Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Due to the high abundance and diverse functions of lysine residues, both in the interior and on the surface of proteins, the development of new methods to characterize their reactivity and ligandability could significantly expand the pool of druggable targets. To date, only a limited number of aminophilic electrophiles have been assessed for interactions with the lysine proteome, resulting in a substantial fraction remaining inaccessible to current probes. Here, to the best of our knowledge, we report the first oxidant-triggered bioconjugation platform for in-depth profiling of lysines. We quantified over 7000 covalently modifiable lysine residues, which significantly expands the coverage of ligandable lysines in the whole proteome. Chemical proteomics enabled the mapping of more than 100 endogenous kinases, thus providing a comprehensive landscape of ligandable catalytic lysines within the kinome. Moreover, we identified a suite of new ligandable lysines such as K60 of ENO1 and K31 of PPIA, offering insights for exploring new functional and targetable residues. These findings could provide valuable clues for the development of targeted covalent inhibitors (TCIs).
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1002/anie.202418473 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Investigation of a cryptic ligand binding site on Plasmodium falciparum Hsp90.
Bioorg Med Chem
August 2025
Department of Chemistry, Duke University, Durham, NC, USA; Department of Molecular Genetics & Microbiology, Duke Medical School, Durham, NC, USA. Electronic address:
The molecular chaperone heat shock protein 90 (Hsp90) has an important role in maintaining proteostasis in Plasmodium parasites, the causative agents of malaria, and is of interest as a potential antimalarial drug target. Inhibitors targeting its well-characterized N-terminal ATP-binding site are lethal, but the development of high-affinity binders with selectivity for the Plasmodium over the human homolog has been challenging given the high conservation of this domain. A binding site in the less conserved Hsp90 C-terminus has been reported to interact with nucleotides and inhibitors in other eukaryotic systems, which could offer an alternative route for antimalarial design.
View Article and Find Full Text PDFActivity-Based Profiling of Reactive Nucleophilic Cysteine Sites from Tissue Proteomes for Drug Discovery Applications.
Methods Mol Biol
June 2025
Merck & Co., Inc., Cambridge, MA, USA.
Identifying engaged nucleophilic sites in a proteome-wide manner has become a powerful means to leverage activity-based protein profiling toward assessing the target landscape of covalent compounds ranging from fragments to approved drugs. In this chapter, we provide a detailed protocol for reactive cysteine profiling from tissue lysates using a low-input high throughput-compatible workflow based on multiplexing via TMT-16pro. We apply this method to a representative biological context, human heart tissue lysates treated with highly reactive and promiscuous electrophilic scout fragments.
View Article and Find Full Text PDFProteome-wide ligandability maps of drugs with diverse cysteine-reactive chemotypes.
Nat Commun
May 2025
State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing, China.
Covalent drug discovery has experienced a revival since the 2013 approval of the first cysteine-targeting kinase inhibitors. Many drugs that were discovered by serendipity also possess the ability to react with cysteine residues, leading to interactions with multiple proteins. This widespread interaction, known as promiscuity, necessitates a comprehensive study of how these drugs engage with cysteines throughout the proteome.
View Article and Find Full Text PDFAdvancing Covalent Ligand and Drug Discovery beyond Cysteine.
Chem Rev
July 2025
Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States.
Targeting intractable proteins remains a key challenge in drug discovery, as these proteins often lack well-defined binding pockets or possess shallow surfaces not readily addressed by traditional drug design. Covalent chemistry has emerged as a powerful solution for accessing protein sites in difficult to ligand regions. By leveraging activity-based protein profiling (ABPP) and LC-MS/MS technologies, academic groups and industry have identified cysteine-reactive ligands that enable selective targeting of challenging protein sites to modulate previously inaccessible biological pathways.
View Article and Find Full Text PDFLysine-Targeting, Covalent Inhibitors of Bromodomain BD1 of BET Proteins in Live Cells and Animals.
Angew Chem Int Ed Engl
July 2025
Department of Pharmacology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
The bromodomain extra-terminal (BET) family of proteins are valuable therapeutic targets for cancer and other diseases. The adverse events of current pan-BET inhibitors (BETi) make the development of BET BD1- or BD2-selective inhibitors as a fresh avenue to overcome safety challenges. On the basis of various lysine-reactive covalent warheads herein we report a set of activity-based probes (ABPs; P3-P7) capable of global profiling of ligandable lysines within bromodomains (BRDs) in live cells and animals.
View Article and Find Full Text PDF