Applications of Fluorescent Polymer Superquenching to High Throughput Screening Assays for Protein Kinases

Measuring Kinase Activity-A Global Challenge

The kinase enzymes within a cell, known collectively as the kinome, play crucial roles in many signaling pathways, including survival, motility, differentiation, stress response, and many more. Aberrant signaling through kinase pathways is often linked to cancer, among other diseases. A major area of scientific research involves understanding the relationships between kinases, their targets, and how the kinome adapts to perturbations of the cellular system. This review will discuss many of the current and developing methods for studying kinase activity, and evaluate their applications, advantages, and disadvantages. J. Cell. Biochem. 118: 3595-3606, 2017. © 2017 Wiley Periodicals, Inc.

Streptavidin sensor and its sensing mechanism based on water-soluble fluorescence conjugated polymer

Fluorescence quenching effect of water-soluble anionic conjugated polymer (CP) (poly[5-methoxy-2-(3-sulfopoxy)-1,4-phenylenevinylene] (MPS-PPV)) by [Re(N-N)(CO)3(py-CH2-NH-biotin)](PF6) [N-N=2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline; py-CH2-NH-biotin=N-[(4-pyridyl) methyl] biotinamide] (Re-Biotin) and fluorescence recovery in the presence of streptavidin (or avidin) were investigated using Re-Biotin as quencher tether ligand (QTL) probe. Meanwhile, the mechanisms of fluorescence quenching and recovery were discussed to provide new thoughts to design biosensor based on water-soluble CPs. The results indicate that the sensing mechanisms of streptavidin sensor or avidin sensor, using Re-Biotin as QTL probe, are the same and stable, whether in non-buffer system (aqueous solution) or different buffer systems [0.01 mol·L(-1) phosphate buffered solution (pH=7.4), 0.1 mol·L(-1) ammonium carbonate buffered solution (pH=8.9)]. There exists specific interactions between streptavidin (or avidin) and biotin of Re-Biotin. Fluorescence quenching and recovery processes of MPS-PPV are reversible. Mechanisms of Re-Biotin quenching MPS-PPV fluorescence can be interpreted as strong electrostatic interactions and charge transferences between Re-Biotin and MPS-PPV. Fluorescence recovery mechanisms of Re-Biotin-MPS-PPV system can be interpreted as specific interactions between streptavidin (or avidin) and biotin of Re-Biotin making Re-Biotin far away from MPS-PPV. Avidin or strptavidin as re-Biotin probe can not only be quantitatively determinated, but also be identified.

Modification of agarose: 6-aminoagarose mediated syntheses of fluorogenic pyridine carboxylic acid amides

A facile 6-aminoagarose (AA) mediated synthesis of new fluorogenic amides of agarose with nicotinic (AA-NA) and picolinic acids (AA-PA) employing carbodiimide chemistry have been described. 6-Amino agarose (AA) was synthesized in a facile Mitsunobu-inspired microwave mediated method involving the reaction of agarose with phthalimide in presence of diisopropyl azodicarboxylate and triphenylphosphene (DIAD/TPP) followed by hydrazinolysis. All compounds were characterized by GPC, UV spectrophotometry, fluorescence spectroscopy, FT-IR, (1)H and (13)C NMR spectra. The fluorescence emissions (λmax 430 and 412 nm) of 1 × 10(-3)M solutions of AA-NA and AA-PA in water were significantly higher (ca. 82% and ca. 90%) than those of the molar equivalents (0.2mg) of NA and PA present in the 1 × 10(-3)M solutions of the amides, respectively. These fluorogenic pyridine carboxylic acid amides of agarose may find applications as sensors in biomedical and pharmaceutical industries.

Phosphorylation assay based on multifunctionalized soluble nanopolymer

Quantitative phosphorylation analysis is essential to understanding cellular signal transductions. Here we present a novel technology for the highly efficient assay of protein phosphorylation in high-throughput format without the use of phospho-specific antibodies. The technique is based on a water-soluble, nanosize polymer, termed pIMAGO, that is multifunctionalized with titanium(IV) ions for specific binding to phosphoproteins and with biotin groups that allow for enzyme-linked spectrometric detection. The sensitivity, specificity, and quantitative nature of pIMAGO for phosphorylation assays were examined with standard phosphoproteins and with purified phosphoproteins from whole cell extracts. As low as 100 pg of phosphoprotein can be measured quantitatively with the pIMAGO chemiluminescence assay. The pIMAGO assay was applied to an in vitro kinase assay, kinase inhibitor screening, and measurement of endogenous phosphorylation events. The technique provides a universal, quantitative method for global phosphorylation analysis with high sensitivity and specificity.

