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

Abstract

Background

The 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.

Objective

To develop and evaluate engineered protein-based RNA binders (PROTEIMERs) that selectively target the APP 5′-UTR to inhibit translation.

Methods

We 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.

Results

PROTEIMERs 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.

Conclusions

These 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.