Fragment Covalent Bond Formation at SOS1 Tyr-884 Inhibits KRAS Nucleotide Exchange

Abstract

The activation of the KRAS oncogene from its inactive GDP-bound state to its active GTP-bound state is mediated by Son of Sevenless (SOS) exchange factors. Small-molecule inhibition of SOS1 has been achieved, with three compounds currently in clinical trials. These compounds bind to SOS1 and disrupt a crucial interaction between SOS1 Tyr-884 and KRAS Arg-73. Here, we screen libraries of aryl sulfonyl fluorides to explore covalent bond formation at Tyr-884 as a strategy for covalent inhibition of SOS1-KRAS binding. Initially, ten fragments were tested and several inhibited KRAS nucleotide exchange by SOS1. X-ray crystal structures revealed that one reaction site for the fragments was Tyr-884, but mass spectrometry and nucleotide exchange assays with wild-type and mutant SOS1 indicated additional reaction sites. To identify candidates specific to Tyr-884, we conducted a larger screen and identified fragment 11 (SOF-599). The fragment formed an adduct predominantly at Tyr-884 and inhibited KRAS nucleotide exchange by SOS1 in a time- and concentration-dependent manner. Fragment 11 (SOF-599) exhibited a half-maximal inactivation concentration (KI) of 12 micromolar and a reaction half-life of 6 h. These findings establish 11 (SOF-599) as a promising starting point for the development of covalent SOS1 inhibitors as an alternative strategy to existing non-covalent antagonists.