Conditional Covalent Lethality Driven by Oncometabolite Accumulation

Hereditary leiomyomatosis and renal
cell carcinoma (HLRCC) is a
cancer predisposition syndrome driven by mutation of the tumor suppressor
fumarate hydratase (FH). Inactivation of FH causes accumulation of
the electrophilic oncometabolite fumarate. In the absence of methods
for reactivation, tumor suppressors can be targeted via identification
of synthetic lethal interactions using genetic screens. Inspired by
recent advances in chemoproteomic target identification, here, we
test the hypothesis that the electrophilicity of the HLRCC metabolome
may produce unique susceptibilities to covalent small molecules, a
phenomenon we term conditional covalent lethality. Screening a panel
of chemically diverse electrophiles, we identified a covalent ligand,
MP-1, that exhibits FH-dependent cytotoxicity. Synthesis and structure–activity
profiling identified key molecular determinants underlying the molecule’s
effects. Chemoproteomic profiling of cysteine reactivity together
with clickable probes validated the ability of MP-1 to engage an array
of functional cysteines, including one lying in the Zn-finger domain
of the tRNA methyltransferase enzyme TRMT1. TRMT1 overexpression rescues
tRNA methylation from inhibition by MP-1 and partially attenuates
the covalent ligand’s cytotoxicity. Our studies highlight the
potential for covalent metabolites and small molecules to synergistically
produce novel synthetic lethal interactions and raise the possibility
of applying phenotypic screening with chemoproteomic target identification
to identify new functional oncometabolite targets.