Diverse Redoxome Reactivity Profiles of Carbon Nucleophiles

Targeted covalent
inhibitors have emerged as a powerful approach
in the drug discovery pipeline. Key to this process is the identification
of signaling pathways (or receptors) specific to (or overexpressed
in) disease cells. In this context, fragment-based ligand discovery
(FBLD) has significantly expanded our view of the ligandable proteome
and affords tool compounds for biological inquiry. To date, such covalent
ligand discovery has almost exclusively employed cysteine-reactive
small-molecule fragments. However, functional cysteine residues in
proteins are often redox-sensitive and can undergo oxidation in cells.
Such reactions are particularly relevant in diseases, like cancer,
which are linked to excessive production of reactive oxygen species.
Once oxidized, the sulfur atom of cysteine is much less reactive toward
electrophilic groups used in the traditional FBLD paradigm. To address
this limitation, we recently developed a novel library of diverse
carbon-based nucleophile fragments that react selectively with cysteine
sulfenic acid formed in proteins via oxidation or hydrolysis reactions.
Here, we report analysis of sulfenic acid-reactive C-nucleophile fragments
screened against a colon cancer cell proteome. Covalent ligands were
identified for >1280 S-sulfenylated cysteines
present
in “druggable” proteins and orphan targets, revealing
disparate reactivity profiles and target preferences. Among the unique
ligand–protein interactions identified was that of a pyrrolidinedione
nucleophile that reacted preferentially with protein tyrosine phosphatases.
Fragment-based covalent ligand discovery with C-nucleophiles affords
an expansive snapshot of the ligandable “redoxome” with
significant implications for covalent inhibitor pharmacology and also
affords new chemical tools to investigate redox-regulation of protein
function.