Why epitope mapping?

Epitope mapping –  instrumental in therapeutic antibody development

Pepscan invented peptide-based epitope mapping. Building on 25 years in advanced and applied peptide chemistry, we provide accurate, clear and directly applicable epitope definitions for our client’s antibodies. Combining our scientists’ experience in immunology, biochemistry, structural and cell biology, and their expertise with our in-house developed peptide arrays and proprietary CLIPS™ technology provides us with a unique platform allowing to serve our clients in numerous purposes.

Functional understanding and selection of antibodies

Determining the binding site will establish how the epitope relates to an antibody’s functional aspects, e.g. does binding take place at a similar site as the ligand. In addition, epitope mapping can be used to select antibodies that target specific parts of a protein, e.g. for (diagnostic) assay development or therapeutic drug development.

Intellectual property and regulatory filings

Epitope mapping is a crucial and inevitable step in therapeutic antibody development. It plays a key role in IP protection and FDA/EMA approval, and therefore in protecting your company’s interests. Surprisingly, though, less than 10% of antibody patents filed mention epitope mapping. In the majority of 2019 European patents that did mention epitope mapping, Pepscan was the company of choice.

  • Intellectual property– Information on the precise binding sites, the epitopes, is helpful in arguing novelty of patent claims and in satisfying the written description requirement for broader antibody claims. Epitope mapping data is also supportive in arguing freedom to operate if analysis shows that a granted antibody claim is actually directed to an epitope that is different than that of your own antibody. In some cases, IP aspects may come down to subtle differences at the amino acid level, which can be resolved using our fine mapping technology.
  • Regulatory filings – FDA and EMA both recommend the inclusion of specific binding site information in regulatory dossiers for novel antibodies

Our epitope mapping platform supports not only your Intellectual Property claims but also builds a functional understanding that allows selection of the best candidate antibodies with preferred specificity by:

  • Comparing two antibodies with a similar epitope
  • Classifying different antibodies into separate binding bins based on discovered epitopes
  • Identifying essential and variable amino acid positions within an epitope
  • A detailed understanding of amino acid requirement for a cross-species or multi-strain reactivity analysis

Most of these aspects can be mapped with either our linear, conformational or discontinuous mapping, while sometimes a more in-depth approach is needed to characterize single amino acid properties using fine mapping.