Improving lanthanide-based resonance energy transfer detection by increasing donor-acceptor distances

General Stepwise Approach to Optimize a TR-FRET Assay for Characterizing the BRD/PROTAC/CRBN Ternary Complex

Proteolysis-targeting chimeras (PROTACs) degrade target proteins by engaging the ubiquitin-proteasome system. Assays detecting target-PROTAC-E3 ligase ternary complexes are critical for PROTAC development. Both time-resolved fluorescence energy transfer (TR-FRET) assays and amplified luminescent proximity homogeneous assays can characterize ternary complexes and assess PROTAC efficacy; stepwise optimization protocols for these assays are lacking. To identify assay conditions that can be applied to various targets and PROTACs, we used a stepwise approach to optimize a TR-FRET assay of BRD2(BD1)/PROTACs/CRBN ternary complexes. This assay is sensitive and specific and responds to the bivalent PROTACs dBET1, PROTAC BET Degrader-1, and PROTAC BET Degrader-2 but not to non-PROTAC ligands of BRD2(BD1) or CRBN. The activity rank order of dBET1, PROTAC BET Degrader-1, and PROTAC BET Degrader-2 in the TR-FRET assay corresponded with previously reported cell growth inhibition assays, indicating the effectiveness of our assay for predicting PROTAC cellular activity. The TR-FRET ternary complex formation assay for BRD2(BD1)/PROTAC/CRBN can be configured to characterize the binding activities of BRD2(BD1) and CRBN ligands with the same compound activity rank order as that of previously reported binary binding assays for individual targets but with the advantage of simultaneously assessing the ligand activities for both targets. Our assay is modular in nature, as BRD2(BD1) can be replaced with other BRDs and successfully detect ternary complexes without modifying other assay conditions. Therefore, the TR-FRET ternary complex assay for BRDs provides a general assay protocol for establishing assays for other targets and bivalent molecules.

FRET-based screening assay using small-molecule photoluminescent probes in lysate of cells overexpressing RFP-fused protein kinases

An assay was developed for the characterization of protein kinase inhibitors in lysates of mammalian cells based on the measurement of FRET between overexpressed red fluorescent protein (TagRFP)-fused protein kinases (PKs) and luminophore-labeled small-molecule inhibitors (ARC-Photo probes). Two types of the assay, one using TagRFP as the photoluminescence donor together with ARC-Photo probes containing a red fluorophore dye as acceptor, and the other using TagRFP as the acceptor fluorophore in combination with a terbium cryptate-based long-lifetime photoluminescence donor, were used for FRET-based measurements in lysates of the cells overexpressing TagRFP-fused PKs. The second variant of the assay enabled the performance of the measurements under time-resolved conditions that led to substantially higher values of the signal/background ratio and further improved the reliability of the assay.

Characterization of the weak calcium binding of trimeric globular adiponectin

Adiponectin is secreted from adipose tissue and functions as a protein hormone in regulating glucose metabolism and fatty acid catabolism. Adiponectin plays an important role as a novel risk factor and potential diagnostic and prognostic biomarker in cancer. Crystal structures of globular adiponectin have been resolved with three calcium-binding sites on the top of its central tunnel. However, the calcium-binding property of adiponectin remains elusive. Mouse globular adiponectin was cloned into pET11a and expressed in Escherichia coli. The folding of adiponectin was indicated by the spread of resonances in HSQC spectrum. Luminescence resonance energy transfer was used to obtain the binding constant (K(d)) of Tb(3+) and the inhibitor constant (K(i)) of Ca(2+) for globular adiponectin. The obtained calcium-binding affinity to adiponectin is relatively low (~2 mM), which indicates that the high concentration of adiponectin in circulating system may function as calcium storage bank and buffer the free calcium concentration.

Development and characterization of a novel membrane assay for full-length BACE-1 at pH 6.0

β-Site amyloid precursor protein cleaving enzyme-1 (BACE-1) is a transmembrane aspartic protease that mediates the initial cleavage of the amyloid precursor protein (APP), leading to the generation of amyloid-β (Aβ) peptides that are thought to be causative of Alzheimer's disease (AD). Consequently, inhibition of BACE-1 is an attractive therapeutic approach for the treatment of AD. In general, in vitro biochemical assays to monitor BACE-1 activity have used the extracellular domain of the protein that contains the catalytic active site. This form of BACE-1 is catalytically active at acidic pH and cleaves APP-based peptide substrates at the β-site. However, this form of BACE-1 does not mimic the natural physiology of BACE-1 and shows minimal activity at pH 6.0, which is more representative of the pH within the intracellular compartments where BACE-1 resides. Moreover, high-throughput screens with recombinant BACE-1 at pH 4.5 have failed to identify tractable leads for drug discovery, and hence, BACE-1 inhibitor development has adopted a rational drug design approach. Here we describe the development and validation of a novel membrane assay comprising full-length BACE-1 with measurable activity at pH 6.0, which could be used for the identification of novel inhibitors of BACE-1.

