Development of a Transcreener Kinase Assay for Protein Kinase A and Demonstration of Concordance of Data with a Filter-Binding Assay Format

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1 Development of a Transcreener Kinase Assay for Protein Kinase A and Demonstration of Concordance of Data with a Filter-Binding Assay Format KAREN L. HUSS, PAULINE E. BLONIGEN, and ROBERT M. CAMPBELL A Transcreener kinase fluorescence polarization (FP) assay has been developed for the serine/threonine kinase protein kinase A (PKA). The PKA Transcreener kinase assay is an homogenous, competitive antibody-based FP assay that uses Far Red Alexa Fluor 633-labeled adenosine 5 disphosphate (ADP) tracer and mouse monoclonal anti-adp antibody. The Transcreener PKA assay was validated with both known PKA inhibitors and library compounds. The Transcreener PKA assay is resistant to low-wavelength (or common) fluorescent interference from small-molecule library compounds and generates results comparable with current radioactive filter-binding assay. (Journal of Biomolecular Screening 2007: ) Key words: Transcreener, protein kinase A, fluorescence polarization, Alexa Fluor 633 INTRODUCTION HOSPHORYLATION BY PROTEIN KINASES is one of the most P widespread and well-studied signaling mechanisms in eukaryotic cells. Aberrant phosphorylation-driven signaling is the basis of many human diseases, making protein kinases attractive therapeutic drug discovery targets. Protein kinases mediate signal transduction by catalyzing the transfer of the γ-phosphoryl group from adenosine 5 triphosphate (ATP) to a kinase-specific substrate serine, threonine, and tyrosine hydroxyl group and releasing adenosine 5 disphosphate (ADP). Historically, kinase drug discovery efforts have focused on assessing the in vitro activity of protein kinases in the presence of inhibitors by monitoring the phosphorylation state of the kinase peptide/protein substrate via radioactive phosphate incorporation (e.g., filter-binding assay, scintillation proximity assay). A number of fluorescence and chemiluminescence-based homogenous assay kits have been developed in the past 10 years that use novel ways of assessing phosphate incorporation into peptide substrates (PolarScreen fluorescence polarization [FP], homogenous time-resolved fluorescence [HTRF ], immobilized metal affinity polarization [IMAP ], ALPHA Screen, and Z LYTE are but a few). 1 Although most of these formats enable high-throughput screening Lilly Research Laboratories, a division of Eli Lilly and Company, Indianapolis, Indiana. Received Dec 1, 2006, and in revised form Jan 5, Accepted for publication Jan 15, Journal of Biomolecular Screening 12(4); 2007 DOI: / (HTS), they require significant lead time to develop and are limited in their use because each kit works for only a subset of kinases (as these assays are peptide substrate based formats). 2 The Transcreener Kinase Assay Kit, developed by BellBrook Labs (Madison, WI), 3 is a unique fluorescence polarization (FP) assay that uses an ADP-antibody/tracer pair for detection. Because the Transcreener kinase assay measures the invariant kinase reaction product (the donor product, ADP) instead of the variant reaction product (the phospho-peptide acceptor), this format can potentially be used for any protein kinase independent of protein/peptide substrate. Finally, by using a highly specific antibody for ADP, the Transcreener kinase assay detects ADP accumulation without the use of an enzyme-coupled ADP detection system as in the ADP Quest kit. 4 We chose protein kinase A (PKA) as the kinase enzyme target for our evaluation because of the large amount of historical assay data on this target. For the past 6 years, we have used a generic PKA enzyme assay as an in-house tool for evaluating several kinase assay formats including filter binding, Polarscreen FP (red and green kits; PanVera/Invitrogen, Carlsbad, CA), ProFluor (Promega, Madison, WI), Z LYTE (Invitrogen), and ElectroCapture (Nanogen, San Diego, CA) assays. 5,6 Founded on this experience, we have determined that when assay conditions are kept the same for comparisons and the target biochemistry is well understood, most, if not all, assay formats (aside from instances of compound-specific assay interference) will provide equivalent data. 7 Based on the knowledge gained from our previous technology evaluations and our in-house expertise in FP, we were optimistic that this technology would have utility in our kinase platform structure-activity relationship (SAR) and HTS efforts. We report here the results of our evaluation of the PKA Society for Biomolecular Sciences

