Molecular and Computational Biology, Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA.
Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
Nat Commun. 2024 Apr 5;15(1):2862. doi: 10.1038/s41467-024-46593-1.
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 IC 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.
DNA 损伤反应 (DDR) 蛋白 DNA 聚合酶θ (Polθ) 与同源重组 (HR) 因子具有合成致死性，因此是 BRCA1/2 突变癌症中有前途的药物靶点。我们发现了一类具有 4-6 nM IC 的别构 Polθ 抑制剂 (Polθi)，它选择性地杀死 HR 缺陷细胞，并在多种遗传背景下与 PARP 抑制剂 (PARPi) 协同作用。X 射线晶体学和生物化学揭示，Polθi 通过诱导契合机制选择性地抑制 B 型 DNA/DNA 上封闭构象中的 Polθ 聚合酶 (Polθ-pol)。相比之下，Polθi 无法抑制酶在开放构象中结合的 A 型 DNA/RNA 上的 Polθ-pol 催化活性。值得注意的是，Polθi 与 Polθ-pol:DNA/DNA 封闭复合物的结合将聚合酶滞留在 DNA 上超过四十分钟，这阐明了其作用机制。这些数据揭示了一种独特的小分子 DNA 聚合酶：DNA 捕获机制，可在 HR 缺陷细胞中诱导合成致死，并增强 PARPi 的活性。
