Bookmark and Share
BioAssay: AID 624394

Luminescence-based cell-based high throughput dose response assay for agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3)

Name: Luminescence-based cell-based high throughput dose response assay for agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3). ..more
_
   
 Tested Compounds
 Tested Compounds
All(225)
 
 
Active(203)
 
 
Inactive(22)
 
 
 Tested Substances
 Tested Substances
All(225)
 
 
Active(203)
 
 
Inactive(22)
 
 
AID: 624394
Data Source: The Scripps Research Institute Molecular Screening Center (NR2E3-CELL_AG_LUMI_1536_3XIC50 DRUN)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
BioAssay Version:
Deposit Date: 2012-07-19
Modify Date: 2012-09-05

Data Table ( Complete ):           Active    All
Target
BioActive Compounds: 203
Depositor Specified Assays
Show more
AIDNameTypeComment
2300TR-FRET-based primary biochemical high throughput screening assay to identify agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3).screeningPrimary screen (NR2E3 agonists in singlicate)
2325Summary of probe development efforts to identify agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3).summarySummary (NR2E3 agonists)
463256TR-FRET-based biochemical high throughput dose response assay to identify NR2E3 inverse agonistsconfirmatoryDose response (NR2E3 inverse agonists in triplicate)
463257Counterscreen for NR2E3 inverse agonists: TR-FRET-based biochemical high throughput dose response assay to identify inverse agonists of the interaction between peroxisome proliferator-activated receptor gamma (PPARg) and nuclear receptor co-repressor 2 (NCOR2)confirmatoryDose response counterscreen (PPARg and NCOR2 interaction inverse agonists in triplicate)
504787Counterscreen for agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3): TR-FRET-based biochemical high throughput assay to identify agonists of the interaction between peroxisome proliferator-activated receptor gamma (PPARg) and nuclear receptor co-repressor 2 (NCOR2)screeningCounterscreen (PPARg and NCOR2 interaction agonists in triplicate)
602229Luminescence-based cell-based high throughput primary screening assay to identify agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3)screeningPrimary screen (NR2E3 agonists in singlicate: Cell-based)
624378Luminescence-based cell-based high throughput confirmation assay for agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3)screeningPrimary screen (NR2E3 agonists in singlicate: Cell-based)
624379Counterscreen for agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3): Luminescence-based cell-based high throughput screening assay to identify agonists of the Herpes Virus Virion Protein 16 (VP16)screeningCounterscreen (VP16 modulators in triplicate: Cell-based)
651846Late Stage Counterscreen for agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3): Luminescence-based cell-based high throughput dose response screening assay to identify agonists of the Herpes Virus Virion Protein 16 (VP16)confirmatory
651849Late stage Luminescence-based cell-based high throughput dose response assay for agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3)confirmatory
Description:
Source (MLPCN Center Name): The Scripps Research Institute Molecular Screening Center
Affiliation: The Scripps Research Institute, TSRI
Assay Provider: Konstantin Petrukhin, Columbia University
Network: Molecular Library Probe Production Centers Network (MLPCN)
Grant Proposal Number: 1 R21 NS061718-01 Fast Track
Grant Proposal PI: Konstantin Petrukhin, Columbia University
External Assay ID: NR2E3-CELL_AG_LUMI_1536_3XIC50 DRUN

Name: Luminescence-based cell-based high throughput dose response assay for agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3).

Description:

Nuclear receptors are small molecule- and hormone-regulated transcription factors with discrete DNA-binding and ligand-binding domains, and are essential during development and for maintenance of proper cell function in adults. Small pharmacological compounds that bind to the cleft of the ligand-binding domain could alter receptor conformation and subsequently modify transcription of target genes. Such ligands (agonists and antagonists) have been designed for 23 nuclear receptors among the 48 identified in the human genome (1-3). NR2E3 is an orphan nuclear receptor expressed exclusively in rod and cone photoreceptor cells of the retina (4-7). In its unliganded state, NR2E3 acts as a transcriptional repressor (4, 8, 9) due to interaction with co-repressors such as retinal RetCOR (10), NCOR (11) or SMRT (11). Defects in this gene are a cause of several retinopathies (12-15). Studies showing that mice with a spontaneous deletion in the Nr2e3 gene develop late-onset, progressive retinal degeneration (7), suggest that this nuclear receptor is essential for photoreceptor development and survival. The identification of selective NR2E3 agonists would provide useful tools for the understanding of the biological role of NR2E3 in retinal diseases.

