The biological and pathological functions of cathepsin
B occur
in acidic lysosomes and at the neutral pH of cytosol, nuclei, and
extracellular locations. Importantly, cathepsin B displays different
substrate cleavage properties at acidic pH compared to neutral pH
conditions. It is, therefore, desirable to develop specific substrates
for cathepsin B that measure its activity over broad pH ranges. Current
substrates used to monitor cathepsin B activity consist of Z-Phe-Arg-AMC
and Z-Arg-Arg-AMC, but they lack specificity since they are cleaved
by other cysteine cathepsins. Furthermore, Z-Arg-Arg-AMC monitors
cathepsin B activity at neutral pH and displays minimal activity at
acidic pH. Therefore, the purpose of this study was to design and
validate specific fluorogenic peptide substrates that can monitor
cathepsin B activity over a broad pH range from acidic to neutral
pH conditions. In-depth cleavage properties of cathepsin B were compared
to those of the cysteine cathepsins K, L, S, V, and X via multiplex
substrate profiling by mass spectrometry at pH 4.6 and pH 7.2. Analysis
of the cleavage preferences predicted the tripeptide Z-Nle-Lys-Arg-AMC
as a preferred substrate for cathepsin B. Significantly, Z-Nle-Lys-Arg-AMC
displayed the advantageous properties of measuring high cathepsin
B specific activity over acidic to neutral pHs and was specifically
cleaved by cathepsin B over the other cysteine cathepsins. Z-Nle-Lys-Arg-AMC
specifically monitored cathepsin B activity in neuronal and glial
cells which were consistent with relative abundances of cathepsin
B protein. These findings validate Z-Nle-Lys-Arg-AMC as a novel substrate
that specifically monitors cathepsin B activity over a broad pH range.