Oral Presentation AUS-oMicS 2025

Can PROTACs degrade proteins in the CNS? We want to know for TDP-43 (#89)

Michael Gotsbacher 1 , Cynthia Zhao 1 , Nicholas McAndrew 1 , Margie Sunde 1 , William Alexander Donald 2 , Rob Capon 3 , Nicholas Geraghty 4
  1. University of Sydney, Sydney, NSW, Australia
  2. University of New South Wales, Sydney, NSW, Australia
  3. IMB, University of Queensland, Brisbane, QLD, Australia
  4. University of Wollongong, Wollongong, NSW, Australia

Molecular degraders (esp. PROTACs) are seeing immense interest as new modalities to combat difficult to treat diseases. After the first PROTACs (ARV-110/ARV-471) showed positive phase I/II results in cancer treatments (e.g., NCT03888612), ARV-471 was granted Fast Track designation by the FDA in 02/2024 for monotherapy for ER+/HER2- advanced or metastatic breast cancer.

While the cancer space is exploding with projects on degrader candidates, degraders for neurodegenerative disorders are understudied due to the perceived drug-unlikeness of PROTACs paired with CNS-delivery concerns. However, degrading certain CNS-proteins constitutes a promising therapeutic strategy for dependent proteinopathies. Its translatability is thus worth exploring.1

In this ongoing work, we focus on TDP-43, a nuclear RNA-binding protein that, when translocating to the cytosol, can form neurotoxic aggregates which are correlated with motor neuron disease (>97% of case) and frontotemporal degeneration (~50% of cases).2, 3 Our synthetic campaign starts via a known, moderate-affinity ligand (nTRD22)4 to synthesise PROTACs in a high-throughput format using bioconjugatable moieties on the ligand, the linkers and E3 ligase recruiters. This allows to rapidly generate PROTACs on analytical scale for high-throughput screening in a flow cytometric assay. In parallel, we perform an affinity selection mass spectrometry screening assay against aggregates-on-a-chip that represent the pathological aggregate conformations to identify more avid binders, and map protein-ligand/-PROTAC interactions via native mass spectrometry.

(1) Farrell K., Jarome T. Is PROTAC technology really a game changer for central nervous system drug discovery? Exp Op Drug Disc 2021, 16(8):833

(2) Wilson D. et al. Hallmarks of neurodegenerative diseases. Cell 2023, 186(4):693.

(3) Scheres S. et al. Molecular pathology of neurodegenerative diseases by cryo-EM of amyloids. Nature 2023, 621(7980):701.

(4) Mollasalehi N. et al. An Allosteric Modulator of RNA Binding Targeting the N-Terminal Domain of TDP-43 Yields Neuroprotective Properties. ACS Chem Biol 2020, 15(11):2854.