References:

1. Evans, R.M., The nuclear receptor superfamily: a rosetta stone for physiology. Mol Endocrinol, 2005. 19(6): p. 1429-38.
2. Kliewer, S.A., Lehmann, J.M., and Willson, T.M., Orphan nuclear receptors: shifting endocrinology into reverse. Science, 1999. 284(5415): p. 757-60.
3. Li, Y., Lambert, M.H., and Xu, H.E., Activation of nuclear receptors: a perspective from structural genomics. Structure, 2003. 11(7): p. 741-6.
4. Chen, J., Rattner, A., and Nathans, J., The rod photoreceptor-specific nuclear receptor Nr2e3 represses transcription of multiple cone-specific genes. J Neurosci, 2005. 25(1): p. 118-29.
5. Cheng, H., Khanna, H., Oh, E.C., Hicks, D., Mitton, K.P., and Swaroop, A., Photoreceptor-specific nuclear receptor NR2E3 functions as a transcriptional activator in rod photoreceptors. Hum Mol Genet, 2004. 13(15): p. 1563-75.
6. Haider, N.B., Naggert, J.K., and Nishina, P.M., Excess cone cell proliferation due to lack of a functional NR2E3 causes retinal dysplasia and degeneration in rd7/rd7 mice. Hum Mol Genet, 2001. 10(16): p. 1619-26.
7. Akhmedov, N.B., Piriev, N.I., Chang, B., Rapoport, A.L., Hawes, N.L., Nishina, P.M., Nusinowitz, S., Heckenlively, J.R., Roderick, T.H., Kozak, C.A., Danciger, M., Davisson, M.T., and Farber, D.B., A deletion in a photoreceptor-specific nuclear receptor mRNA causes retinal degeneration in the rd7 mouse. Proc Natl Acad Sci U S A, 2000. 97(10): p. 5551-6.
8. Gerber, S., Rozet, J.M., Takezawa, S.I., dos Santos, L.C., Lopes, L., Gribouval, O., Penet, C., Perrault, I., Ducroq, D., Souied, E., Jeanpierre, M., Romana, S., Frezal, J., Ferraz, F., Yu-Umesono, R., Munnich, A., and Kaplan, J., The photoreceptor cell-specific nuclear receptor gene (PNR) accounts for retinitis pigmentosa in the Crypto-Jews from Portugal (Marranos), survivors from the Spanish Inquisition. Hum Genet, 2000. 107(3): p. 276-84.
9. Kobayashi, M., Hara, K., Yu, R.T., and Yasuda, K., Expression and functional analysis of Nr2e3, a photoreceptor-specific nuclear receptor, suggest common mechanisms in retinal development between avians and mammals. Dev Genes Evol, 2008. 218(8): p. 439-44.
10. Takezawa, S., Yokoyama, A., Okada, M., Fujiki, R., Iriyama, A., Yanagi, Y., Ito, H., Takada, I., Kishimoto, M., Miyajima, A., Takeyama, K., Umesono, K., Kitagawa, H., and Kato, S., A cell cycle-dependent co-repressor mediates photoreceptor cell-specific nuclear receptor function. EMBO J, 2007. 26(3): p. 764-74.
11. Kapitskaya, M., Cunningham, M.E., Lacson, R., Kornienko, O., Bednar, B., and Petrukhin, K., Development of the high throughput screening assay for identification of agonists of an orphan nuclear receptor. Assay Drug Dev Technol, 2006. 4(3): p. 253-62.
12. Bernal, S., Solans, T., Gamundi, M.J., Hernan, I., de Jorge, L., Carballo, M., Navarro, R., Tizzano, E., Ayuso, C., and Baiget, M., Analysis of the involvement of the NR2E3 gene in autosomal recessive retinal dystrophies. Clin Genet, 2008. 73(4): p. 360-6.
13. Coppieters, F., Leroy, B.P., Beysen, D., Hellemans, J., De Bosscher, K., Haegeman, G., Robberecht, K., Wuyts, W., Coucke, P.J., and De Baere, E., Recurrent mutation in the first zinc finger of the orphan nuclear receptor NR2E3 causes autosomal dominant retinitis pigmentosa. Am J Hum Genet, 2007. 81(1): p. 147-57.
14. Gire, A.I., Sullivan, L.S., Bowne, S.J., Birch, D.G., Hughbanks-Wheaton, D., Heckenlively, J.R., and Daiger, S.P., The Gly56Arg mutation in NR2E3 accounts for 1-2% of autosomal dominant retinitis pigmentosa. Mol Vis, 2007. 13: p. 1970-5.
15. Sharon, D., Sandberg, M.A., Caruso, R.C., Berson, E.L., and Dryja, T.P., Shared mutations in NR2E3 in enhanced S-cone syndrome, Goldmann-Favre syndrome, and many cases of clumped pigmentary retinal degeneration. Arch Ophthalmol, 2003. 121(9): p. 1316-23.

