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.
Highlights
Because of their specificity and affinity, antibodies are commonly used in biomedical research to bind to a specific target protein
The set of three residue sockets on Epidermal growth factor receptor (EGFR) that interact with single residue knobs from Cetuximab clearly defines the epitope surface
This interaction surface is shown as grey triangles, while free sockets without any interaction are shown in white
Summary
Because of their specificity and affinity, antibodies are commonly used in biomedical research to bind to a specific target protein. In a study by Honarvar et al, a HER2 specific peptide A9 with nanomolar affinity was derived from transtuzumab-Fab portion and was used as a 111In radio labeled imaging probe for HER2 positive tumor tissue[18] These peptides bind with high affinities (KD in nanomolar range) the studies involve tedious and time consuming in vitro or in silico screening process to identify the peptides against a target. Structure based peptide design utilizes the crystallographic structural information from the interface of a protein-protein interaction to direct the design of a peptide’s binding specificity This approach often uses computational modeling and docking studies as tools in peptide design. This knob-socket code can be applied in the rational design of a peptide that can bind to a specific site of a protein by mimicking the packing mode of protein-protein interaction
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