Cu(II)-Assisted Novel Covalent Warheads for Proteome-wide Cysteine Profiling

In the realm of residue-specific labeling of amino acids within the proteome, cysteine (-SH) emerges as a particularly nucleophilic residue and plays a pivotal role in covalent drug discovery. Despite significant strides in targeting cysteine sites, there remains a substantial expanse of unexplored site space. We discovered that a nucleophilic phenol (DBA)/Cu2+ ‘complex’ serves as a potent warhead for traditionally "inert" cysteines. In the context of a general chemoproteomics profiling, the DBA-1 probe exhibits higher reactivity than IAA toward approximately 45% of quantifiable Cys sites. Dose-dependent profiling experiments suggest that Cu2+ may function not only as an oxidizing agent of phenol but also as a chelating agent of polar residues in proteins. Given its reliance on structural characteristics of proteins for site targeting, this novel (DBA)/Cu2+ ‘complex’ fits the scope of ‘structure-based protein profiling’ (SBPP), highlighting the role of metal ion in the design of effective warheads and the virtue of new proteomic microenvironmental chemistry ‘hunting’.