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

TL;DR

This paper explores how to design covalent chemical probes that selectively target cysteine residues in proteins, particularly kinases like BTK, using tunable aromatic sulfoxide and sulfone warheads.

Contribution

The study introduces a 48-member library of SNAr warheads with tunable reactivity and demonstrates their use in creating traceless covalent probes for kinases.

Findings

Structure–reactivity relationships were established for aromatic sulfoxide and sulfone warheads.

A pyrazine-based warhead was identified as effective for cellular labeling of BTK.

The ibrutinib-derived probe Ibr-2 enabled potent and traceless BTK labeling while preserving enzymatic activity.

Abstract

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
(SNAr). 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 Ibr-2 with optimized warhead-Cys481
geometry. Ibr-2 enabled potent and traceless BTK labeling
in cells while preserving enzymatic activity. These findings highlight
the potential of tunable SNAr warheads for the development
of traceless covalent probes targeting kinases with noncatalytic cysteines.

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