A First-in-Class Therapy Targeting Transcription-Replication Conflicts Drives Synthetic Lethality in Homologous Recombination Deficient Cancers

Oncogenic signaling drives unchecked proliferation by subverting cellular processes, often at the expense of genome integrity. To survive this inherent genotoxic stress, cancer cells have developed a critical reliance on non-oncogenic stress response pathways to safeguard their genome. Capitalizing on this therapeutic vulnerability, we exploited the dependency of cancer cells on stress-mitigating mechanisms during DNA replication to identify a naturally occurring compound — Molephantin. Here, the derivatization of Molephantin produces NYH002 with cancer-specific toxicity at nanomolar potency. As a small-molecule inhibitor (∼450 Da), NYH002 selectively binds the ILF2 complex to disrupt the activity of downstream helicases essential for R-loop resolution. Progressive accumulation of unresolved RNA:DNA hybrids increases the frequency of head-on collisions with the replication machinery, resulting in catastrophic genome-wide DNA double-strand breaks. While elevated cyclin E and E2F1 levels predict NYH002 sensitivity, homologous recombination deficient cancer cells exhibit greater vulnerability, as evidenced by the selective lethality observed in both in vitro and in vivo models. Collectively, the ILF2 plays a central role in coordinating a series of helicases to safeguard R-loop resolution, which NYH002 leverages to restrict tumor malignancy.