Epitope mapping is a fundamental step in the study of macromolecular interactions, particularly in the development of vaccines, drugs and diagnostics. For example, this approach can provide in-depth analysis of the interaction site between a drug and its target or, in the case of vaccines, of the mechanisms underlying anti-pathogen immunity. NMR spectroscopy and X-ray co-crystallography are gold standards in epitope mapping, but are very laborious, costly and not always applicable. Array-based scanning of overlapping synthetic oligopeptides is a simpler and more widely used method, which is useful in the characterization of linear epitopes. Phage display technologies, in which artificial oligopeptides are expressed on filamentous phage vectors, are also limited to the characterization of linear continuous epitopes.

  • What is a linear epitope? Although linear epitopes probably do not exist in reality (the surface of molecules, like those of all objects, are tridimensional), they can be operationally defined as the epitopes that can be mimicked by short amino acid sequences. Linear epitopes are only a small minority of all epitopes.
  • A conformational epitope is defined by its tri-dimensional conformation and is made up by non adjacent segments in the protein sequence, brought together in space by loops and folds.

Since vast majority of antibodies (including therapeutic antibodies) bind to conformational epitopes, Scylla Biotech, devoloped PROFILER®, a  comprehensive technology using long fragments of the antigen of interest, which can fully reconstitute the conformation of the epitope.

PROFILER® combines the power of next-generation sequencing with the efficiency of an improved phage display system to identify conformational epitopes with unprecedented precision. The whole procedure takes a few days, including data analysis, and can simultaneously process hundreds of samples. In addition, PROFILER® can provide dozens of high-affinity epitope mimics which can be used to speed up and streamline further structural studies (e.g. by X-ray crystallography or nuclear magnetic resonance). These mimics can also be used as immunogens for epitope-based vaccination and rational vaccine design. Finally PROFILER® provides functional insights by quickly identifying the molecular regions, which are required for antibody binding. These regions may involve contact points with the antibodies or areas that are located far from the antigen binding sites, but are important for the correct folding of the epitope.

Precise epitope mapping by PROFILER® is suited for:

  • Defining the conformation of drug binding sites on a target protein
  • Intellectual Property (IP) purposes in establishing IP rights in development of therapeutic antibodies and other drugs
  • Regulatory filings: FDA and EMA require description of structural and functional properties of binding site for approval of novel antibodies

PROFILER® is characterized by a number of unique features and benefits:

No risk of failure: we guarantee the identification of the epitope in 15 days

High-throughput information: Comparative mapping and epitope fingerprinting of 96 samples in a single run (ideally suited for selection of therapeutic antibody candidates)

Broad applicability: identifies any type of epitope, both linear and conformational (with the exception of epitopes involving multimeric protein complexes).