Microwave-induced facile synthesis of water-soluble fluorogenic alginic acid derivatives

A facile microwave-induced method was developed for synthesizing water-soluble fluorescent derivatives of alginic acid (ALG) with four different diamines, hydrazine (HY), ethylenediamine (EDA), 1,6-hexanediamine (HDA), and 1,4-cyclohexanediamine (CHDA), followed by a cross-linking reaction with a natural cross linker genipin. The ethylenediamine derivative of alginic acid (ALG-EDA) exhibited good fluorescent activity, which upon cross linking was enhanced threefold. The other amide derivatives, for example, ALG-HY, ALG-HDA, and ALG-CHDA, were not fluorescent, but their respective crosslinked products exhibited excellent fluorescent activity. The fluorescence intensity had an inverse correlation with the number of carbon atoms present in the amine, which in turn was a function of degree of substitution (DS). These fluorescent polysaccharide derivatives are of potential utility in the domain of sensor applications.

Biomimetic silica microspheres in biosensing

Lipid vesicles spontaneously fuse and assemble into a lipid bilayer on planar or spherical silica surfaces and other substrates. The supported lipid bilayers (SLBs) maintain characteristics of biological membranes, and are thus considered to be biomembrane mimetic systems that are stable because of the underlying substrate. Examples of their shared characteristics with biomembranes include lateral fluidity, barrier formation to ions and molecules, and their ability to incorporate membrane proteins into them. Biomimetic silica microspheres consisting of SLBs on solid or porous silica microspheres have been utilized for different biosensing applications. The advantages of such biomimetic microspheres for biosensing include their increased surface area to volume ratio which improves the detection limits of analytes, and their amenability for miniaturization, multiplexing and high throughput screening. This review presents examples and formats of using such biomimetic solid or porous silica microspheres in biosensing.

A new light-harvesting conjugated polyelectrolyte microgel for DNA and enzyme detections

A new fluorescent microgel containing the CP moiety (PFP-NIPAm) was prepared with the size within 100 nm. Covalent linking of the conjugated polyelectrolyte moiety into the microgel prevents leakage of the fluorophore while keeping its fluorescence property. The new fluorescent microgel can be used as an optical platform to detect DNA and enzyme. More importantly, because the electrostatic attraction dominates the interactions between cationic PFP-NIPAm microgel and negatively charged target, washing with high ionic strength aqueous solution can block their interactions and displace the target from the PFP-NIPAm microgel. Thus, PFP-NIPAm can be readily reusable for detection. Another unique feature is that the PFP-NIPAm microgel extends the detection media from homogeneous solution to solid phase, which shows great potential for biodetection in the real world using conjugated polymers. Furthermore, the detection can be carried out under UV light, and no expensive detection instrumentation is needed. In principle, such an assay system could be expanded to a high-throughput assay.

A fluorescence lifetime based binding assay to characterize kinase inhibitors

The authors present a fluorescence lifetime-based kinase binding assay that identifies and characterizes compounds that bind to the adenosine triphosphate (ATP)-binding pocket of a range of tyrosine and serine/threonine kinases. The assay is based on displacement of an Alexa Fluor 647 conjugate of staurosporine from the ATP-binding site of a kinase, which is detected by a change in the fluorescence lifetime of the probe between the free (displaced) and kinase-bound states. The authors screened 257 kinases for specific binding and displacement of the Alexa Fluor 647-staurosporine probe and found that approximately half of the kinases tested could potentially be assayed with this method. They present inhibitor binding data against 4 selected serine/threonine kinases and 4 selected tyrosine kinases, using 6 commonly used kinase inhibitors. Two of these kinases were chosen for further studies, in which inhibitor binding data were compared to inhibition of kinase activity using 2 separate activity assay formats. Rank-order potencies of compounds were similar, but not identical, between the binding and activity assays. It was postulated that these differences could be caused by the fact that the assays are measuring distinct phenomena, namely, activity versus binding, and in a purified recombinant kinase preparation, there can exist a mixture of active and nonactivated kinases. To explore this possibility, the authors compared binding affinity for the probe using 2 kinases in their respective nonactivated and activated (phosphorylated) forms and found a kinase-dependent difference between the 2 forms. This assay format therefore represents a simple method for the identification and characterization of small-molecule kinase inhibitors that may be useful in screening a wide range of kinases and may be useful in identifying small molecules that bind to kinases in their active or nonactivated states.

