Synthesis and evaluation of naphthoquinone-based probes for activity-based protein profiling of oxidoreductases

Abstract

Activity-based protein profiling (ABPP) has become a highly valuable proteomic technique over the past decades especially in the investigation of hydrolytic enzymes. Oxidoreductases have so far received less attention as their catalytic function usually depends on cofactors, which requires different strategies for warhead design for probe molecules. We describe the design and total synthesis of novel activity-based probes based on an α-fluoromethyl naphthoquinone warhead. Starting from inexpensive and commercially available mequinol, our synthetic route utilizes an intramolecular Friedel–Crafts acylation as the key step for the formation of an annulated aryl ring bearing the ligation handle for the linker. In total, three novel probes were synthesized in 13 to 18 sequential steps, respectively. Initial ABPP experiments with flavin-dependent reductases and murine liver revealed the promiscuous reactivity of the warhead.

Graphical abstract: Synthesis and evaluation of naphthoquinone-based probes for activity-based protein profiling of oxidoreductases

Supplementary files

Article information

Article type
Paper
Submitted
12 Aug 2025
Accepted
07 Oct 2025
First published
08 Oct 2025
This article is Open Access
Creative Commons BY license

Org. Biomol. Chem., 2025, Advance Article

Synthesis and evaluation of naphthoquinone-based probes for activity-based protein profiling of oxidoreductases

L. Krammer, B. Darnhofer and R. Breinbauer, Org. Biomol. Chem., 2025, Advance Article , DOI: 10.1039/D5OB01320H

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements