Tunable Aromatic Sulfoxides and Sulfones as Cysteine-Targeting Warheads: Exploring the Structure–Reactivity Relationship

Covalent modalities are powerful tools in medicinal chemistry and chemical biology, enabling selective protein inhibition and functional labeling through precise tuning of warhead reactivity. We report the design and synthesis of a 48-member library of aromatic sulfoxide and sulfone warheads capable of nucleophilic aromatic substitution (S_NAr). Systematic variation of the aromatic core, leaving-group electronics, and sulfur oxidation state revealed structure-reactivity relationships, correlating intrinsic reactivity with structural features. Kinetic assays demonstrated chemoselectivity toward cysteine thiols, with rates primarily dictated by the aromatic scaffold. Selected warheads were incorporated into ligand-directed probes targeting Bruton's tyrosine kinase (BTK), identifying a pyrazine-based warhead suitable for cellular applications. Molecular dynamics guided the design of the ibrutinib-derived probe <b>Ibr-2</b> with optimized warhead-Cys481 geometry. <b>Ibr-2</b> enabled potent and traceless BTK labeling in cells while preserving enzymatic activity. These findings highlight the potential of tunable S_NAr warheads for the development of traceless covalent probes targeting kinases with noncatalytic cysteines.