Molecularly Imprinted Polymer Nanogels as Synthetic Peptide Antibodies for Protein Recognition: Validation of the Epitope Approach by STD NMR Spectroscopy

Molecularly imprinted polymers (MIPs) are tailor-made synthetic antibodies that carry specific binding cavities designed for a target molecule. Nowadays, MIPs for protein targets are routinely synthesized by imprinting a short surface-exposed fragment of the protein, called an epitope or antigenic determinant. A seven-amino acid-long N-terminal peptide epitope, Asp1-Trp2-Val3-Ile4-Pro5-Pro6-Ile7, was employed to prepare MIP nanogel (MIP-NG) that recognized recombinant E- and N-cadherins with a high affinity and selectivity. In order to obtain detailed structural binding information on the epitope peptide at an atomic level within the MIP-NG, we used STD NMR spectroscopy complemented with peptide molecular modeling tools. The combination of the two methods proved to be highly effective in interpreting the molecular interaction of the epitope peptide and other potential binding peptides with MIP-NG. A binding epitope map was constructed from STD NMR build-up curves at increasing saturation times and showed that the amino acids with protruding side chains, Ile7, Ile4, and Trp2, were those in closest contact with the MIP receptor. Importantly, the specific epitope-imprinted binding cavity did not host the nonbinder peptide having the Trp2 substituted by Ala2, as observed by the absence of STD signals.