Protease activity is tightly regulated in both normal and disease conditions. However, it is often difficult to monitor the dynamic nature of this regulation in the context of a live cell or whole organism. To address this limitation, we developed a series of quenched activity-based probes (qABPs) that become fluorescent upon activity-dependent covalent modification of a protease target. These reagents freely penetrate cells and allow direct imaging of protease activity in living cells. Targeted proteases are directly identified and monitored biochemically by virtue of the resulting covalent tag, thereby allowing unambiguous assignment of protease activities observed in imaging studies. We report here the design and synthesis of a selective, cell-permeable qABP for the study of papain-family cysteine proteases. This probe is used to monitor real-time protease activity in live human cells with fluorescence microscopy techniques as well as standard biochemical methods.

Purpose To evaluate the accuracy and reproducibility of quantitative chemical shift-encoded MRI (CSE-MRI) to quantify proton-density fat-fraction (PDFF) in a fat-water phantom across sites, vendors, field strengths and protocols. Methods Six sites (three vendors: GE/Philips/Siemens) participated in this study. A phantom containing multiple vials with various oil-water suspensions (PDFF:0–100%) was built, shipped to each site and scanned at 1.5T and 3T using two CSE protocols per field strength. Confounder-corrected PDFF maps were reconstructed using a common algorithm. To assess accuracy, PDFF bias and linear regression with the known PDFF were calculated. To assess reproducibility, measurements were compared across sites, vendors, field strengths and protocols using analysis of covariance (ANCOVA), Bland-Altman analysis and the intra-class correlation coefficient (ICC). Results PDFF measurements showed overall absolute bias (across sites, field strengths and protocols)=0.22% with 95% CI:(0.07%,0.38%), and R2>0.995 relative to the known PDFF at each site, field strength and protocol (slopes: 0.96–1.02, intercepts: −0.56%–1.13%). ANCOVA did not show effects of field strength (p=0.36), or protocol (p=0.19). There was a significant effect of vendor (F=25.13,p=1.07×10−10), with bias= −0.37% (Philips) and −1.22% (Siemens) relative to GE. The overall ICC was 0.999. Conclusion CSE-based fat quantification is accurate and reproducible across sites, vendors, field strengths and protocols.

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SUMMARY The widespread resistance of malaria parasites to all affordable drugs has made the identification of new targets urgent. Dipeptidyl aminopeptidases (DPAPs) represent potentially valuable new targets that are involved in hemoglobin degradation (DPAP1) and parasite egress (DPAP3). Here we use activity-based probes to demonstrate that specific inhibition of DPAP1 by a small molecule results in the formation of an immature trophozoite that leads to parasite death. Using computational methods we designed stable, non-peptidic covalent inhibitors that kill Plasmodium falciparum at low nanomolar concentrations. These compounds show signs of slowing parasite growth in a murine model of malaria, which suggests that DPAP1 might be a viable anti-malarial target. Interestingly, we found that re-synthesis and activation of DPAP1 after inhibition is rapid, suggesting that effective drugs would need to sustain DPAP1 inhibition for a period of 2–3h.

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