Homogeneous detection of avidin based on switchable lanthanide luminescence

We have developed switchable lanthanide luminescence-based binary probe technology for homogeneous detection of avidin, which is a tetrameric protein. Two different nonluminescent label moieties--a light-absorbing antenna ligand and a lanthanide ion carrier chelate--were conjugated to separate biotins, which is known as avidin's natural ligand. The assay was based on binding of the two differently labeled biotins on separate binding sites on the target protein and consequent self-assembly of a luminescent complex from the two label moieties. Specific luminescence signal was observed only at the presence of the target protein. The characteristics of the switchable lanthanide luminescence assay were compared to the reference assay, based on lanthanide resonance energy transfer. Both assays had a limit of detection in the low-picomolar concentration range; however, the lanthanide chelate complementation-based assay had wider dynamic range and its optimization was more straightforward. The switchable lanthanide luminescence technology could be further applied to generic protein detection, using reagents that are analogous to the proximity ligation assay principle.

Eu(III) complexes of functionalized octadentate 1-hydroxypyridin-2-ones: stability, bioconjugation, and luminescence resonance energy transfer studies

The synthesis, stability, and photophysical properties of several Eu(III) complexes featuring the 1-hydroxypyridin-2-one (1,2-HOPO) chelate group in tetradentate and octadentate ligands are reported. These complexes pair highly efficient emission with exceptional stabilities (pEu ∼ 20.7-21.8) in aqueous solution at pH 7.4. Further analysis of their solution behavior has shown the observed luminescence intensity is significantly diminished below about pH ∼ 6 because of an apparent quenching mechanism involving protonation of the amine backbones. Nonetheless, under biologically relevant conditions, these complexes are promising candidates for applications in Homogeneous Time-Resolved Fluorescence (HTRF) assays and synthetic methodology to prepare derivatives with either a terminal amine or a carboxylate group suitable for bioconjugation has been developed. Lastly, we have demonstrated the use of these compounds as the energy donor in a Luminescence Resonance Energy Transfer (LRET) biological assay format.

A new quinoline sensitizer-centered lanthanide chelate and its use for protein labling on Ni-NTA beads for TR LRET assays

A quinoline sensitizer-centered lanthanide chelate system of novel design for TR-LRET was prepared; it exhibited high labelling efficiency with a his-tagged protein (ERalpha-LBD) on the Ni-NTA beads, using a mixed metal chelate protocol, and it functioned well in TR-LRET protein-protein interaction assays.

Particulate and soluble Eu(III)-chelates as donor labels in homogeneous fluorescence resonance energy transfer based immunoassay

Many well-established homogeneous separation free immunoassays rely on particulate label technologies. Particles generally contain a high concentration of the embedded label and they have a large surface area, which enables conjugation of a large amount of protein per particle. Eu(III)-chelate dyed nanoparticles have been successfully used as labels in heterogeneous and homogeneous immunoassays. In this study, we compared the characteristics of two homogeneous competitive immunoassays using either soluble Eu(III)-chelates or polystyrene particles containing Eu(III)-chelates as donors in a fluorescence resonance energy transfer based assay. The use of the particulate label significantly increased the obtained sensitized emission, which was generated by a single binding event. This was due to the extremely high specific activity of the nanoparticle label and also in some extent the longer Förster radius between the donor and the acceptor. The amount of the binder protein used in the assay could be decreased by 10-fold without impairing the obtainable sensitized emission, which subsequently led to improved assay sensitivity. The optimized assay using particulate donor had the lowest limit of detection (calculated using 3 x S.D. of the 0 nM standard) 50pM of estradiol in the assay well, which was approximately 20-fold more sensitive than assays using soluble Eu(III)-chelates.

Recommendations for the reduction of compound artifacts in time-resolved fluorescence resonance energy transfer assays

Time-resolved (TR) fluorescence resonance energy transfer (FRET) is a widely accepted technology for high throughput screening (HTS), being able to detect and quantify the interactions of specific biomolecules in a homogeneous format. TR-FRET has several advantages for HTS applications that reduce assay artifacts such as compound interference. However, in some cases artifacts due to compound autofluorescence, color quenching, or signal stability are still observed. This report presents strategies addressing these issues by several means. One recommendation is the recording and visualization of differences in the donor/acceptor fluorescence, which allows the identification of compound artifacts. Another suggestion is to adjust the time delay, between excitation and recording of the fluorescence, in order to reduce compound interference. Furthermore, configuring the assay to allow the TR-FRET measurement to be taken at different time points, creating a reaction time course, allows background correction for each sample. Finally, the optimization of the FRET pair, to ensure assay signal stability under screening conditions, can improve the assay quality. This report presents examples of how these simple steps can be applied to enhance the quality of TR-FRET screening campaigns.