ABPP-CoDEL: Activity-Based Proteome Profiling-Guided Discovery of Tyrosine-Targeting Covalent Inhibitors from DNA-Encoded Libraries

J Am Chem Soc. 2023 Nov 22;145(46):25283-25292. doi: 10.1021/jacs.3c08852. Epub 2023 Oct 19.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA
  • Drug Discovery / methods
  • Ligands
  • Proteome* / chemistry
  • Small Molecule Libraries / pharmacology
  • Tyrosine*

Substances

  • Proteome
  • Tyrosine
  • Small Molecule Libraries
  • Ligands
  • sulfuryl fluoride
  • DNA