Allosteric Modulation of Pathological Ataxin‐3 Aggregation: A Path to Spinocerebellar Ataxia Type‐3 Therapies

Spinocerebellar ataxia type 3 (SCA3) is a rare neurodegenerative disorder caused by the expansion of a polyglutamine (polyQ) repeat in ataxin‐3 (Atx3) for which no disease‐modifying therapies are available. The presence of protein inclusions enriched in polyQ‐expanded Atx3 in neurons suggests that inhibiting its self‐assembly may provide targeted therapies. Here, it is demonstrated that the supramolecular tweezer CLR01 binds to a lysine residue on a positively charged patch of the Atx3 catalytic Josephin domain, decreasing conformational fluctuations of the distal helical hairpin, without altering its ubiquitin hydrolase activity. This reduces exposure of the aggregation‐prone region that initiates Atx3 self‐assembly, ultimately delaying Atx3 amyloid fibril formation and reducing the secondary nucleation rate, a process linked to fibril proliferation and toxicity. CLR01's effects translate into the reversal of synapse loss in SCA3 cultured cortical neuron model, improve locomotor function in a Caenorhabditis elegans SCA3 model, and delay disease onset with reduced severity of motor symptoms in a SCA3 mouse model. These insights reveal a novel allosteric site for developing CLR01‐inspired therapies targeting pathological aggregation while preserving essential functional sites. They also highlight that targeting allosteric sites in amyloid‐forming proteins may provide new opportunities for safe therapeutic strategies for various protein misfolding disorders.