Disrupting the Base Excision Repair (BER) Pathway by Targeting the Abasic Site Enhances the Sensitivity of PARP Inhibitor in HR-Proficient Cancer Cells

Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPis) are clinically effective in homologous recombination (HR)-deficient cancers but have limited efficacy in HR-proficient cancers; therefore, new strategies are needed to address this therapeutic limitation. Since PARP1 recognizes abasic sites as intermediates to repair single-strand breaks (SSBs) in the base excision repair (BER) pathway, we demonstrate that targeting these DNA abasic sites with a fused-quinoxaline-diazepine amine derivative (BA-6) can enhance the effectiveness of the PARPi Olaparib in HR-proficient Cancer cells (MDA-MB-231, HeLa, and SKOV3). BA-6 cleaves abasic sites via β- and β,δ-elimination mechanisms, generating unusable substrates for DNA Polymerase β, such as 3'-α,β-unsaturated aldehyde and 3'-phosphate products, thereby disrupting the BER pathway and leading to the accumulation of SSBs. Upon combination with a low micromolar dosage of Olaparib, BA-6 exhibited potent synergistic effects in HR-proficient Cancer cells by reducing cell viability and clonogenic survival. Interestingly, the following synergy is attributed to PARP trapping at BA-6-induced SSBs, leading to DNA double-strand breaks (DSBs) during replication, as evidenced by an increased comet tail length and γH2AX expression, ultimately inducing S-phase arrest and Apoptosis in HR-proficient Cancer cells. Furthermore, combining BA-6 with alkylating agents like Temozolomide (TMZ) and methylmethanesulfonate (MMS), which elevate abasic sites, remarkably increased the Olaparib potency (∼55-fold) in HR-proficient Cancer cells. Overall, this study established that targeting DNA abasic sites with diazepine hybrids such as BA-6, in combination with known PARPi, acts as a rational strategy to enhance the therapeutic efficacy even in HR-proficient cancers.