Assay principle for modulators of protein-protein interactions and its application to non-ATP-competitive ligands targeting protein kinase A

Targeting sites that modulate protein-protein interactions represents an ongoing challenge for drug discovery. We have devised an assay principle, named ligand-regulated competition (LiReC), in an effort to find non-ATP competitive small-molecule regulators for type Ialpha cAMP-dependent Protein kinase (PKA-Ialpha), a protein complex that is implicated in disease. Our assay based on the LiReC principle utilizes a competitive fluorescent peptide probe to assess the integrity of the PKA-Ialpha complex upon introduction of an allosteric ligand. The developed fluorescence polarization method screens for small molecules that specifically protect (antagonists) or conversely activate (agonists) this protein complex. In high-throughput format, various cyclic nucleotide-derived agonists and antagonists are successfully detected with high precision. Furthermore, assay performance (Z'-factors above 0.7) far exceeds the minimum requirement for small-molecule screening. To identify compounds that operate through novel modes of action, our method shields the ATP-binding site and purposely excludes ATP-competitive ligands. These proof-of-principle experiments highlight the potential of the LiReC technique and suggest its application to other protein complexes, thereby providing a novel approach to identify and characterize modulators (small molecules, proteins, peptides, or nucleic acids) of protein-protein systems.

Biotinylated Peptides for Rapid Identification of Substrates and Inhibitors of Kinases and Phosphatases with Fluorescence Superquenching

Aberrant regulation of kinase and phosphatase activities is implicated in various diseases, including cancer, diabetes, and inflammation. Thus, high-throughput screening (HTS) has become a focused strategy for the identification of kinase and phosphatase inhibitors. With a growing number of these enzymes becoming available for HTS, rapid identification of substrates has become pertinent. Several substrate panel screening assays exist that allow the researcher to test dye-labeled peptides for kinase or phosphatase activity. Here we introduce a method that uses readily available biotinylated peptides instead of dye-labeled substrates, which are costly and limited in availability. After enzymatic phosphorylation, biotinylated peptides are coupled to streptavidin-quencher conjugates, which then associate with a fluorescent polymer via phosphate-metal ion interaction between the reacted biotinylated peptide complex and the polymer. As a result, quencher and polymer are brought into a proximity that allows electron transfer from the polymer to the dye. The Dylight(647) (Pierce, Rockford, IL) dye was identified as an efficient electron transfer molecule that allows assays to be monitored using two emission wavelengths simultaneously, 490 nm from the polymer and 685 nm from the transferred emission of the dye. Assays are homogeneous and show comparable sensitivities to assays performed with direct-labeled dyes. When applied to a limited screen using previously characterized peptides, substrates for two kinases and one phosphatase were correctly identified. Further, ratiometric analysis of polymer quenching and transferred emission accurately detected inhibitors in a compound screen against protein kinase A, protein kinase Calpha, and protein tyrosine phosphatase 1B with limited interferences from colored compounds and with Z factors of >0.7.

Time-resolved fluorescence resonance energy transfer kinase assays using physiological protein substrates: Applications of terbium–fluorescein and terbium–green fluorescent protein fluorescence resonance energy transfer pairs

Fluorescence-based kinase assays using peptide substrates are an established format for high-throughput screening and profiling of kinases. Among fluorescence-based formats, time-resolved fluorescence resonance energy transfer (TR-FRET) using a lanthanide donor species has advantages over other fluorescent formats in being resistant to many types of optical interference such as autofluorescent compounds, scattered light from precipitated compounds, or colored compounds that absorb excitation or emission radiation ("color quenchers"). By taking advantage of the fact that acceptors such as fluorescein or green fluorescent protein (GFP) can be paired with a terbium donor in a TR-FRET assay, we have developed TR-FRET kinase assays that use physiologically relevant native protein substrates, either labeled with fluorescein or expressed as GFP fusions. Phosphorylation of the labeled protein substrate results in an increase in TR-FRET when incubated with a terbium-labeled antibody that specifically recognizes the phosphorylated product. Thus, a strategy of using terbium-based TR-FRET can be applied to develop kinase assays, and the unique properties of terbium lead to a high degree of flexibility with regard to specific assay design.

Homogeneous time-resolved fluorescence and its applications for kinase assays in drug discovery

The rapidly growing interest in kinases as potential targets for therapeutic intervention has prompted the development of many kinase assay technologies. One exciting example is homogeneous time-resolved fluorescence (HTRF). An HTRF assay utilizes the signal generated by the fluorescence resonance energy transfer between donor and acceptor molecules in close proximity. Dual-wavelength detection helps to eliminate media interference, and the final signal is proportional to the extent of product formation. Thus far, the reported applications of this technology for in vitro kinase assays have mainly focused on high-throughput screening. In this report, we extend the applications of HTRF technology to the areas of enzyme and inhibitor characterization, some aspects of which were previously believed impossible. We describe the methods developed for determining the kinetic parameters of an enzyme, such as K(m) and k(cat), and the procedures for inhibitor mechanistic studies including ATP competitiveness and slow-binding and dissociation kinetics. These assays can be readily applied to any kinase and are valuable in advancing a program through the early stages of drug discovery.

Quantitative methods for the analysis of protein phosphorylation in drug development

Most signal transduction and cell signaling pathways are mediated by protein kinases. Protein kinases have emerged as important cellular regulatory proteins in many aspects of neoplasia. Protein kinase inhibitors offer the opportunity to target diseases such as cancer with chemotherapeutic agents specific for the causative molecular defect. In order to identify possible targets and assess kinase inhibitors, quantitative methods for analyzing protein phosphorylation have been developed. This review examines some of the current formats used for quantifying kinase function for drug development.

Overcoming the Hurdle of Fluorescent Compounds in Kinase Screening: A Case Study

In the field of screening in general and especially in the kinase area, taking into consideration throughput and cost, fluorescence- and luminescence-based assays have been developed as alternatives to radioactivity-based assays. However, fluorescence-based technologies are not devoid of pitfalls. One of the main problems is interference from autofluorescent compounds and the incidence of false-positives as exemplified here with a fluorescence polarization (FP)-based assay. Using the scintillation proximity assay as the in-house standard, we assessed several alternatives to radioactive methods, namely, the amplified luminescent proximity homogeneous assay screen (ALPHAScreen, Perkin-Elmer Life Sciences, Boston, MA), enzyme fragment complementation, FP, and nanofluidics-based fluorescence intensity. Data comparing the sensitivity, robustness, relative sensitivity to autofluorescent compounds, enzyme consumption, and relative costs of each assay for one common kinase are presented. Results obtained seem to favor the nanofluidics mobility shift assay as a method of choice, followed by the direct FP approach, using generic high-molecular-weight phosphate group-binders.

Supramolecular photochemical self-assemblies for fluorescence “turn on” and “turn off” assays for chem-bio-helices

We describe the development of an optical sensing system for the high-throughput screening (HTS) of a broad range of biological molecules, whole cells, organisms and pathogens, and illustrate the technology applications by a hyaluronidase enzyme activity assay as a specific example. At the core of the technology described in this paper, is the exciton concept that is relevant to molecular aggregation. J-aggregates of cyanine dyes have a narrower, red-shifted absorption band compared to monomer. We demonstrate that self-assembly may be driven by the helicogenic nature of the cyanine dye, converting the linear polymers of hyaluronic acid or carboxymethyl cellulose into supramolecular helical assemblies. This self-assembly is accompanied by an intense, sharp, red-shifted J-aggregate fluorescence. We utilized this property to develop an assay for the enzyme hyaluronidase, based upon the concept of "scaffold destruction," whereby the disruption/destruction of the hyaluronic acid polymer by hyaluronidase is accompanied by an attenuation of light emission from the J-aggregate. The extent of light attenuation provides an index of hyaluronidase activity. Other polymers of carbohydrates, proteins, nucleic acids and chemical polymers (such as the carbon nanotube) might provide a similar scaffold for helicogenic dyes upon which molecular aggregation can occur. A key feature of these assays is that they are label-free.

Superquenching as a detector for microsphere-based flow cytometric assays

BACKGROUND

Fluorescent conjugated polymers display high fluorescence quantum yields and enhanced sensitivity to quenching (superquenching) by oppositely charged quenchers through energy or electron transfer. Fluorescent polymers and their quenchers are used in bead-based biosensor applications where the polymers are coated on particles. In this work, we investigate a detection method that utilizes superquenching on microspheres, which can be used for flow cytometric assays.

METHODS

Microspheres were coated with the fluorescent cationic polyelectrolyte poly(p-phenylene-ethynylene) (PPE), and its superquenching by 9,10-anthraquinone-2,6-disulfonic acid (AQS) was examined by fluorometric methods in presence and in absence of a barrier to superquenching in the form of an anionic lipid bilayer.

RESULTS

Flow cytometry detected superquenching of PPE on microspheres (MS-PPE) by AQS where high levels of reduction in fluorescence were observed. Adding different concentrations of AQS to MS-PPE yielded a Stern-Volmer quenching constant of 0.8x10(6) M-1. While forming an anionic lipid bilayer around the MS-PPE acted as a barrier to superquenching by AQS, disrupting the lipid bilayer allowed superquenching to take place.

