Reactive chemistry for covalent probe and therapeutic development

Advances in Activity‐Based Protein Profiling of Functional Tyrosines in Proteomes

“…[15] To expand the protein classes addressable by ABPP, new reactive groups are being developed to investigate protein sites beyond active site residues (e. g., catalytic serines) and intrinsically nucleophilic residues (e. g., cysteines). [21] Electrophilic groups for ABPP investigations of protein sites containing a tyrosine residue are emerging and enabling biochemical and cell biological investigations. [36f,46c,47a-f] The SuTEx electrophile, for example, has advanced ABPP analyses of tyrosines by (i) facilitating the global discovery of ligandable tyrosines in the human proteome, [36f] (ii) established a prioritization strategy to identify functional tyrosine sites based on reactive/structural features, [36f] (iii) demonstrated capabilities for tuning the reactivity and selectivity of sulfonyl-triazoles for a tyrosine site of interest using medicinal chemistry, [47a] (iv) provided a facile means for target identification in cell lysate and phenotypic screening formats, [67] and (v) established proof-of-concept for late stage functionalization for developing targeted covalent inhibitors with an embedded SuTEx reactive group.…”

“…Biotin‐avidin‐based interaction is widely‐used for affinity chromatography for ABPP. The proteins or peptides labeled by the (desthio)biotin‐containing ABPs can be enriched with immobilized avidin beads and eluted (in the case of desthiobiotin‐tagged ABPs) for ABPP analysis [21] …”

“…ABPP analyses are typically performed using a "bottomup" proteomics approach that measures peptide fragments generated from proteolysis to infer the identity of probe-bound protein. [21] In most bottom-up proteomic workflows the proteins are solubilized and denatured. Disulfide bonds are reduced, and cysteine thiol groups are carbamidomethylated using iodoacetamide (IAA).…”

An Activity-Based Oxaziridine Platform for Identifying and Developing Covalent Ligands for Functional Allosteric Methionine Sites: Redox-Dependent Inhibition of Cyclin-Dependent Kinase 4

“…Covalent small molecules that target specific amino acid residues are powerful chemical tools that can reveal fundamental new protein function and identify lead candidates for accelerating drug discovery. − Indeed, led by advances across broad fields encompassing organic chemistry, chemical biology, cell biology, and bioinformatics, covalent therapeutics now constitute approximately 30% of enzyme-targeting FDA-approved drugs . In this context, activity-based protein profiling (ABPP), where chemical probes measure protein function rather than protein abundance, , has enabled new modalities for fragment-based drug discovery by applying small-molecule screening efforts in conjunction with chemoproteomics for target and site identification and characterization. − These technologies rely on residue-specific covalent warheads that can be used from proteins to proteomes, ,− yet the majority of reactive probe development to tackle this vast undruggable space has targeted cysteine , or lysine, ,,, with relatively limited expansion of this chemical toolbox to other nucleophilic residues like tyrosine and glutamate/aspartate. , …”

Exploring the boundaries of ferrocenesulfonyl fluoride chemistry

“…The sulfonyl fluorides are therefore stable under an amazing range of reaction conditions but they can also react with a nucleophile in smooth conditions, if properly activated via hydrogenbonding or by a Lewis acid. As a consequence, sulfonyl fluorides have found applications in chemical biology, [9][10][11][12][13][14][15] the func-tional group acting as a warhead to react with enzymes, and in material science to reach original materials. 16,17 This was accompanied with main developments in the synthesis of sulfonyl fluorides, 18,19 the study of their orthogonal reactivity, 20 and the optimization of various SuFEx reaction conditions.…”