR. The designed peptide, Pep11, bound to EGFR with KD of 252 nM. Cytotoxicity of Monomethyl Auristatin E (MMAE)-EGFR-Pep11 peptide-drug conjugate was more than 2,000 fold higher against EGFR overexpressing cell lines A431, MDA MB 468 than control HEK 293 cells which lack EGFR overexpression. MMAE-EGFR-Pep11 conjugate also showed more than 90-fold lower cytotoxicity towards non-EGFR overexpressing HEK 293 cells when compared with cytotoxicity of MMAE itself. In conclusion, a method that can rationally design peptides using knob-socket model is presented. This method was successfully applied to create peptides based on the antigen-antibody interaction to mimic the specificity, affinity and functionality of antibody.

Publication types

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

MeSH terms

  • Amino Acid Motifs
  • Antibodies, Monoclonal / metabolism*
  • Cell Death
  • Cell Line, Tumor
  • Cell Survival
  • Drug Delivery Systems
  • Drug Design*
  • ErbB Receptors / metabolism
  • HEK293 Cells
  • Humans
  • Kinetics
  • Molecular Docking Simulation
  • Peptides / chemistry
  • Peptides / metabolism*
  • Phosphorylation
  • Protein Binding
  • Protein Structure, Secondary
  • Surface Plasmon Resonance

Substances

  • Antibodies, Monoclonal
  • Peptides
  • ErbB Receptors