2 Transcreener kinase assay for use in SAR lead optimization biology assay. MATERIALS AND METHODS Transcreener kinase assay technology Transcreener Kinase Assay Fluorescence polarization is a detection method that is used to study molecular interactions by monitoring changes in the apparent size of fluorescently labeled or inherently fluorescent molecules. 8 When a small fluorescent molecule (tracer) is excited with plane-polarized light, the emitted light is largely depolarized because the molecule rotates rapidly in solution during the fluorescence event (the time between excitation and emission). However, if the tracer is bound to a much larger receptor, thereby increasing its effective molecular volume, its rotation is slowed sufficiently to emit light in the same plane in which it was excited and the emitted light is largely polarized. To measure FP, the emission intensity is measured in both the vertical and horizontal planes, which are parallel and perpendicular to the vertically polarized excitation light. The emission light defines polarization (P) as follows: P = [( )/( + )]. The Transcreener kinase assay technology uses a far-red Alexa Fluor 633-labeled ADP tracer and a mouse monoclonal ADP-selective antibody to measure the amount of ADP generated in the kinase reaction using FP. In the Transcreener kinase assay, ADP displaces the Alexa Fluor 633-labeled ADP tracer from the antibody, allowing the tracer to rotate freely, which is measured as a decrease in polarization (see details in Fig. 1). Transcreener kinase assay enzyme titration protocol A PKA enzyme titration experiment was run to determine the appropriate concentration of enzyme needed in the Transcreener kinase assay to achieve adequate signal versus background but remain within the initial velocity kinetics of the reaction (usually achieved when between 0% to 10%-20% of the initial substrate has been converted to product). The protein kinase C α- pseudosubstrate peptide (RFARKGSLRQKNV) used as the substrate in the filter-binding assay was also used as the phosphate acceptor for PKA Transcreener. The kinase reactions for the PKA enzyme titration experiment consisted of 23 mm HEPES (Invitrogen) ph 7.4, 0.034% Triton X-100 (Pierce, Rockford, IL), 2 mm MgCl 2, mm DTT, 4% DMSO, 10 µm (20*K M ) RFARKGSLRQKNV (AnaSpec, San Jose, CA), 10 µm (1*K M ) ATP, and 0 to 1.6 U/mL human PKA-c α enzyme (Upstate Biotech, Billerica, MA). Kinase reactions were performed in black, half-area, flat-bottom, 96-well polystyrene plates (COSTAR). Reagents were added to the plate as follows: 5 µl 20% DMSO, 10 µl PKA and RFARKGSLRQKNV peptide, and FIG. 1. Transcreener kinase fluorescence polarization (FP) assay. The Transcreener adenosine 5 disphosphate (ADP) detection mix is added at the end of the kinase reaction. ADP formed during the reaction displaces the bound ADP AlexaFluor 633 tracer from the mouse monoclonal ADP antibody. The displaced tracer rotates freely, resulting in a decrease in FP (relative to antibody-bound tracer). 10 µl 25 µm ATP. Kinase reactions were incubated at room temperature for 60 min, and then the reactions were quenched by the addition of 25 µl ADP detection mix containing Stop and Detect Buffer: 50 mm HEPES, 4 M NaCl, 0.2% Brij-35, 200 mm EDTA, ph 7.5, with 4 nm ADP Far Red tracer, and 20 µg/ml ADP antibody. After quench, the plates were incubated in darkness at room temperature for 2 to 16 h, and then FP was measured at λ ex = 610, λ em = 670, on an Tecan Ultra 384 (Tecan, Männedorf, Switzerland) plate reader. The concentration of ADP product per well was calculated from millipolarization (mp) using a prepared ADP/ATP competitor dilution series as a standard curve. The PKA concentration in U/mL was then plotted versus ADP µm product formed for each enzyme concentration tested, and linear regression analysis was performed (GraphPad Prism ; GraphPad Software, San Diego, CA). The data are presented in Figure 2. Based on these results, we decided to use a PKA enzyme concentration of 0.06 U/mL (final reaction), which produced 1 µm ADP product (10% ADP/ATP conversion) in the 60-min