Small-Molecule KRAS Inhibitors by Tyrosine Covalent Bond Formation

Abstract

The development of the KRAS G12C inhibitor sotorasib is a major advance toward drugging KRAS. However, the G12C mutation is only found in about 10% of KRAS-driven tumors. KRAS possesses several tyrosine amino acids that could provide alternative sites for covalent drug development. Here, a library of aryl sulfonyl fluorides identified 1 (SOF-436) as an inhibitor of KRAS nucleotide exchange by guanine exchange factor SOS1 and KRAS binding to effector protein rapidly accelerated fibrosarcoma kinase (RAF). Tyr-64 is the major reaction site of 1 (SOF-436), although minor reaction at Tyr-71 is also observed. The fragment binds to the Switch II pocket of KRAS based on whole protein mass spectrometry, nucleotide exchange, effector protein binding, and nuclear magnetic resonance studies. Cocrystal structures of smaller fragments covalently bound to KRAS at Tyr-71 provide a strategy for the development of Switch I/II KRAS covalent inhibitors. A bioluminescent resonance energy transfer (NanoBRET) assay reveals that the compounds inhibit KRAS binding to RAF in mammalian cells. Although not yet suitable as chemical probes, these fragments provide starting points to develop small molecules to investigate tyrosine as a nucleophile for covalent inhibition of KRAS in tumors.