Solid-Phase Synthesis of ProTide Fluorogenic Probes Enables Systematic Profiling of Carboxypeptidase Activity

ABSTRACT Carboxypeptidases play diverse roles in physiological and pathological processes, yet comprehensive analysis of their activities in complex biological samples remains challenging. Here we report a solid-phase synthesis strategy for fluorogenic ProTide-based probes that enables systematic profiling of carboxypeptidase activities based on defined C-terminal amino acid motifs. By modular synthesis of dipeptide–fluorophore conjugates, we generated a focused probe set that revealed distinct substrate preferences among carboxypeptidases, including carboxypeptidase A and B family enzymes. Integration of these probes with a single-molecule enzyme activity assay allowed ultrasensitive detection of circulating carboxypeptidase activities in human blood samples. Application of this platform to clinical specimens demonstrated that specific carboxypeptidase activities are elevated in patients with pancreatic cancer compared with healthy controls, whereas closely related enzymes showed limited diagnostic value. These results establish a scalable chemical strategy for activity-based profiling of exopeptidases and highlight circulating carboxypeptidase activity as a functional enzymatic signature associated with pancreatic cancer. Competing Interest Statement Y. K. is a cofounder, employee and shareholder of Cosomil, Inc. M. M. and H. H.. are employees of Cosomil, Inc. T. K. and K. H. are advisors and shareholders of Cosomil, Inc. T. K. and Y. U. are inventors of a patent describing the design strategies of fluorogenic probes. This study was supported in part by Cosomil, Inc. through a collaborative research agreement with the University of Tokyo.