other positions. Researchers analyzed the importance of each nonanchor residue by comparing a very large set of peptides. They found that charged residues (positive or negative) are deleterious to binding, whereas aromatic residues are generally favorable. This allows researchers to predict with high efficiency the binding capacity of peptides that bear a given motif. In general, a peptide bearing one of the favored residues has about a 25-percent chance of binding, but when it contains one favored residue and none of the deleterious residues the chances of high-affinity binding increase to approximately 80 percent.
Binding Affinity and Immunogenicity. Based on the literature, about 90 percent of normal T-cell epitopes bind to the restriction element with high affinity, defined as a KD of 50 nanomolar. Peptides that are naturally processed by MHC also tend to fall into this high-affinity category. High-affinity peptides from transgenic mice also tended to be preferred immunogens. When researchers repeated this analysis for known epitopes of viral and tumor antigens, however, they found that 90 percent of viral epitopes are high-affinity binders for MHC, while less than half of tumor epitopes are high-affinity binders. Because tolerance tends to favor high-affinity, immunodominant peptides, a possible vaccine in situations of significant tolerance would be to shift to subdominant, lower-affinity peptides as potential immunogens.
In order to vaccinate with these peptides, researchers decided to include a “helper epitope” along with the classical CTL epitope. To this they added palmitic acids, which according to the literature enhance the immunogenicity of peptides. The data showed that the lipidated helper-CTL epitopes was a very efficient immunogen, and that it is equally efficient to a similar construct without the lipid but using IFA as an adjuvant.
Peptide-Mediated HBV Vaccine. Based on these findings, researchers proceeded to construct a CTL vaccine for hepatitis B. The rationale for such a vaccine was that CTL responsiveness was known to be associated with (1) clearance of acute HBV infection, (2) spontaneous clearance of chronic HBV infection, and (3) successful IFN-alpha therapy.
The vaccine used in preliminary studies consisted of an immunodominant epitope derived from the HBV core (18–27), combined with a helper epitope from tetanus toxin (830–843, which is relatively MNH-unrestricted), plus lipids. Phase I clinical data showed a clear immune response (measured in CTL activity) in normal subjects at a dosage of 500 micrograms of antigen, administered with a single booster shot. Higher and lower doses produced corresponding responses.
Preliminary Phase II clinical data show similar responses in about one dozen patients with chronic HBV infection who were given two injections of lipidated peptide as antigen. The “ALT flare” refers to liver damage with release of transaminase enzymes, which would be expected to follow the induction of CTL and is in fact an important indicator of CTL response. A similar flare can be observed in patients treated with IFN-alpha who clear the virus. DNA levels