Rui Jin and Xiaojie Lu

https://doi.org/10.1016/j.sbi.2025.103163

Abstract

DNA-encoded library (DEL) technology has enabled efficient discovery of both non-covalent and covalent inhibitors. Covalent DELs (CoDELs) incorporating diverse electrophilic warheads have expanded the scope of covalent targeting beyond cysteine to residues like lysine, tyrosine, arginine, and glutamic acid. The integration of CoDEL with activity-based protein profiling (ABPP) has further enabled the identification of potential protein targets for CoDEL screening using residue-selective warheads. Additionally, proteome profiling with fully functionalized tags has guided target identification for focused DELs with privileged structures. This review highlights recent advances in CoDEL technologies for targeting both cysteine and non-cysteine residues and discusses how proteomics facilitates hit discovery through CoDELs and focused DELs.

Summary

This review article discusses the recent advancements in DNA-encoded libraries (DELs), particularly focusing on covalent DELs (CoDELs). CoDELs have shown significant potential in discovering covalent inhibitors targeting various amino acid residues, not just cysteine. The article highlights the use of CoDELs in identifying inhibitors for a range of targets, including viral proteins and oncoproteins. It also explores the integration of CoDEL technology with proteomics strategies such as activity-based protein profiling (ABPP) and proteome profiling using fully functionalized tags to guide the construction of focused DELs and improve hit discovery. The review emphasizes the importance of these integrative approaches in expanding the scope of covalent drug design and accelerating the discovery of novel therapeutic agents.

Highlights

- Covalent DNA-encoded libraries (CoDELs) have expanded covalent targeting to residues beyond cysteine, including lysine, tyrosine, arginine, and glutamic acid.

- Integration of CoDEL with activity-based protein profiling (ABPP) enables the identification of potential protein targets for covalent inhibitors.

- Proteome profiling using fully functionalized tags guides the construction of focused DELs with privileged structures, enhancing hit discovery.

- Recent studies demonstrate the discovery of covalent inhibitors for viral proteins and oncoproteins using CoDELs, showcasing their translational potential.

- The review emphasizes the importance of combining proteomics with CoDEL technology to improve target selection and hit identification.

Conclusion

Over the past decade, DNA-encoded library (DEL) technology has undergone rapid development, with significant advancements in the expansion of on-DNA chemical reactions and the construction of diverse libraries. Covalent DELs (CoDELs) have emerged as a powerful tool for discovering covalent inhibitors targeting various amino acid residues. The integration of CoDEL with proteomics strategies such as activity-based protein profiling (ABPP) and proteome profiling using fully functionalized tags has significantly enhanced the efficiency of hit discovery and target identification. As the field progresses, the continued expansion of CoDEL applications and the incorporation of proteomic data to guide library design and target engagement represent promising frontiers for both covalent and non-covalent DELs, potentially leading to the discovery of novel therapeutic agents with improved efficacy and selectivity.