reaction time. Transcreener kinase assay protocol The kinase reactions for the PKA Transcreener kinase determinations consisted of 23 mm HEPES (Invitrogen) ph 7.4, 0.034% Triton X-100 (Pierce), 2 mm MgCl 2, mm DTT, 4% DMSO, 10 µm (20*K M ) RFARKGSLRQKNV peptide (AnaSpec), 10 µm (1*K M ) ATP, and 0.06 U/mL human PKA-c α enzyme (Upstate Biotech). Compound inhibitors were solubilized at 10 mm in 100% DMSO then diluted to 100 µm with 20% DMSO. Compound serial dilutions (1:3) were prepared on a Tecan Genesis over a range from 100 µm to µm. Kinase reactions were performed in black, half-area, flat-bottom, 96-well polystyrene plates (COSTAR). Reagents were added to the plate using the same volumes specified in the Journal of Biomolecular Screening 12(4);

3 Huss et al. FIG. 2. Transcreener kinase assay: adenosine 5 disphosphate (ADP)/ adenosine 5 triphosphate (ATP) standard curve and protein kinase A (PKA) enzyme titration. (A) Data for Transcreener kinase ADP/ATP standard curve. (B) Enzyme titration data for the Transcreener kinase assay reaction indicates that the reaction was linear to 0.1 U/mL PKA and 1.5 mm ADP; these data agree well with previous PKA enzyme titration data generated with a filter-binding assay (K. L. Huss, unpublished observations). PKA enzyme titration protocol. Eight determinations and 16 controls (8 uninhibited MAX and mm EDTA inhibited MIN control wells) were performed per 96-well plate. Kinase reactions were incubated at room temperature for 60 min, and then the reactions were quenched by the addition of ADP detection mix. After quench, the plates were incubated in darkness at room temperature for 3 to 16 h, and then FP was measured at λ ex = 610, λ em = 670, on an Tecan Ultra 384 (Tecan) plate reader. The concentration of ADP product per well was calculated from mp using a prepared ADP/ATP competitor dilution series as a standard curve. Absolute compound values were determined by first converting the calculated µm ADP product per well to percentage inhibition with respect to on-plate MIN and MAX controls and then fitting the percentage inhibition values and 10-point dose-response data to a 4-parameter logistic equation using ActivityBase (version 4.2; IDBS, Guildford, UK). Filter-binding assay protocol The kinase reactions for the filter-binding determinations were similar to those specified in the Transcreener protocol with the exception of the following: 0.04 U/mL hpka α, 2 um (4*Km) RFARKGSLRQKNV peptide, and 0.5 µci [γ 33 P] ATP (ICN) were added per reaction. Reagents were added to 96-well polystyrene plates (COSTAR) as follows: 20 µl 20% DMSO, 40 µl PKA, 40 µl RFARKGSLRQKNV, and 25 µm ATP. The reactions were quenched by the addition of 125 µl of 10% H 3 PO 4, and the quenched reactions (100 µl) were then transferred using a Multimek-96 (Beckman, Fullerton, CA) to Multiscreen anionic phosphocellulose 96-well filter plated (Millipore, Billerca, MA) and filtered and washed with 0.5% H 3 PO 4 on a Zoom filter plate processor (Titertek, Huntsville, AL). After addition of Microscint 20 scintillation cocktail (Packard, Waltham, MA), the plates were read on a Microbeta scintillation Journal of Biomolecular Screening 12(4); 2007

4 Transcreener Kinase Assay Table 1. Nonselective Protein Kinase A Inhibitor Comparison by Format µm p µm Compound Transcreener FP Filter Binding Transcreener FP Filter Binding Staurosporine H H H H HA HA Lilly Library The table shows the and p values determined in Transcreener kinase fluorescence polarization (FP) and filter-binding assay formats for known nonselective (noncolored) protein kinase A inhibitors. counter (PerkinElmer, Waltham, MA). Absolute compound values were determined by first converting counts per minute to percentage inhibition with respect to on-plate MIN and MAX controls and then fitting the percentage inhibition values and 10- point dose-response data to a 4-parameter logistic equation using ActivityBase (version 4.2; IDBS). Assay technology comparison protocol Three separate experiments were conducted to evaluate and compare PKA assays developed using the Transcreener FP and filter-binding formats. The initial proof-of-concept experiment used a small set of known PKA inhibitors. This set included staurosporine, H-7, H-8, H-9, H-89, HA-100, and HA-1004 (Sigma, St. Louis, MO), and a Lilly library compound. The 2nd experiment used a set of 