IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-51351-4.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-51351-4
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-51351-4?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. 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.
    2. 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.
    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Anne Margriet Heijink & Colin Stok & David Porubsky & Eleni Maria Manolika & Jurrian K. Kanter & Yannick P. Kok & Marieke Everts & H. Rudolf Boer & Anastasia Audrey & Femke J. Bakker & Elles Wierenga , 2022. "Sister chromatid exchanges induced by perturbed replication can form independently of BRCA1, BRCA2 and RAD51," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. William Fried & Mrityunjay Tyagi & Leonid Minakhin & Gurushankar Chandramouly & Taylor Tredinnick & Mercy Ramanjulu & William Auerbacher & Marissa Calbert & Timur Rusanov & Trung Hoang & Nikita Boriso, 2024. "Discovery of a small-molecule inhibitor that traps Polθ on DNA and synergizes with PARP inhibitors," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Megan E. Luedeman & Susanna Stroik & Wanjuan Feng & Adam J. Luthman & Gaorav P. Gupta & Dale A. Ramsden, 2022. "Poly(ADP) ribose polymerase promotes DNA polymerase theta-mediated end joining by activation of end resection," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    4. Yuxin Huang & Wenjing Li & Tzeh Foo & Jae-Hoon Ji & Bo Wu & Nozomi Tomimatsu & Qingming Fang & Boya Gao & Melissa Long & Jingfei Xu & Rouf Maqbool & Bipasha Mukherjee & Tengyang Ni & Salvador Alejo & , 2024. "DSS1 restrains BRCA2’s engagement with dsDNA for homologous recombination, replication fork protection, and R-loop homeostasis," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    5. Daniel J. Laverty & Shiv K. Gupta & Gary A. Bradshaw & Alexander S. Hunter & Brett L. Carlson & Nery Matias Calmo & Jiajia Chen & Shulan Tian & Jann N. Sarkaria & Zachary D. Nagel, 2024. "ATM inhibition exploits checkpoint defects and ATM-dependent double strand break repair in TP53-mutant glioblastoma," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    6. John J. Krais & David J. Glass & Ilse Chudoba & Yifan Wang & Wanjuan Feng & Dennis Simpson & Pooja Patel & Zemin Liu & Ryan Neumann-Domer & Robert G. Betsch & Andrea J. Bernhardy & Alice M. Bradbury &, 2023. "Genetic separation of Brca1 functions reveal mutation-dependent Polθ vulnerabilities," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    7. Yonina R. Murciano-Goroff & Alison M. Schram & Ezra Y. Rosen & Helen Won & Yixiao Gong & Anne Marie Noronha & Yelena Y. Janjigian & Zsofia K. Stadler & Jason C. Chang & Soo-Ryum Yang & Diana Mandelker, 2022. "Reversion mutations in germline BRCA1/2-mutant tumors reveal a BRCA-mediated phenotype in non-canonical histologies," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    8. J. A. Kamp & B. B. L. G. Lemmens & R. J. Romeijn & S. C. Changoer & R. Schendel & M. Tijsterman, 2021. "Helicase Q promotes homology-driven DNA double-strand break repair and prevents tandem duplications," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    9. Jeffrey Patterson-Fortin & Heta Jadhav & Constantia Pantelidou & Tin Phan & Carter Grochala & Anita K. Mehta & Jennifer L. Guerriero & Gerburg M. Wulf & Brian M. Wolpin & Ben Z. Stanger & Andrew J. Ag, 2023. "RETRACTED ARTICLE: Polymerase θ inhibition activates the cGAS-STING pathway and cooperates with immune checkpoint blockade in models of BRCA-deficient cancer," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    10. Georgia Zoumpoulidou & Carlos Alvarez-Mendoza & Caterina Mancusi & Ritika-Mahmuda