Abstract IA06: Design and chemoproteomic characterization of novel covalent ligands

Abstract Covalent ligands that effectively balance chemical reactivity with molecular recognition provide pharmacodynamic and pharmacokinetic advantages and offer a means to target proteins traditionally deemed undruggable. By forming covalent bonds with nucleophilic residues such as catalytic cysteine, serine, threonine, tyrosine, or lysine residues, these compounds inhibit the enzymatic activity of diverse protein classes. In addition to active site targeting, covalent modification of reactive residues in allosteric regions can modulate protein function and protein-protein interactions. More recently, covalent ligands have been successfully employed in small molecule-induced proximity strategies, expanding their utility beyond simple inhibition. Cysteine-directed covalent warheads are already a component of many FDA-approved drugs, and advanced chemoproteomic studies have uncovered thousands of cysteines that can be covalently modified by small molecules. However, these sites have been identified using a relatively limited number of electrophilic chemotypes. Thus, there remains an unmet need for novel electrophilic scaffolds whose reactivity and selectivity can be rationally tuned to address protein targets of interest. In this presentation, I will describe our efforts to expand the scope of electrophilic chemotypes with significant potential to selectively engage reactive cysteines using a chemoproteomics platform integrated with phenotypic screening. Our initial efforts have focused on exploring unique and underexplored electrophilic moieties inspired by natural product scaffolds. We have developed a modular synthetic strategy to rapidly incorporate a natural product-derived electrophilic warhead into a diverse fragment library and mapped reactive sites (e.g., C113 of PIN1, C319 of BLK, and C481 of BTK). This study highlighted their promise for enabling inverse drug design strategies and late-stage functionalization in covalent ligand discovery. Additionally, we have characterized a reactive heterocyclic scaffold targeting therapeutically important proteins such as HSP60 and PREP. Our ongoing efforts aim to further refine the reactivity of these electrophilic warheads and optimize ligand scaffolds to enhance potency, selectivity, and overall drug-like properties. Citation Format: Euna Yoo. Design and chemoproteomic characterization of novel covalent ligands [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2025 Oct 22-26; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2025;24(10 Suppl):Abstract nr IA06.