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

William Fried, Mrityunjay Tyagi, Leonid Minakhin, Gurushankar Chandramouly, Taylor Tredinnick, Mercy Ramanjulu, William Auerbacher, Marissa Calbert, Timur Rusanov, Trung Hoang, Nikita Borisonnik, Robert Betsch, John J. Krais, Yifan Wang, Umeshkumar M. Vekariya, John Gordon, George Morton, Tatiana Kent, Tomasz Skorski, Neil JohnsonWayne Childers, Xiaojiang S. Chen, Richard T. Pomerantz

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Article number2862
JournalNature communications
Volume15
Issue number1
DOIs
StatePublished - Dec 2024

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