Evaluation of α,β-unsaturated ketone-based probes for papain-family cysteine proteases

Zhimou Yang, Marko Fonović, Steven H.L. Verhelst, Galia Blum, Matthew Bogyo*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


The field of activity-based proteomics makes use of small molecule active site probes to monitor distinct subsets of enzymatic proteins. While a number of reactive functional groups have been applied to activity-based probes (ABPs) that target diverse families of proteases, there remains a continual need for further evaluation of new probe scaffolds and reactive functional groups for use in ABPs. In this study we evaluate the utility of the, α,β-unsaturated ketone reactive group for use in ABPs targeting the papain-family of cysteine proteases. We find that this reactive group shows highly selective labeling of cysteine cathepsins in both intact cells and total cell extracts. We observed a variable degree of background labeling that depended on the type of tag and linker used in the probe synthesis. The relative ease of synthesis of this class of compounds provides the potential for further derivatization to generate new families of cysteine protease ABPs with unique specificity and labeling properties.

Original languageAmerican English
Pages (from-to)1071-1078
Number of pages8
JournalBioorganic and Medicinal Chemistry
Issue number3
StatePublished - 1 Feb 2009
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by the National Institutes of Health National Technology Center for Networks and Pathways Grant U54 RR020843, R01 EB005011, P01 CA072006, and a Stanford Chemical and Systems Biology training grant (to S.V.).


  • Active site labeling
  • Activity-based probes
  • Cysteine protease
  • Irreversible inhibitor


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