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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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    1. Wataru Sakai & Elizabeth M. Swisher & Beth Y. Karlan & Mukesh K. Agarwal & Jake Higgins & Cynthia Friedman & Emily Villegas & Céline Jacquemont & Daniel J. Farrugia & Fergus J. Couch & Nicole Urban & , 2008. "Secondary mutations as a mechanism of cisplatin resistance in BRCA2-mutated cancers," Nature, Nature, vol. 451(7182), pages 1116-1120, February.
    2. Wanjuan Feng & Dennis A. Simpson & Juan Carvajal-Garcia & Brandon A. Price & Rashmi J. Kumar & Lisle E. Mose & Richard D. Wood & Naim Rashid & Jeremy E. Purvis & Joel S. Parker & Dale A. Ramsden & Gao, 2019. "Genetic determinants of cellular addiction to DNA polymerase theta," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    3. Wouter Koole & Robin van Schendel & Andrea E. Karambelas & Jane T. van Heteren & Kristy L. Okihara & Marcel Tijsterman, 2014. "A Polymerase Theta-dependent repair pathway suppresses extensive genomic instability at endogenous G4 DNA sites," Nature Communications, Nature, vol. 5(1), pages 1-10, May.
    4. Hannah Farmer & Nuala McCabe & Christopher J. Lord & Andrew N. J. Tutt & Damian A. Johnson & Tobias B. Richardson & Manuela Santarosa & Krystyna J. Dillon & Ian Hickson & Charlotte Knights & Niall M. , 2005. "Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy," Nature, Nature, vol. 434(7035), pages 917-921, April.
    5. Raphael Ceccaldi & Jessica C. Liu & Ravindra Amunugama & Ildiko Hajdu & Benjamin Primack & Mark I. R. Petalcorin & Kevin W. O’Connor & Panagiotis A. Konstantinopoulos & Stephen J. Elledge & Simon J. B, 2015. "Homologous-recombination-deficient tumours are dependent on Polθ-mediated repair," Nature, Nature, vol. 518(7538), pages 258-262, February.
    6. Stacey L. Edwards & Rachel Brough & Christopher J. Lord & Rachael Natrajan & Radost Vatcheva & Douglas A. Levine & Jeff Boyd & Jorge S. Reis-Filho & Alan Ashworth, 2008. "Resistance to therapy caused by intragenic deletion in BRCA2," Nature, Nature, vol. 451(7182), pages 1111-1115, February.
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