An efficient selection platform enables discovery of novel lysine targeting covalent inhibitors

In a study published in Angewandte Chemie International Edition, the researchers integrated activity-based protein profiling (ABPP) data with covalent DNA-encoding chemical library (Codel) technology to identify structurally novel lysine target covalent inhibitors with diverse mechanisms of action.

The team is led by Lu Xiaojie of the Shanghai Institute of Materials and Media, China Academy of Sciences, and is working with Zhou Lu and Sun Yi of Fudan University at Zhejiang University School of Medicine.

Covalent drugs function by forming covalent bonds with specific amino acid residues, allowing for sustained regulation of target proteins. Compared to cysteine ​​intergating strategies, lysine acts as an alternative covalent binding site that avoids limitations on cysteine ​​rarity in the ligand binding pocket and broadens the landscape of drag agent targets. In recent years, structure-based drug design has accelerated the development of lysine targeted shared sharing inhibitors.

Codell technology is rapidly emerging as an important platform for the discovery of shared organisms. Lu Xiaojie’s team, together with collaborators, applied the technology to discover novel cysteine ​​target covalent covalent inhibitors of proteins and develop an integrated ABPP codel strategy to identify tyrosine target covalent inhibitors.

However, a systematic code cell selection platform specifically designed for lysine target inhibitors has not yet been established. Furthermore, due to the wide distribution of lysine throughout the human proteome, random target selection is not efficient for screening.

By integrating the compound-based and warhead-based ABPP datasets, the researchers constructed protein datasets enriched for lysine residues that exhibit both high reactivity and ligand properties, thereby facilitating rational target selection for screening. Eight lysine targeting shared warheads were then incorporated with eight lysine targeting shared warheads with distinct reaction mechanisms for synthesizing codes containing 107 million compounds.

Covalent selection identified lysine target covalent inhibitors for phosphoglycerate mutase 1 (PGAM1), bromodomain (BRD) family proteins, and lysine target covalent inhibitors for the ubiquitin-conjugated enzyme E2N (UBE2N).

Among them, compound 1 served as a light-covalent probe for the active site of PGAM1, and compound 4 formed a reversible covalent bond with previously unopened sites within the bromodomain of the BRD family protein.

In particular, compound 9 irreversibly bound to UBE2N induces conformational changes in the UBE2N/UBE2V2 complex, disrupting the formation of polyubiquitin chains and impairs its downstream functional activity. This new mechanism provided a new strategy to regulate the ubiquitination pathway.

This study establishes an efficient platform for selecting covalent inhibitors targeting lysine by integrating proteome data and coding technology. This strategy not only expands the applicability of covalent organisms in target selection, but also provides technical support for the rational design of covalent inhibitors.