Allosteric Inhibitors of the SARS-COV-2 Papain-like Protease Domain Induce Proteasomal Degradation of Its Parent Protein NSP3

  • ACS Chem Biol. 2024 Jan 19;19(1):22-36. doi: 10.1021/acschembio.3c00312.
Peter E Cockram  1  2 ,  Benjamin T Walters  3 ,  Aaron Lictao  3 ,  Frances Shanahan  2 ,  Ingrid E Wertz  2 ,  Scott A Foster  2 ,  Joachim Rudolph  1
Affiliations
  • 1. Discovery Chemistry, Genentech, South San Francisco, California 94080, United States.
  • 2. Discovery Oncology, Genentech, South San Francisco, California 94080, United States.
  • 3. Biochemical and Cellular Pharmacology, Genentech, South San Francisco, California 94080, United States.
PMID: 38150587 DOI: 10.1021/acschembio.3c00312
Abstract

The papain-like protease of SARS-COV-2 is essential for viral replication and pathogenesis. Its location within a much larger multifunctional protein, NSP3, makes it an ideal candidate for a targeted degradation approach capable of eliminating multiple functions with a single-molecule treatment. In this work, we have developed a HiBiT-based cellular model to study NSP3 degradation and used this platform for the discovery of monovalent NSP3 degraders. We present previously unreported degradation activity of published papain-like Protease Inhibitors. Follow-up exploration of structure-activity relationships and mechanism-of-action studies points to the recruitment of the ubiquitin-proteasome machinery that is solely driven by site occupancy, regardless of molecular features of the ligand. Supported by HDX data, we hypothesize that binding-induced structural changes in NSP3 trigger the recruitment of an E3 Ligase and lead to proteasomal degradation.

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