Applying bioinformatics for antibody epitope prediction using affinity-selected mimotopes – relevance for vaccine design

Abstract

To properly characterize protective polyclonal antibody responses, it is necessary to examine epitope specificity. Most antibody epitopes are conformational in nature and, thus, cannot be identified using synthetic linear peptides. Cyclic peptides can function as mimetics of conformational epitopes (termed mimotopes), thereby providing targets, which can be selected by immunoaffinity purification. However, the management of large collections of random cyclic peptides is cumbersome. Filamentous bacteriophage provides a useful scaffold for the expression of random peptides (termed phage display) facilitating both the production and manipulation of complex peptide libraries. Immunoaffinity selection of phage displaying random cyclic peptides is an effective strategy for isolating mimotopes with specificity for a given antiserum. Further epitope prediction based on mimotope sequence is not trivial since mimotopes generally display only small homologies with the target protein. Large numbers of unique mimotopes are required to provide sufficient sequence coverage to elucidate the target epitope. We have developed a method based on pattern recognition theory to deal with the complexity of large collections of conformational mimotopes. The analysis consists of two phases: 1) The learning phase where a large collection of epitope-specific mimotopes is analyzed to identify epitope specific “signs” and 2) The identification phase where immunoaffinity-selected mimotopes are interrogated for the presence of the epitope specific “signs” and assigned to specific epitopes. We are currently using computational methods to define epitope “signs” without the need for prior knowledge of specific mimotopes. This technology provides an important tool for characterizing the breadth of antibody specificities within polyclonal antisera.

Bioinformatics Resources and Tools for Conformational B-Cell Epitope Prediction

“…In 2007, Bublil et al applied this method to conformational B-cell epitope prediction and presented the tool as Mapitope [70]. A continuous work by Denisova et al took all possible space pairs, including pairs separated by one residue, two residues, three residues, and so on in mimotopes into account and identified epitopes by pattern recognition theory [71–73]. This method is specially designed for elucidating epitope specificity within antiserum.…”

Peptide modulators of alpha‐glucosidase

“…Cyclized peptides thus present a more uniform structure than linear peptides. Furthermore, they are less prone to enzymatic degradation than linear peptides 27,34 . Peptide rigidity aside, phage clones isolated with a non-specific elution approach (C1 and C2) appeared to have a higher affinity towards the target than those obtained with specific elution with acarbose/voglibose.…”

Bioinformatics Resources and Tools for Phage Display

“…The same fact might have also been noticed by other groups. In a recent method based on pattern recognition theory, all possible space pairs (for example, pairs separated by one residue, two residues, three residues, and so on) in mimotope sequences are taken into account [ 41 , 42 ]. This new method can be regarded as a derivative of Mapitope.…”