69 nonfluorescent Lilly library compounds. The 3rd experiment used a set of 30 colored and/or fluorescent Lilly library compounds. The latter set of compounds had been identified during routine SAR screening as fluorescent (and were confirmed to interfere) in the phosphopeptide-based PKA PolarScreen FP green assay format using a fluorescein-labeled (λ ex = 485, λ em = 530) peptide tracer (data not shown); thus, these latter compounds represent a worst-case compound set to test to determine the susceptibility of the Transcreener FP assay to compound fluorescent interference. For all 3 data sets, the values were converted to p, and then the p values were analyzed in JMP (SAS Institute, Cary, NC) using the Fit Y by X Regression Platform. RESULTS AND DISCUSSION Results for the Transcreener enzyme titration The enzyme titration and ADP/ATP standard curve data for the Transcreener kinase assay format are summarized in Figure 2. The data indicate that the Transcreener PKA assay reaction was linear to 0.1 U/uL PKA and 1.5 µm ADP, which FIG. 3. Correlation of nonselective protein kinase A (PKA) inhibitor comparison by format. The JMP Y X regression analysis demonstrates that good correlation of p results for the Transcreener kinase fluorescence polarization assay (TS FP) and filter-binding (FB) assays were obtained for the set of PKA inhibitors. agrees well with historical filter-binding results for PKA (K. L. Huss, unpublished observations). Results for known PKA inhibitors The and p values obtained in the filter-binding and Transcreener kinase assay formats for the known PKA inhibitor set are summarized in Table 1. The values obtained by the Transcreener FP assay were comparable, within 3-fold of those obtained in the filter binding, and the p values showed a significant correlation (R 2 = 0.970) in the JMP regression analysis (Fig. 3). These results confirm that for at least these nonselective PKA inhibitors, the Transcreener FP and filterbinding assay provide equivalent concentration-response data. Journal of Biomolecular Screening 12(4);

5 Huss et al. FIG. 4. Correlation of nonfluorescent library compounds by format. The JMP Y X regression analysis demonstrates that good correlation of p results for the Transcreener kinase fluorescence polarization assay (TS FP) and filter-binding (FB) assays were obtained for this set of 68 compounds across a 4-log range of activity. FIG. 5. Correlation of fluorescent library compounds by format. The JMP Y X regression analysis demonstrates that good correlation of p results for the Transcreener kinase fluorescent polarization assay (TS FP) and filter-binding (FB) assays were obtained for this set of 20 compounds. Results for nonfluorescent library inhibitor set The values obtained by the Transcreener FP assay for the nonfluorescent compound set were comparable, within 3-fold of those obtained in the filter binding. The scatter plots and linear regression analysis of the p values obtained in the filter-binding and Transcreener kinase assay formats for the nonfluorescent library inhibitor set are summarized in Figure 4. JMP regression analysis indicated a significant correlation (R 2 = 0.963) between the 2 assays. These results confirm that for these nonfluorescent inhibitors, the Transcreener FP and filter-binding assay provide equivalent concentration-response data. Results for fluorescent compound set Only 20 of the 30 compounds tested in this set were found to have measurable values against PKA; 10 compounds were found to be inactive in both formats. As previously observed with the nonfluorescent compound set, the p values obtained by the Transcreener FP assay for the fluorescent compound set were comparable, within 3-fold of those obtained in the filterbinding assay. The scatter plots and linear regression analysis of the p values obtained in the filter-binding and Transcreener kinase assay formats for the fluorescent library inhibitor set are summarized in Figure 5. Regression analysis indicates a significant correlation (R 2 = 0.978) between the 2 assay formats. Furthermore, these compounds did not have the >15% increase in well-level total fluorescence (calculated by parallel + 2*perpendicular) relative to control wells and the concomitant shift in potency (lower) that was observed in the phosphopeptidebased PKA PolarScreen FP green assay format (see Miick et al 6 for details on the detection of compound fluorescence interference). Taken together, these results confirm that the Transcreener FP assay provides equivalent concentrationresponse data to filter binding while remaining highly resistant to low-wavelength interference by fluorescent compounds. CONCLUSIONS We have developed a Transcreener kinase FP PKA assay using kit reagents (ADP-tracer, anti-adp antibody, and quench buffer) supplied from BellBrook Labs. The PKA Transcreener kinase FP assay is sensitive, reproducible, and robust, providing a good signal window and acceptable Z factor (Table 2). 