Design of Cyclic Vinyl Sulfones as WRN Covalent Inhibitors from Noncovalent Binders

Werner syndrome helicase (WRN) is a DNA damage response protein selectively required for the survival of tumors with high microsatellite instability (MSI-H). We identified a noncovalent WRN inhibitor 1 via an extensive screening and hit triage. Co-crystal structure of 1 with the WRN helicase domain revealed a unique mechanism of inhibition via stabilization of inactive protein conformation and led to identification of cysteine 727 as a target for covalent inhibition. Structure-based drug design (SBDD) and a computational workflow resulted in the discovery of cyclic vinyl sulfone 4 as a covalent WRN functional inhibitor with improved stability. Further optimization led to potent compound 26 demonstrating exquisite selectivity to WRN in cell proteomic profiling and strong in vivo efficacy in an MSI-H Xenograft tumor model with no effect in microsatellite stable xenograft tumors. Therefore, a proof of concept of synthetic lethal MSI-H tumor cell growth inhibition by covalent inhibitor 26 was achieved.