Lulu Jiang; Sixiu Liu; Xinglong Jia; Qinting Gong; Xin Wen; Weiwei Lu; Jintong Yang; Xinyuan Wu; Xuan Wang; Yanrui Suo; Yilin Li; Motonari Uesugi; Zhi-bei Qu; Minjia Tan; Xiaojie Lu; Lu Zhou
J. Am. Chem. Soc., 2023, 145(46), 25283-25292
https://doi.org/10.1021/jacs.3c08852

Abstract

DNA-encoded chemical library (DEL) has been extensively used for lead compound discovery for decades in academia and industry. Incorporating an electrophile warhead into DNA-encoded compounds recently permitted the discovery of covalent ligands that selectively react with a particular cysteine residue. However, noncysteine residues remain underexplored as modification sites of covalent DELs. Herein, we report the design and utility of tyrosine-targeting DELs of 67 million compounds. Proteome-wide reactivity analysis of tyrosine-reactive sulfonyl fluoride (SF) covalent probes suggested three enzymes (phosphoglycerate mutase 1, glutathione s-transferase 1, and dipeptidyl peptidase 3) as models of tyrosine-targetable proteins. Enrichment with SF-functionalized DELs led to the identification of a series of tyrosine-targeting covalent inhibitors of the model enzymes. In-depth mechanistic investigation revealed their novel modes of action and reactive ligand-accessible hotspots of the enzymes. Our strategy of combining activity-based proteome profiling and covalent DEL enrichment (ABPP-CoDEL), which generated selective covalent binders against a variety of target proteins, illustrates the potential use of this methodology in further covalent drug discovery.