Discovery and mechanistic characterisation of the first oral bioavailable FEN1 inhibitor for treatment of HRD and EWS cancers and combination with various DDR inhibitors

Flap endonuclease 1 (FEN1) has emerged as a critical target in the DNA damage response (DDR) landscape, particularly due to its synthetic lethal interactions with homologous recombination-deficient (HRD) cancers, such as those harboring BRCA mutations. Despite the therapeutic potential of FEN1 inhibition, the development of effective small molecule inhibitors has been limited, with existing compounds exhibiting modest selectivity and lacking oral bioavailability. In this presentation, we highlight the discovery of MSC778, the first potent, selective, and orally bioavailable FEN1 inhibitor and its mechanistic characterization. Utilizing a metal-chelating fragment-based screening approach combined with structure-based optimization, we successfully identified MSC778, which demonstrates strong cellular activity and selectivity and induces cell death in BRCA-deficient cancer cells. Our medicinal chemistry optimization campaign led to the development of oral bioavailable compounds that potentiate the activity of the PARPi niraparib in vivo to induce tumor stasis in a BRCA2 KO DLD-1 mouse xenograft model. Mechanistically we could demonstrate that MSC778 enhances FEN1 retention on chromatin and disrupts active DNA replication, leading to S-phase accumulation and subsequent DNA damage. Our findings also reveal a novel sensitization of Ewing sarcoma (EWS) cells to FEN1 inhibition, driven by the expression of SLFN11. Through CRISPR and drug combination screening, we elucidate a spectrum of synthetic lethal interactions between FEN1 and key DDR factors, including PARP1, USP1, PARG, and ATR, highlighting the synergistic potential of combining FEN1 inhibition with existing and emerging DDR-targeting agents. Together, these data underscore the relevance of FEN1 inhibition as a precision oncology strategy, with significant implications for the treatment of HRD and EWS cancers, as well as potential for combination therapies that leverage the DDR landscape.