Discovery and Optimization of a WRN Helicase Inhibitor Series through Structure-Guided Drug Design from a Covalent Fragment Binding Insight

WRN helicase activity inhibition has emerged as a promising therapeutic approach for targeting cancer cells with specific DNA repair deficiencies, especially those with microsatellite instability (MSI). Herein, we report a novel covalent WRN helicase inhibitor series discovered and optimized by leveraging insights from a covalent fragment investigation. Initial structure-based design led to potency-optimized compounds from this series that exhibited unbound cellular potency in the nanomolar range in both p21 induction and HCT116 CTG viability assays, albeit with high intrinsic warhead reactivity. Further refinement of the ADME properties by modulating the warhead reactivity yielded lead WC-2 with excellent cellular potency, low reactivity toward GSH, excellent plasma and blood stabilities, good oral bioavailability, and long in vivo half-lives in rat (T1/2 = 7.2 h; F = 62%) and dog (T1/2 = 18.9 h). WC-2 has the potential as a next-generation, low-dose WRN helicase clinical candidate for treating patients with MSI-classified tumors.