Keywords:

dose, dose response, titration, triplicate, CHO, cell-based, lumi, luminescence, alternate, nuclear receptor subfamily 2, group E, member 3, NR2E3; RetCOR, corepressor, photoreceptor-specific nuclear receptor; PNR, blindness, age-related macular degeneration, AMD, orphan nuclear receptor, agonist, activator, HTS, 1536, Scripps, Scripps Florida, Research Institute Molecular Screening Center, SRIMSC, Molecular Libraries Probe Production Centers Network, MLPCN.
Protocol
Assay Overview:

The purpose of this assay is to determine dose response curves for available compounds identified as active in a set of previous experiments entitled, "Luminescence-based cell-based high throughput primary screening assay to identify agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3)" (AID 602229).

In this assay, the nuclear receptor interaction domain of NCOR is fused to the Gal4 DNA binding domain (pGALDBD_NCOR plasmid), while the NR2E3 fragment containing the hinge and ligand-binding domains is fused to VP16 activation domain (pVP16_NR2E3LBD plasmid). CHO-S cells are co-transfected with pGALDBD_NCOR and pVP16_NR2E3LBD plasmids along with the pGL4.31 reporter plasmid containing five GAL4 response elements and expressing luciferase. NR2E3-NCOR interaction inside CHO-S cells results in increased luciferase expression due to recruitment of the VP16 activator to the promoter. Agonistic ligands would induce NCOR release thus reducing luciferase expression. Compounds were tested in triplicate using a 10-point, 1:3 dilution series starting at a nominal concentration of 40 uM.

Protocol Summary:

The CHO-S cell line was routinely cultured in 850 sq cm smooth surface, vented cap roller bottles at 37 C, 95% relative humidity (RH) and shaken at 135-155 rpm. The growth media consisted of Freestyle CHO Expression Medium supplemented with 8 mM L-Glutamine and 1X antibiotic mix (penicillin, streptomycin, and neomycin).

CHO-S cells were suspended in roller bottles at a density of 0.6 million cells/mL in CHO Expression Medium supplemented with 8 mM L-Glutamine. The following day, cells were diluted to a density of 1 million cells/mL and transfected one of two ways: one population was transfected with 0.112 ug/mL of pGL4.31 reporter plasmid, 0.54 ug/mL of pGALDBD_NCOR plasmid and 0.54 ug/mL of pVP16_NR2E3LBD plasmid, complexed with 1.2 uL/mL of Freestyle Max Reagent in 38.4 uL/mL of OptiPRO SFM according to the Freestyle Max Reagent manufacturer's protocol (+NR2E3 cells). The second poplulation was transfected with 0.112 ug/mL of pGL4.31 reporter plasmid and 0.54 ug/mL of pGALDBD_NCOR plasmid, complexed with 1.2 uL/mL of Freestyle Max Reagent in 38.4 uL/mL of OptiPRO SFM according to the Freestyle Max Reagent manufacturer's protocol (-NR2E3 cells). Sixteen hours after transfection, 3750 cells in 5 uL of media were seeded into each well of 1536 well microtiter plates. The -NR2E3 cell population was dispensed to column 1 and 2 and was used as a high control mimicking inhibition. The +NR2E3 cell population was dispensed over the rest of the plate, with the exception of column 48 that received only media. Next, 20 nL of test compound in DMSO, or DMSO alone were dispensed to the appropriate wells. The plates were then incubated for 24 hours at 37 C, 5% CO2, and 95 % RH.

Luciferase levels were measured by adding 5 uL of One-Glo Luciferase Assay (prepared according to the manufacturer's protocol) to each well; followed by 10 minute incubation at room temperature. Then, Well Luminescence was read on the ViewLux plate reader. The percent inhibition for each compound was calculated as follows:

%_Inhibition = ( ( Ratio_Test_Compound - Median_Ratio_Low_Control ) / ( Median_Ratio_High_Control - Median_Ratio_Low_Control ) ) * 100

Where:

High_Control is defined as wells containing DMSO and -NR2E3 cells.
Test_Compound is defined as wells containing test compounds, DMSO and +NR2E3 cells.
Low_Control is defined as wells containing DMSO and +NR2E3 cells.

