DNA damage induced by G-quadruplex ligand PyBI and its synthetic lethality with DNA repair inhibitors in cancer cells

The existence of G-quadruplexes (G4s) in vivo verified by diverse techniques, accompanied with their regulatory roles in cellular processes, highlight G4s as a target for various disease treatment. Targeting G-quadruplex DNAs to cause DNA damage has a good prospect for cancer therapy. However, previous studies on DNA damage induced by G4 ligands and its repair response thereof mainly focused on limited scaffolds such as CX series drugs, PDS families, etc. Here, we systematically investigated the DNA damage and repair mechanism induced by a good G4 stabilizer with bis(benzimidazole)pyridine as its key scaffold, which we termed as PyBI. PyBI can stabilize G4s both in vitro and in vivo, and cause DNA double strand breaks (DSB) and genome instability during DNA replication, resulting in cell cycle stagnation in G2/M phase and the increase of RAD51 and 53BP1 foci. Significantly, we applied Cleavage Under Targets and Tagmentation (CUT&Tag) for genome-wide mapping DNA damage sites induced by PyBI in cancer cells. Together with its G4 mapping result by CUT&Tag, we revealed that DNA damage caused by PyBI might be mediated by G4 stabilization. Moreover, we thoroughly investigated the synthetic lethality of PyBI with a small library of DNA repair inhibitors. PyBI exhibited good synthetic lethality effects with RAD51 and DNA-PK inhibitor, providing a new prospect for the treatment of genetically defective cancers.