Discovery of a small-molecule inhibitor that traps Polθ on DNA and synergizes with PARP inhibitors

  • Nat Commun. 2024 Apr 5;15(1):2862. doi: 10.1038/s41467-024-46593-1.
William Fried  #  1 ,  Mrityunjay Tyagi  #  2 ,  Leonid Minakhin  2 ,  Gurushankar Chandramouly  2 ,  Taylor Tredinnick  2 ,  Mercy Ramanjulu  3 ,  William Auerbacher  2 ,  Marissa Calbert  2  4 ,  Timur Rusanov  5 ,  Trung Hoang  6 ,  Nikita Borisonnik  7 ,  Robert Betsch  8 ,  John J Krais  8 ,  Yifan Wang  8 ,  Umeshkumar M Vekariya  4  9 ,  John Gordon  4 ,  George Morton  10 ,  Tatiana Kent  2 ,  Tomasz Skorski  4  9 ,  Neil Johnson  8 ,  Wayne Childers  3  10 ,  Xiaojiang S Chen  1  3 ,  Richard T Pomerantz  11  12
Affiliations
  • 1. Molecular and Computational Biology, Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA.
  • 2. Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
  • 3. Recombination Therapeutics, Pennsylvania Biotechnology Center, Doylestown, PA, 18902, USA.
  • 4. Fels Cancer Institute for Personalized Medicine, Philadelphia, PA, USA.
  • 5. Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA.
  • 6. Janssen Biotech, Malvern, PA, 19355, USA.
  • 7. Polysciences, Inc., Huntingdon Valley, PA, USA.
  • 8. Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
  • 9. Department of Cancer and Cellular Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA.
  • 10. Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA, USA.
  • 11. Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA. [email protected].
  • 12. Recombination Therapeutics, Pennsylvania Biotechnology Center, Doylestown, PA, 18902, USA. [email protected].
  • # Contributed equally.
PMID: 38580648 DOI: 10.1038/s41467-024-46593-1
Abstract

The DNA damage response (DDR) protein DNA Polymerase θ (Polθ) is synthetic lethal with homologous recombination (HR) factors and is therefore a promising drug target in BRCA1/2 mutant cancers. We discover an allosteric Polθ inhibitor (Polθi) class with 4-6 nM IC50 that selectively kills HR-deficient cells and acts synergistically with PARP inhibitors (PARPi) in multiple genetic backgrounds. X-ray crystallography and biochemistry reveal that Polθi selectively inhibits Polθ polymerase (Polθ-pol) in the closed conformation on B-form DNA/DNA via an induced fit mechanism. In contrast, Polθi fails to inhibit Polθ-pol catalytic activity on A-form DNA/RNA in which the enzyme binds in the open configuration. Remarkably, Polθi binding to the Polθ-pol:DNA/DNA closed complex traps the polymerase on DNA for more than forty minutes which elucidates the inhibitory mechanism of action. These data reveal a unique small-molecule DNA polymerase:DNA trapping mechanism that induces synthetic lethality in HR-deficient cells and potentiates the activity of PARPi.

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