CONCLUSIONS

The sensitivity of flow cytometry in detecting fluorescence of microspheres and the amplified quenching sensitivity of fluorescent conjugated polymers both offer advantages over other fluorometric methods and conventional quenching detection. This study used superquenching of fluorescent polymers as a new tool in flow cytometry, thus combining the advantages offered by both method and detector. In addition, we employed the formation and the disruption of a supported lipid bilayer in mediating superquenching to offer new biosensing applications.

Biosensors based on binding-modulated donor-acceptor distances

The promising recognition characteristics exhibited by biomolecules have caused significant interest in biomolecule-based sensor strategies. Here we review several emerging biosensor designs that use modulated electron or energy transfer to a bio-specific ligand as the signaling mechanism. The efficiencies of both electron transfer and energy transfer are strongly dependent on donor-acceptor distance. When coupled with the large conformational changes sometimes associated with biomolecular recognition, these distance-dependent processes provide a robust means for generating optical and electronic signals.

High-throughput kinase assays with protein substrates using fluorescent polymer superquenching

BACKGROUND

High-throughput screening is used by the pharmaceutical industry for identifying lead compounds that interact with targets of pharmacological interest. Because of the key role that aberrant regulation of protein phosphorylation plays in diseases such as cancer, diabetes and hypertension, kinases have become one of the main drug targets. With the exception of antibody-based assays, methods to screen for specific kinase activity are generally restricted to the use of small synthetic peptides as substrates. However, the use of natural protein substrates has the advantage that potential inhibitors can be detected that affect enzyme activity by binding to a site other than the catalytic site. We have previously reported a non-radioactive and non-antibody-based fluorescence quench assay for detection of phosphorylation or dephosphorylation using synthetic peptide substrates. The aim of this work is to develop an assay for detection of phosphorylation of chemically unmodified proteins based on this polymer superquenching platform.

RESULTS

Using a modified QTL Lightspeed assay, phosphorylation of native protein was quantified by the interaction of the phosphorylated proteins with metal-ion coordinating groups co-located with fluorescent polymer deposited onto microspheres. The binding of phospho-protein inhibits a dye-labeled "tracer" peptide from associating to the phosphate-binding sites present on the fluorescent microspheres. The resulting inhibition of quench generates a "turn on" assay, in which the signal correlates with the phosphorylation of the substrate. The assay was tested on three different proteins: Myelin Basic Protein (MBP), Histone H1 and Phosphorylated heat- and acid-stable protein (PHAS-1). Phosphorylation of the proteins was detected by Protein Kinase Calpha (PKCalpha) and by the Interleukin -1 Receptor-associated Kinase 4 (IRAK4). Enzyme inhibition yielded IC50 values that were comparable to those obtained using peptide substrates. Statistical parameters that are used in the high-throughput community to determine assay robustness (Z'-value) demonstrate the suitability of this format for high-throughput screening applications for detection of inhibitors of enzyme activity.

CONCLUSION

The QTL Lightspeed protein detection system provides a simple mix and measure "turn on" assay for the detection of kinase activity using natural protein substrates. The platform is robust and allows for identification of inhibitors of kinase activity.

Magnetically assisted DNA assays: high selectivity using conjugated polymers for amplified fluorescent transduction

We report a strategy for conjugated polymer (CP)-based optical DNA detection with improved selectivity. The high sensitivity of CP-based biosensors arises from light harvesting by the CP and the related amplified fluorescent signal transduction. We demonstrate that the use of magnetic microparticles significantly improves the selectivity of this class of DNA sensors. Compared with previously reported DNA sensors with CP amplification, this novel sensing strategy displays excellent discrimination against non-cognate DNA in the presence of a protein mixture or even human serum. We also demonstrate that the magnetically assisted DNA sensor can conveniently identify even a single-nucleotide mismatch in the target sequence.

Metal ion-mediated polymer superquenching for highly sensitive detection of kinase and phosphatase activities

An assay technology for high-throughput screening of kinase and phosphatase activities is introduced. The format is based upon superquenching of fluorescent-conjugated polymers by dye-labeled kinase/phosphatase peptide substrates. The sensor platform is composed of highly fluorescent-conjugated polyelectrolytes colocated with the phosphate coordinating metal ion gallium on microspheres. Phosphorylated peptide substrates containing a quencher bind specifically to the metal ions by means of phosphate groups, resulting in quench of polymer fluorescence. The modulation of fluorescence signal is proportional to kinase or phosphatase activity and is monitored as a turn-off or turn-on signal, respectively. The assay is homogeneous and simple and can be run either as an endpoint measurement or in a kinetic mode. The assay meets the sensitivity required for high-throughput screening of kinase or phosphatase inhibitors and is a valuable tool for drug discovery. A modified version of the assay allows for the detection of protein phosphorylation.