Background: A major challenge is the induction of neutralizing antibodies (nAbs) in the vaccinee. We propose to meet this challenge by developing recombinant vaccines based on the corresponding epitopes recognized by known and well defined nAbs. These “neutralizing epitopes” are concealed within the pathogen's envelope proteins and by means of negative selection have evolved to be inaccessible or highly conformational, and therefore of suppressed immunogenicity in the context of intact pathogen.
Hypothesis: Reconstituted neutralizing epitopes used as isolated immunogens are able to elicit nAbs. To test this hypothesis we have to overcome two major obstacles: (i) mapping the neutralizing epitope at the atomic level, and (ii) reconstitution of the epitope as an independent subunit-immunogen.
Model system and results: 80R is an extremely potent nAb directed against the receptor binding domain (RBD) of the SARS virus spike protein. The 80R neutralizing epitope was initially mapped using novel bioinformatic tools, and subsequently confirmed by co-crystallization. The epitope is comprised of 32 contacts that are located on a large and extended surface of approximately 1000 angstrom2, encompassing two beta strands, one alpha-helix and two random structures. The isolated 80R epitope is predicted to be efficient as an immunogen able to elicit an 80R-like humoral response and serves as a model for epitope-based vaccine construction against other viruses such as HIV. In order to reconstitute the epitope into a functional and short recombinant peptide, a novel approach has been developed: “conformer libraries”. Such libraries use the bona fide peptide-segments of the RBD interconnected by a variety of linkers that stabilize the epitope segments in a vast collection of different conformations. Four different epitope-libraries were built using the phage display technique and screened against 80R that was used as a monitor for the desired native conformation. A number of epitope-conformers were isolated that bind 80R well. These epitope-conformers are vaccine candidates currently being evaluated as immunogens.