Predicting Mimotopes of Amyloid beta (Aβ₄₂) from Non-Coding DNA as candidates for Synthetic Peptide Vaccine Design against Alzheimer’s Disease

Introduction: What could be an ideal raw material for developing a drug or a vaccine? In line with the research on different biomolecules like DNA, RNA, protein, and peptide, we explore the potential use of non-coding DNA in designing lifesaving vaccines and drugs.

Methods: Using computational approaches, a multi-parametric virtual library of novel peptides from the intergenic regions of the Escherichia coli genome was generated, and their therapeutic potential was studied. The potential antigens from the peptides were analyzed for their B cell epitopes and MHC binding T cell epitopes, which find application in epitope-based vaccine design. Alzheimer's disease (AD) immunotherapy was selected as an example to demonstrate the possible application of the non-coding DNA-derived peptides as promising candidates for Synthetic Peptide Vaccine Design.

Results: Sequence and structure comparison studies between toxic amyloid beta (Aβ₄₂) peptides and the non-coding DNA-derived peptides revealed promising matches. The structural mimics of Aβ₄₂ with potential mimotopes were further studied through mimotope-antibody docking and molecular dynamic simulation for their affinity towards the antibody's antigen-binding fragment (Fab).

Conclusion: Our study put forward a novel method to identify therapeutic peptides from non-coding DNA, which offers a non-obvious source of potential mimotope candidates for designing novel synthetic vaccines against Alzheimer’s Disease.