Epitope mapping

Epitope mapping is the process of experimentally identifying the binding sites, or 'epitopes', of antibodies on their target antigens. Identification and characterization of the binding sites of antibodies can aid in the discovery and development of new therapeutics, vaccines, and diagnostics. Characterization of epitopes can also help elucidate the mechanism of binding for an antibody and facilitate the prediction of B cell epitopes using robust algorithms. Epitopes can be generally divided into two main classes: linear and conformational. Linear epitopes are formed by a continuous sequence of amino acids in a protein, while conformational epitopes are composed of amino acids that are discontinuous in the protein sequence but are brought together upon three-dimensional protein folding.The vast majority of antigen-antibody interactions rely upon binding to conformational epitopes.

Epitope mapping is an important component in the development of therapeutic monoclonal antibodies (mAbs) and vaccines. Specifically, epitope mapping can allow determination of the therapeutic mechanism of action of individual mAbs e.g. blocking ligand binding or trapping a protein in a non-functional state. However, many therapeutic antibodies target conformational epitopes that are particularly difficult to map because they are only formed in the native structure of a protein. New techniques such as high-throughput mutagenesis have been developed to address these challenging epitopes. Epitope mapping is also crucial to developing vaccines against prevalent viral diseases such as Dengue virus. Epitope mapping helps develop these challenging vaccines by determining antigenic elements (or epitopes) that confer long-lasting immunization effects. 

Epitope mapping of complex target antigens, such as integral membrane proteins or multi-subunit proteins, is often challenging because of the difficulty in expressing and purifying these types of antigens. Human membrane proteins and receptors, key targets for therapeutic antibodies, often have short antigenic regions that fold correctly only in the context of a lipid bilayer. As a result, mAb epitopes on these types of targets are often conformational, making them difficult to map.

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