DNA-encoded libraries (DELs) are constructed using split-and-pool strategies that enable the systematic assembly of diverse chemical building blocks [1,2]. Supported by an expanding array of DNA-compatible chemical reactions, this approach facilitates efficient exploration of vast chemical space during library synthesis [3, 4, 5, 6]. DELs with varied structural architectures can be pooled and screened in parallel against specific biological targets [7]. High-throughput sequencing (NGS) then enables rapid identification of enriched binders via their unique DNA barcodes. Benefitting from their large chemical space and highly efficient screening capabilities, DELs have yielded hits across a broad range of targets, including traditionally challenging classes such as E3 ligases [8, 9, 10] and G protein-coupled receptors (GPCRs) [11, 12, 13]. Notably, several DEL-derived hits have progressed into clinical trials, underscoring the translational potential of this technology [14, 15, 16, 17, 18, 19]. Novel modalities, such as PROTACs and molecular glues, have also emerged from specially designed DEL platforms [20, 21, 22]. In parallel, covalent DEL technology (CoDEL) has been developed to discover covalent ligands, particularly those bearing Michael acceptors that target reactive cysteine residues within protein binding pockets [23, 24, 25]. More recently, additional covalent warheads have been incorporated into DELs to enable the targeting of alternative nucleophilic residues such as lysine, tyrosine, and others.

Covalent inhibitors offer high selectivity, sustained efficacy, and typically require lower doses. Multiple platforms have been established for their discovery, particularly to address traditionally undruggable targets [26]. CoDEL adopts an “electrophile-first” strategy, in which electrophilic warheads are incorporated into DEL scaffolds, sometimes as one cycle of BBs [27]. While reversible covalent hits can be identified through standard affinity-based selection, the discovery of irreversible covalent inhibitors requires modification to the DEL screening platform, generally involving denaturing washes or thermal treatments to eliminate non-covalent binders. Early efforts have primarily focused on targeting cysteine residues within or near binding sites, which limited the scope of CoDEL applications. This review summarizes recent advances in CoDEL-enabled covalent inhibitor discovery and the incorporation of proteome profiling to guide DEL construction and target identification.