De novo design of a β -helix tau protein scaffold: An oligomer-selective vaccine immunogen candidate for Alzheimer’s disease

Abstract

Tau pathology is associated with many neurodegenetive disorders, including Alzheimer’s disease (AD), where the spatio-temporal pattern of tau neurofibrillary tangles strongly correlates with disease progression, which motivates therapeutics selective for misfolded tau. Here, we introduce a new avidity-enhanced, multi-epitope approach for protein misfolding immunogen design, which is predicted to mimic the conformational state of an exposed epitope in toxic tau oligomers. A predicted oligomer-selective tau epitope 343 KLDFK 347 was scaffolded by designing a β -helix structure that incorporated multiple instances of the 16-residue tau fragment 339 VKSEKLDFKDRVQSKI 354 . Largescale conformational ensemble analyses involving Jensen-Shannon Divergence and the embedding depth 𝒟 showed that the multi-epitope scaffolding approach, employed in designing the β -helix scaffold, was predicted to better discriminate toxic tau oligomers than other “monovalent” strategies utilizing a single instance of an epitope for vaccine immunogen design. Using Rosetta, 10,000 sequences were designed and screened for the linker portions of the β -helix scaffold, along with a C-terminal stabilizing α -helix that interacts with the linkers, to optimize the folded structure and stability of the scaffold. Structures were ranked by energy, and the lowest 1% (82 unique sequences) were verified using AlphaFold. Several selection criteria involving AlphaFold are implemented to obtain a lead designed sequence. The structure was further predicted to have free energetic stability by using Hamiltonian replica exchange molecular dynamics (MD) simulations. The synthesized β -helix scaffold showed direct binding in surface plasmon resonance (SPR) experiments to several antibodies that were raised to the structured epitope using a designed cyclic peptide. Moreover the strength of binding of these antibodies to in vitro tau oligomers correlated with the strength of binding to the β -helix construct, suggesting that the construct presents an oligomer-like conformation and may thus constitute an effective oligomer-selective immunogen.