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

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.