- Determine the activity of a de-neddylating protease in an HTS compatible format
- Use of a ﬂuorophore with a long ﬂuorescence lifetime to extend the assay window
- PHERAstar® enables measurement due to speed and accuracy
Table of contents
Cullin-RING E3 ubiquitin ligases (CRLs) are activated by neddylation and inactivated by de-neddylation that is accomplished by the COP9 signalosome (CSN). Trapping CRLs in their inactive state is reported to elevate tumor suppressors. Therefore, inhibition of CSN is a potential modality for cancer treatment.
Here, we show the development of a high-throughput de-neddylation assay for a CRL substrate that was used to find inhibitors of CSN. The fluorescence polarization assay was optimized using a fluorophore with comparatively long fluorescence lifetime.
Performing the assay in a 384 well plate and reading it on a PHERAstar® microplate reader provided an assay window of 130 mP. The reader's capability of simultaneous detection of the two polarization channels accelerated the measurement and enabled kinetic reads. Hence, the assay is applicable for both CSN inhibitor finding and characterization.
The COP9 signalosome (CSN) catalyzes the de-neddylation of cullin-RING E3 ubiquitin ligases (CRLs) turning the ligase into the inactive state. Literature evidence suggests that trapping CRLs in the inactive state will keep selected tumor suppressors at elevated levels. Therefore, the inhibition of CSN’s proteolytic subunit CSN5 represents a potential novel modality for the treatment of cancer (Fig. 1).
A biochemical protease assay to probe the de-neddy-lating activity of CSN was developed in order to identify by high-throughput screening (HTS) chemical starting points for drug discovery.
A major complication for establishing an appropriate enzyme activity assay was the fact that CSN5 is only proteolytically active in the context of the CSN complex. In addition, CSN-catalyzed de-neddylation requires neddylated cullin complexes as substrate (i.e., CRNB-DDB1-DDB2-Rbx-Nedd8). Hence, both the enzymatically active protease and the corresponding substrate are multi-domain protein complexes. As a consequence, the assay had to be adapted for detecting the release of the 8 kDa ubiquitin-like protein Nedd8 from an approx. 270 kDa CRL complex (Fig. 2a).
As assay readout, we applied ﬂuorescence polarization (FP), which relies on rotational movement of molecules in solution. Large molecules rotate slower than small molecules. Therefore, ﬂuorophores tightly bound to small molecules depolarize emission light stronger than those bound to larger molecules. In order to optimize the assay window for the protease activity assay with respect to the expected mass changes, we selected the ﬂuorophore PureTime-22 (PT22) as the FP probe. PT22 is an acridone dye exhibiting a remarkable long ﬂuorescence lifetime (FLT) of 22 ns. Since the FP value depends on both, the molecular mass of the protein and the FLT of the probe, the use of the long FLT probe PT22 offers an obvious advantage over the use of frequently used probes such as Alex Fluor® 488, which have a FLT in the range of only 3-4 ns. The long FLT of the PT22 probe signiﬁcantly increases the window of the FP assay when proteins or protein complexes of high molecular mass are under investigation (Fig. 2b).
Materials & Methods
- CliniPlates (ThermoScientiﬁc) 384 well black
- Cul4A E3 ligase modiﬁed with ﬂuorophore-labeled NEDD81 (ﬂuorophore PT22, GE Healthcare, TTP Labtech)
- CSN complex1
- PHERAstar® FS, BMG LABTECH
The CSN enzyme solution (12.5 µl, ﬁnal concentration 150 pM) was added to 0.25 µl of test compound to preincubate at room temperature for 1 h. The reaction was started by addition of the Cul-NEDD8-PT22 sub-strate (12.5 µl, ﬁnal concentration 150 nM)1.
For the comparative TR-FRET assay a terbium labelled anti-His antibody was used in combination with an Alexa 488-coupled substrate. Please contact BMG LABTECH for further information.
|Optic settings|| |
FP 540 590 590 optic module
Emission: (parallel and
LanthaScreen optic module
Tb emission: 488
Alexa488 emission: 520
|Focus and gains adjusted before measurement, target mP 75|| |
Integration start: 70 µs
Integration time: 500 µs
|General settings||10 flashes (flash lamp)|
|0.1 s settling time|
|Measurement mode||Kinetic parameters: |
Plate mode, 60 s cycle time, 240 cycle number or endpoint
|Shaking||Shaking 5 s before first cycle, double orbital 500 rpm||5 s before first cycle, double orbital 500 rpm|
Results & Discussion
The PT22 ﬂuorophore with a comparatively long ﬂuorescence lifetime of 22 ns was employed to monitor the proteolytic activity of CSN5 resulting in the release of PT22-NEDD8 from the Cul4A ubiquitin ligase. The proteolytic activity results in a decrease of the FP value. With increasing concentrations of CSN5, the FP value decreased more rapidly. The overall assay window of 130 mP is sufﬁcient for both, screening and subsequent inhibitor validation and characterization activities².
When used for hit ﬁnding and during the hit-lead and lead-optimization phase, the FP assay performed well compared to a previously established TR-FRET activity assay (Fig 4). The TR-FRET assay employed a Tb chelate introduced via streptavidin-biotin system and an Alexa488 ﬂuorophore bound to the Nedd8 corresponding donor-acceptor pair. We witnessed that many highly potent CSN5 small molecule inhibitors tested during the later stage of the drug discovery project interfered with the TR-FRET but not with the FP assay readout.
The ﬂuorescence polarization assay presented here allows to screen for inhibitors of the CSN5, a metallo-protease regulating the activity of ubiquitin ligases and implicated in cancer. The assay window was optimized by choosing an FP probe with a remarkable long ﬂuorescence lifetime, because the FP value depends on both, the molecular mass of the protein and the ﬂuorescence lifetime of the probe. The high sensitivity of the PHERAstar reader together with the simultaneous detection of both emission channels enabled for fast FP measurements. Consequently, this allowed for running the assay in a continuous manner, i.e., without quenching the protease activity prior to plate reading, and hence for a lean and economic workﬂow in HT screening and inhibitor characterization.
1. A. Schlierf et al. (2016) Nat. Commun. 2016; 7: 13166.
2. J. Woelcke and U Hassiepen (2009) CRC Press 2009, Taosheng Chen