Ahmed & Milly Denman & Christopher D. Steele & Maxime Tarabichi & Errin Roy & Lauren R. Davies & Jiten Manji & Camilla, 2021. "Therapeutic vulnerability to PARP1,2 inhibition in RB1-mutant osteosarcoma," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    11. Neil J. Rzechorzek & Simone Kunzelmann & Andrew G. Purkiss & Mariana Silva Dos Santos & James I. MacRae & Ian A. Taylor & Kasper Fugger & Stephen C. West, 2023. "Mechanism of substrate hydrolysis by the human nucleotide pool sanitiser DNPH1," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    12. Heathcliff Dorado García & Fabian Pusch & Yi Bei & Jennifer Stebut & Glorymar Ibáñez & Kristina Guillan & Koshi Imami & Dennis Gürgen & Jana Rolff & Konstantin Helmsauer & Stephanie Meyer-Liesener & N, 2022. "Therapeutic targeting of ATR in alveolar rhabdomyosarcoma," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    13. Sundarraj Jayakumar & Manthan Patel & Fanny Boulet & Hadicha Aziz & Greg N. Brooke & Hemanth Tummala & Madapura M. Pradeepa, 2024. "PSIP1/LEDGF reduces R-loops at transcription sites to maintain genome integrity," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    14. Zizhi Tang & Ming Zeng & Xiaojun Wang & Chang Guo & Peng Yue & Xiaohu Zhang & Huiqiang Lou & Jun Chen & Dezhi Mu & Daochun Kong & Antony M. Carr & Cong Liu, 2022. "Synthetic lethality between TP53 and ENDOD1," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    15. Samuel D. Chauvin & Shoichiro Ando & Joe A. Holley & Atsushi Sugie & Fang R. Zhao & Subhajit Poddar & Rei Kato & Cathrine A. Miner & Yohei Nitta & Siddharth R. Krishnamurthy & Rie Saito & Yue Ning & Y, 2024. "Inherited C-terminal TREX1 variants disrupt homology-directed repair to cause senescence and DNA damage phenotypes in Drosophila, mice, and humans," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
    16. Arindam Datta & Kajal Biswas & Joshua A. Sommers & Haley Thompson & Sanket Awate & Claudia M. Nicolae & Tanay Thakar & George-Lucian Moldovan & Robert H. Shoemaker & Shyam K. Sharan & Robert M. Brosh, 2021. "WRN helicase safeguards deprotected replication forks in BRCA2-mutated cancer cells," Nature Communications, Nature, vol. 12(1), pages 1-22, December.
    17. Meng Wang & Satoshi Fukushima & Yi-Shuan Sheen & Egle Ramelyte & Noel Cruz-Pacheco & Chenxu Shi & Shanshan Liu & Ishani Banik & Jamie D. Aquino & Martin Sangueza Acosta & Mitchell Levesque & Reinhard , 2024. "The genetic evolution of acral melanoma," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    18. Jun Dai & Shuyu Zheng & Matías M. Falco & Jie Bao & Johanna Eriksson & Sanna Pikkusaari & Sofia Forstén & Jing Jiang & Wenyu Wang & Luping Gao & Fernando Perez-Villatoro & Olli Dufva & Khalid Saeed & , 2024. "Tracing back primed resistance in cancer via sister cells," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    19. John Hilton & Karen Gelmon & Philippe L. Bedard & Dongsheng Tu & Hong Xu & Anna V. Tinker & Rachel Goodwin & Scott A. Laurie & Derek Jonker & Aaron R. Hansen & Zachary W. Veitch & Daniel J. Renouf & L, 2022. "Results of the phase I CCTG IND.231 trial of CX-5461 in patients with advanced solid tumors enriched for DNA-repair deficiencies," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    20. Youngho Kwon & Heike Rösner & Weixing Zhao & Platon Selemenakis & Zhuoling He & Ajinkya S. Kawale & Jeffrey N. Katz & Cody M. Rogers & Francisco E. Neal & Aida Badamchi Shabestari & Valdemaras Petrosi, 2023. "DNA binding and RAD51 engagement by the BRCA2 C-terminus orchestrate DNA repair and replication fork preservation," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51351-4. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.