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Structural basis for a Polθ helicase small-molecule inhibitor revealed by cryo-EM

Author

Listed:
  • Fumiaki Ito

    (Los Angeles)

  • Ziyuan Li

    (Los Angeles)

  • Leonid Minakhin

    (Thomas Jefferson University)

  • Gurushankar Chandramouly

    (Thomas Jefferson University)

  • Mrityunjay Tyagi

    (Thomas Jefferson University)

  • Robert Betsch

    (Fox Chase Cancer Center)

  • John J. Krais

    (Fox Chase Cancer Center)

  • Bernadette Taberi

    (Thomas Jefferson University)

  • Umeshkumar Vekariya

    (Temple University)

  • Marissa Calbert

    (Thomas Jefferson University)

  • Tomasz Skorski

    (Temple University)

  • Neil Johnson

    (Fox Chase Cancer Center)

  • Xiaojiang S. Chen

    (Los Angeles)

  • Richard T. Pomerantz

    (Thomas Jefferson University)

Abstract

DNA polymerase theta (Polθ) is a DNA helicase-polymerase protein that facilitates DNA repair and is synthetic lethal with homology-directed repair (HDR) factors. Thus, Polθ is a promising precision oncology drug-target in HDR-deficient cancers. Here, we characterize the binding and mechanism of action of a Polθ helicase (Polθ-hel) small-molecule inhibitor (AB25583) using cryo-EM. AB25583 exhibits 6 nM IC50 against Polθ-hel, selectively kills BRCA1/2-deficient cells, and acts synergistically with olaparib in cancer cells harboring pathogenic BRCA1/2 mutations. Cryo-EM uncovers predominantly dimeric Polθ-hel:AB25583 complex structures at 3.0-3.2 Å. The structures reveal a binding-pocket deep inside the helicase central-channel, which underscores the high specificity and potency of AB25583. The cryo-EM structures in conjunction with biochemical data indicate that AB25583 inhibits the ATPase activity of Polθ-hel helicase via an allosteric mechanism. These detailed structural data and insights about AB25583 inhibition pave the way for accelerating drug development targeting Polθ-hel in HDR-deficient cancers.

Suggested Citation

  • Fumiaki Ito & Ziyuan Li & Leonid Minakhin & Gurushankar Chandramouly & Mrityunjay Tyagi & Robert Betsch & John J. Krais & Bernadette Taberi & Umeshkumar Vekariya & Marissa Calbert & Tomasz Skorski & N, 2024. "Structural basis for a Polθ helicase small-molecule inhibitor revealed by cryo-EM," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51351-4
    DOI: 10.1038/s41467-024-51351-4
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