PEPOP: new approaches to mimic non-continous epitopes
2018
Demolombe, Vincent | de Brevern, Alexandre | Felicori, Liza | Nguyen, Christophe | de Avila, Ricardo Andrez Machado | Valera, Lionel | Jardin-Watelet, Bénédicte | Lavigne, Géraldine | Lebreton, Aurélien | Molina, Franck | Moreau, Violaine | Biochimie et Physiologie Moléculaire des Plantes (BPMP) ; Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) | Laboratoire d'Excellence du Globule Rouge, Villejuif, France | Departamento de Bioquimica | Alcediag | Programa de Pós-Graduação em Ciências da Saúde ; Partenaires INRAE | Bio-Rad Laboratories ; Partenaires INRAE | Department of Haematology | Service d'Hématologie Biologique ; Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12) | Centre National de la Recherche Scientifique (CNRS)
Bioinformatics methods are helpful to identify new molecules for diagnostic or therapeutic applications. For example, the use of peptides capable of mimicking binding sites has several benefits as replacing a protein difficult to produce, or toxic. Using peptides is less expensive. Peptides are easier to manipulate, and can be used as drugs. Continuous epitope predicted by bioinformatics tools are commonly used and these sequential epitopes are used as such in further experiments. Numerous discontinuous epitope predictors have been developed but only two bioinformatics tools proposed so far to predict peptide sequences: Superficial and PEPOP. PEPOP can generate series of peptide sequences that can replace continuous or discontinuous epitopes in their interaction with their cognate antibody. We have developed an improved version of PEPOP dedicated to answer to the experimentalists' need for a tool able to handle proteins and to turn them into peptides. The PEPOP web site has been reorganized by peptide prediction category and is therefore better formulated to experimental designs. Since the first version of PEPOP, 32 new methods of peptide design were developed. In total, PEPOP proposes 35 methods in which 34 deal specifically with discontinuous epitopes, the most represented epitope type in nature. We present the user-friendly, well-structured web-site of PEPOP and its validation through the use of predicted immunogenic or antigenic peptides mimicking discontinuous epitopes in different experimental ways. PEPOP proposes 35 methods of peptide design to guide experimentalists in using peptides potentially capable of replacing the cognate protein in its interaction with an Ab.
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