• Antigen-antibody epitope mapping.
• Protein-protein or protein-peptide interface mapping.
• Bioequivalence of follow-on or biogeneric biologicals.

Epitope mapping is an essential aspect of the discovery and development of diagnostic and therapeutic antibodies. Epitope mapping can streamline the selection of lead candidate molecules, particularly where epitope similarity or dissimilarity issues are involved. Intellectual property considerations of patentability, with freedom to operate consequences, can hinge upon the epitope itself. Furthermore, regulatory agencies recommend that prior to use in humans and whenever possible, the protein bearing the reactive epitope should be biochemically defined and the antigenic epitope itself determined (PTC/FDA, 94D-0259).


While an X-ray co-crystal of the antigen:antibody complex remains the gold standard of epitope determination, it is technically challenging, tedious and not always feasible due to the difficulty of obtaining high quality well diffracting crystals. In the absence of a crystal complex, hydrogen/deuterium exchange (e.g. DXMS, H/D-Ex, etc.) is the next best available option. ExSAR employs hydrogen/deuterium exchange mass spectrometry as a tool to identify binding interfaces. Differences in the rate of exchange serve to highlight the location of an epitope. Hydrogen/deuterium exchange (H/D-Ex) was utilized to identify the epitope of a potent neutralizing antibody to IL-17, a homodimeric cytokine involved in a number of pro-inflammatory signaling pathways. Illustrated in red in the above figure are areas where exchange was significantly reduced upon complex formation. Pink highlighted regions indicate areas that were moderaty affected upon complex formation. The epitope was subsequently validated by the X-ray crystal structure of the complex.

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