DNA damaging properties of G-quadruplex ligand QN-302 are potentiated by the DNA repair inhibitor Olaparib and mitigated by the molecular helicase PhpC

Abstract Background QN-302 is a tetra-substituted naphthalene diimide (NDI) designed to bind G-quadruplex (G4) DNA and is in a phase 1 clinical trial for pancreatic ductal adenocarcinoma (PDAC) and other solid tumors. The mechanistic basis of its anticancer activity remains to be fully understood. Results Using in vitro fluorescence quenching and FRET-melting assays together with cell-based in situ click imaging and γH2AX immunodetection, we show that QN-302 engages cellular G4s and triggers G4-associated DNA damage in human cancer cells. In HeLa cells, short exposures increase G4 foci and double strand break (DSB) markers, whereas pre-incubation with the G4-disruptor PhpC reduces both, supporting a G4-dependent mechanism. In PDAC (MIA PaCa-2) cells, QN-302’s antiproliferative activity synergizes with the PARP1 inhibitor Olaparib. Combination treatment produces supra-additive increases in γH2AX foci and yields Bliss synergy across multiple dose pairs, consistent with chemically induced synthetic lethality. Conclusions QN-302 induces G4-mediated DNA damage that underpins potent antiproliferative effects. Inhibition of DNA repair with Olaparib augments this activity, whereas pharmacological G4 destabilization with PhpC attenuates it. These findings support a defined mechanism of action for QN-302 and provide a rationale for clinical combination strategies in PDAC and potentially other cancer.