Antibody mapping
Protein-protein interactions are key in the functioning of antibodies, enzymes and receptors. Pepscan is a world leader in identification of protein-protein interaction sites (epitopes) to the level of individual amino acids.
Epitope mapping involves the precise definition of the binding site of an antibody to its target protein. Detailed knowledge of the interactions sites on single amino acid level is crucial for understanding the mode of action and biology of an antibody. FDA and EMEA guidelines require such specific binding site information to be included in regulatory dossiers. Also, exact epitope definition is of paramount importance for generating IP protection for novel antibodies.
Pepscan’s CLIPS Epitope Mapping Technology allows defining the protein-protein interaction sites at the level of individual amino acids and can be applied to linear, conformational and discontinuous epitopes. Even discontinuous epitopes involving dimeric or multimeric protein complexes can be mapped. The technology is not restricted to antibodies and antibody scaffolds, but can be used to identify other ligand binding sites or resolve in more detail known interaction sites of proteins.
The CLIPS Epitope Mapping Technology uses a high-throughput synthesis of microarrays of overlapping structurally constrained (surface-immobilized) CLIPS peptides covering the complete sequence of a given protein. Antibody binding studies using a fully automated ELISA-type read-out ultimately identifies the peptides representing the protein interaction site of interest. The peptide microarrays allow for the efficient screening of multiple monoclonal and polyclonal antibodies making the method highly suited for antibody lead selection, benchmarking and IP freedom to operate studies.
Epitope mapping data for anti-FSH mAb in three different formats using i) linear peptides, ii) single-loop CLIPS peptides, and iii) double-loop CLIPS peptides. Introduction of single resp. double loop peptides reveal a discontinuous binding site which was clearly not identified in the linear peptide format
With its CLIPS arrays technology, Pepscan has developed the next generation in epitope mapping: the use of structurally confined/conformational peptides with defined spatial orientations significantly increases the resolving power over traditional mapping with linear peptides.
CLIPS epitope mapping has a number of distinct advantages over other standards technologies. These benefits include providing binding epitope information plus information on the contribution of each single amino acid as required for regulatory and IP filing, the ease of screening multiple samples with exceptionally low material requirements (often only 0.1 mg required), and - unlike X-ray - crystalization is not required. The method is fully synthetic and no recombinant technologies, with intrinsic biological variations, are required.