9,10 The data are comparable to that provided by the historical filter-binding assay format, as confirmed by the significant correlation (R 2 = 0.97, 0.963, and 0.978) of values between the Transcreener kinase FP and filter-binding assay formats for the 3 compound sets tested. The data also indicate that the Transcreener kinase FP assay is highly resistant to low-wavelength (or common) fluorescence interference, as demonstrated by the lack of fluorescent artifacts observed in our evaluation. Clearly, the use of the longer wavelength Alexa Fluor-633 probe (647 nm emission peak) enables this resistance to low-wavelength fluorescent interference from small-molecule libraries, as the use of red-shifted fluorescent probes to avoid compound fluorescent interference in FP assays is well documented in the literature We speculate (based on our experience and on BellBrook Labs data) that large-molecularweight compounds, especially natural product molecules that possess many conjugated bonds, may cause fluorescent interference at the wavelengths used in the assay. 17 It is possible that the Journal of Biomolecular Screening 12(4); 2007

6 Transcreener Kinase Assay Table 2. Assay Statistics for the Filter-Binding and Transcreener Fluorescence Polarization Assays Run in the Evaluation Assay Format S/B SW Z Factor Filter binding 44 ± ± ± 0.09 Transcreener FP 1.64 ± ± ± 0.04 The table summarizes the assay statistics achieved in the format comparison. The average signal-to-background (S/B) was measured in counts per minute for the filterbinding format and in millipolarization units for the fluorescence polarization (FP) assay. Signal window (SW) and Z factor were comparable for the 2 assays during the evaluation. Signal window here is defined as the overall window between the average maximum and average minimum signals as defined in standard deviation units. 9,10 reason we did not observe any fluorescent interference from compounds is because of limited diversity of our compound libraries (and the focus on lower molecular weight compounds). If, in the future, natural product libraries are tested in Transcreener, we believe that any fluorescent compounds should be easily detected based on the increase in compound well total fluorescence (versus control wells). This increase in fluorescence could be flagged in an automated manner using well-level quality control criteria similar to that described in Miick et al, 6 and compounds found to be fluorescent could be retested in the secondary filter-binding assay. Finally, because the Transcreener kinase FP assay uses standard footprint 96- and 384-well plates, most highthroughput screening liquid-handling and fluorescence plate readers can be used for this assay format. Since the successful completion of this evaluation, we have developed a panel of Transcreener kinase FP assays, including 14 protein kinase targets (serine, threonine, and tyrosine) and 1 lipid kinase target. These protein kinase assays use peptides (10) and full-length protein substrates (4, including 1 autophosphorylation assay), ATP concentrations that range from 2 to 100 µm (reaction), and anti-adp antibody concentrations from 2 to 25 µg/ml (final assay). These kinase targets represent 5 of the 7 human kinome families, thus confirming in our hands that the technology can be used with multiple kinase targets and protein, peptide, and lipid substrates (K. L. Huss et al., unpublished observations). 18 These Transcreener kinase FP assays have replaced our traditional filter-binding assays for these targets and are routinely used to provide needed SAR data to support kinase platform lead generation and lead optimization drug discovery projects. In addition, we have successfully completed medium-throughput screen Transcreener kinase format screens (15-80,000 compounds, 384-well single point-version assays) for 4 of the above configured SAR assays with no observed interference from library (small-molecule) compounds. 