224 11 Small Functional Peptides and Their Application in Superfunctionalizing Proteins
11.3.5.1 Peptide Epitopes
The immune response elicited by a given pathogen is specific against certain
exposed fractions of the pathogen’s proteome, called epitopes. For the design of
novel vaccines, approaches are explored where known epitopes are taken out of
their natural (pathogenic) context and inserted into a different protein scaffold
that is, in contrast to the protein of the epitope’s origin, nontoxic and easy to
purify in high yield. It was already shown a decade ago that a permissive site
within B. pertussis adenylate cyclase toxin‐hemolysin (ACT‐Hly) can be used to
deliver a CD8+ T‐cell epitope into antigen‐presenting cells in vivo and induce
protective antiviral as well as therapeutic antitumor cytotoxic T‐cell responses
[91–93]. Adenylate cyclase toxoids can penetrate a variety of immune effector
cells. Variants with disrupted catalytic activity, which are still cell invasive, are
therefore considered a potent scaffold for vaccine design.
Further, the nontoxic B subunit of cholera toxin [12, 94] as well as the hepatitis
B core particle‐forming protein HBcAg (for hepatitis B core antigen) have been
explored as potential vaccine scaffolds by insertion of relevant epitopes, for
example, a hepatitis C‐specific epitope or the HIV‐1‐neutralizing epitope
[95, 96]. More recently, adenovirus (Ad) capsid proteins embody enormous
promise for the realization of diverse vaccines [97–99]. Also computational
strategies have been developed to guide the design of epitope‐equipped protein
scaffolds for conformational stabilization and immune presentation [14–16].
For the design of novel chimeric vaccines, two points can be extracted from
the body of available literature that seem to be most relevant for consideration:
(i) the protein that is supposed to serve as a scaffold should be highly immuno-
genic by itself to elicit – next to the scaffold‐specific response – a high antibody
production against the inserted epitope and (ii) a solvent‐exposed permissive
sites within the scaffold should be known. The second point seems relevant for
two reasons: Firstly, though it was shown that terminal epitope fusions are in
principle able to elicit epitope‐specific immune responses, proteins were prone
to degradation that might interfere with the generation of the response. In con-
trast, proteins with internal insertions were stably expressed [12]. Further and
more importantly, it was shown for HBcAg‐epitope chimeras that insertions in
an internal permissive site showed higher epitope‐specific antibody produc-
tion than terminal fusions, especially when the chimeric protein was designed
such that the inserted epitope replaced another immunogenic region of the
scaffold [100].
Although some proteins with known permissive sites are available and
employed for the design of vaccine chimeras, the field seems limited by novel
scaffolds. Better knowledge on permissive sites and their identification in
potentially attractive scaffolds could thus pave the way for novel vaccine
strategies.11.3.5.2 Peptide Mimotopes
Peptide mimotopes are short aa sequences that mimic small molecules or carbo-
hydrates. By using a protein that naturally binds the target molecule, for exam-
ple, monosaccharide‐binding lectins, mimotopes can be selected from peptide
libraries by phage display. Per definition, a selected peptide is considered