PROTEIMERs as catalytic inhibitors of APP mRNA translation: Toward a new therapeutic for Alzheimer's disease

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BackgroundThe rising prevalence of Alzheimer's disease (AD) highlights the urgent need for novel therapeutic approaches capable of suppressing further neurodegeneration. Aberrant aggregation of the amyloid-β peptide fragment of the amyloid-β protein precursor (APP) has long been considered to be a central feature of AD pathology. However, directly targeting the amyloid-β peptide is complicated by its conformational flexibility. Instead, reducing APP expression at the translational level represents a promising alternative. The highly structured 5' untranslated region (UTR) of APP mRNA provides a targetable element for selective inhibition using RNA-binding therapeutics.ObjectiveTo develop and evaluate engineered protein-based RNA binders (PROTEIMERs) that selectively target the APP 5'-UTR to inhibit translation.MethodsWe applied high-throughput phage display screening techniques to identify two PROTEIMERs with high affinity for the APP 5'-UTR, confirmed via surface plasmon resonance. Domain engineering enabled the fusion of these binders to an RNase domain to facilitate catalytic degradation of APP mRNA.ResultsPROTEIMERs bound the APP 5'-UTR with nanomolar affinity. Structural modeling of the PROTEIMER-RNA complexes revealed that the engineered mutations within the binding pocket predominantly interact with the 5'-AGA-3' cleft of the APP mRNA. RNase-fused PROTEIMERs mediated sequence-specific APP mRNA cleavage in vitro, demonstrating robust target engagement and degradation. The PROTEIMER ProAPPS3-11 effectively inhibited APP translation in SH-SY5Y cells, reducing protein levels by up to 60% in a dose-dependent manner.ConclusionsThese findings establish the feasibility of PROTEIMERs as novel RNA-targeting biologics with therapeutic potential to reduce APP mRNA and protein levels, mitigating downstream AD-related neurodegeneration.