Cyclization Scaffolding for Improved Vaccine Immunogen Stability: Application to Tau Protein in Alzheimer’s Disease

Effective scaffolding of immunogens
is crucial for generating
conformationally
selective antibodies through active immunization, particularly in
the treatment of protein misfolding diseases such as Alzheimer’s
and Parkinson’s disease. Previous computational work has revealed
that a disorder-prone region of the tau protein, when in a stacked
form, is predicted to structurally resemble a small, soluble protofibril,
having conformational properties similar to those of experimental
in vitro tau oligomers. Such an oligomeric structural mimic has the
potential to serve as a vaccine immunogen design for Alzheimer’s
disease. In this study, we developed a cyclization scaffolding method
in Rosetta, in which multiple cyclic peptides are stacked into a protofibril.
Cyclization results in significant stabilization of protofibril-like
structures by constraining the conformational space. Applying this
method to the disorder-prone region of the tau fibril, we evaluated
the metastability of the cyclized tau immunogen using molecular dynamics
simulations, and we identified sequences of two cyclic constructs
having high metastability in the protofibril. We then assessed their
thermodynamic stability by computing the free energy required to separate
a distal chain from the rest of the stacked structure. Our computational
results, based on molecular dynamics simulations and free energy calculations,
demonstrate that two cyclized constructs, cyclo-(VKSEKLDFKDRVQSKIFyN)
and cyclo-(VKSEKLDFKDRVQSKIYvG) (lowercase letters indicate d-form amino acids), possess significantly increased thermodynamic
stability in the protofibril over an uncyclized linear construct VKSEKLDFKDRVQSKI.
The cyclization scaffolding approach proposed here holds promise as
a means to effectively design immunogens for protein misfolding diseases,
particularly those involving liposome-conjugated peptide constructs.