19 ACKNOWLEDGMENTS The authors thank Bruce Wiltermood and Donald Walden for their engineering support, the Lilly Compound Management Team for supply of compound plates, and Larry Stramm, Sitta Sittampalam, and Chris Moxham for their encouragement and support of this work. REFERENCES 1. von Ahsen O, Bomer U: High-throughput screening for kinase inhibitors. Chembiochem 2005;6: Campbell RM, Huss KL, Treadway PJ, Anderson BD: A plethora of kinase assay technologies: considerations for appropriate selection. Paper presented to the Joint SDAT/AOC Special Interest Group at the Society for Biomolecular Sciences 12th annual conference and exhibition, Seattle, WA, September Lowery RG, Kleman-Leyer KM: Transcreener: screening enzymes involved in covalent regulation. Expert Opin Ther Targets 2006;10: Charter NW, Kauffman L, Singh R, Eglen RM: A generic, homogenous method for measuring kinase and inhibitor activity via adenosine 5 - diphosphate accumulation. J Biomol Screen 2006;4: Huss KL, Campbell RM: Evaluation of the Z -LYTE technology for S/T kinase assays: comparions with two other formats for lead optimization of protein kinase A inhibitors. Poster presented at the Society for Biomolecular Screening 11th annual conference and exhibition, Orlando, FL, September Miick SM, Jalali S, Dwyer BP, Havens J, Thomas D, Jimenez MA, et al: Development of a microplate-based, electrophoretic fluorescent protein kinase A assay: comparison with filter-binding and fluorescence polarization assay formats. J Biomol Screen 2005;10: Anderson BD, Campbell RM, Cox K, Eessalu T, Huss K, Kaplan K, et al: Lessons learned from the development and validation of fluorescence polarization kinase assays: setting the bar equal for technology comparisons. Paper presented at the Society for Biomolecular Screening 8th annual conference and exhibition, The Hague, the Netherlands, September Owicki JC: Fluorescence polarization and anisotropy in high-throughput screening: perspectives and primer. J Biomol Screen 2000;5: Sittampalam GS, Iversen PW, Boadt JA, Kahl SD, Bright S, Zock JM, et al: Design of signal windows in high-throughput screening assays for drug discovery. J Biomol Screen 1997;2: Zhang JH, Chung TD, Oldenburg KR: A simple statistical parameter for use in evaluation and validation of high-throughput screening assays. J Biomol Screen 1999;4: Turek-Etienne TC, Small EC, Soh SC, Tianpei AX, Gaitonde PV, Barabee EB, et al: Evaluation of fluorescent compound interference in 4 fluorescence polarization assays: 2 kinases, 1 protease, and 1 phosphatase. J Biomol Screen 2003;2: Banks P, Gosselin M, Prystay L: Impact of red-shifted dye label for highthroughput fluorescence polarization assays of G protein coupled receptors. J Biomol Screen 2000;5: Olive DM: Quantitative methods for analysis of protein phosphorylation in drug development. Expert Rev Proteomics 2004;3: Vedrik KL, Hildegard CE, Hoffman RL, Gibson JR, Kupcho KR, Somberg RL, et al: Overcoming compound interference in fluorescence polarization-based kinase assays using far-red tracers. Assay Drug Dev Technol 2004;2: Comley J: Assay interference a limiting factor in HTS? Drug Discovery World 2003;Summer: Klink TA, Kleman-Leyer KM, Fronczak JA, Westermeyer TA, Staeben M, Lowery RG: ADP detection assay for diverse kinases and ATPases. 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7 Huss et al. Poster presented at the Society for Biomolecular Sciences 12th annual conference and exhibition, Seattle, WA, September Visible and UV spectroscopy [Online]. Retrieved from Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S: The protein kinase complement of the human genome. Science 2002;298: Huss KL, Zhai Y, Britt KS, Yuan XJ, Lorite MJ, Bloem LJ, et al: Development and validation of a panel of Transcreener kinase assays for use in lead generation/optimization biology. Poster presented at the Society for Biomolecular Sciences 12th annual conference and exhibition, Seattle, WA, September Address reprint requests to: Karen L. Huss Lilly Research Laboratories A Division of Eli Lilly and Company Lilly Corporate Center, DC0536 Indianapolis, IN huss_karen_l@lilly.com Journal of Biomolecular Screening 12(4); 2007