For each test compound, percent activation was plotted against compound concentration. A four parameter equation describing a sigmoidal dose-response curve was then fitted with adjustable baseline using Assay Explorer software (Symyx Technologies Inc). The reported IC50 values were generated from fitted curves by solving for the X-intercept value at the 50% activation level of the Y-intercept value. In cases where the highest concentration tested (i.e. 40 uM) did not result in greater than 50% activation, the IC50 was determined manually as greater than 40 uM.

PubChem Activity Outcome and Score:

Compounds with an IC50 greater than 10 uM were considered inactive. Compounds with an IC50 equal to or less than 10 uM were considered active.

Any compound with a percent activity value < 50% at all test concentrations was assigned an activity score of zero. Any compound with a percent activity value >= 50% at any test concentration was assigned an activity score greater than zero.

Activity score was then ranked by the potency of the compounds with fitted curves, with the most potent compounds assigned the highest activity scores.

The PubChem Activity Score range for active compounds is 100-75, for inactive 67-0.

List of Reagents:

Freestyle CHO-S Cells (Invitrogen, part R800-07)
Freestyle CHO-S Expression Medium (Invitrogen, part 12651-022)
Freestyle Max Reagent (Invitrogen, part 16447-100)
OptiPRO SFM (Invitrogen, part 12309-050)
100X Penicillin-Streptomycin-Neomycin mix (Invitrogen, part 15640-055)
L-Glutamine-200mM (Invitrogen, part 25030-081)
BD Falcon Roller Bottles-Smooth Surface (Bd Vacutainer Labware Medical, part 353154 )
pGL4.31 (Promega, part C935)
pGALDBD-NCOR LBD (Assay provider)
pVP16-NR2E3 LBD (Assay provider)
1536-well plates (Corning, part 7298)
Comment
Due to the increasing size of the MLPCN compound library, this assay may have been run as two or more separate campaigns, each campaign testing a unique set of compounds. All data reported were normalized on a per-plate basis. Possible artifacts of this assay can include, but are not limited to: dust or lint located in or on wells of the microtiter plate, and compounds that modulate well luminescence. All test compound concentrations reported above and below are nominal; the specific test concentration(s) for a particular compound may vary based upon the actual sample provided by the MLSMR. The MLSMR was unable to provide all compounds selected for testing.
Categorized Comment
Assay: Dictionary: Version: 0.1

Assay: CurveFit [1]: Equation: =( ( [Maximal Response] * [Concentration]^[Hill Slope] ) / ( [Inflection Point Concentration]^[Hill Slope] + [Concentration]^[Hill Slope] ) ) + [Baseline Response]

Assay: CurveFit [1]: Mask: Excluded Points

Result Definitions
Show more
TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1QualifierActivity Qualifier identifies if the resultant data IC50 came from a fitted curve or was determined manually to be less than or greater than its listed IC50 concentration.String
2IC50*The concentration at which 50 percent of the activity in the inhibitor assay is observed; (IC50) shown in micromolar.FloatμM
3LogIC50Log10 of the qualified IC50 (IC50) from the inhibitor assay in M concentrationFloat
4Inflection Point ConcentrationThe concentration value for the inflection point of the curve.FloatμM
5Hill SlopeThe variable HillSlope describes the steepness of the curve. This variable is called the Hill slope, the slope factor, or the Hill coefficient. If it is positive, the curve increases as X increases. If it is negative, the curve decreases as X increases. A standard sigmoid dose-response curve (previous equation) has a Hill Slope of 1.0. When HillSlope is less than 1.0, the curve is more shallow. When HillSlope is greater than 1.0, the curve is steeper. The Hill slope has no units.Float
6Baseline ResponseAdjustable baseline of the curve fit, minimal response value.Float
7Maximal ResponseThe maximal or asymptotic response above the baseline as concentration increases without bound.Float
8Response RangeThe range of Y.Float
9Chi SquareA measure for the 'goodness' of a fit. The chi-square test (Snedecor and Cochran, 1989) is used to test if a sample of data came from a population with a specific distribution.Float
10RsquareThis statistic measures how successful the fit explains the variation of the data; R-square is the square of the correlation between the response values and the predicted response values.Float
11Excluded PointsFlags to indicate which of the dose-response points were excluded from analysis. (1) means the point was excluded and (0) means the point was not excluded.String
12Number of DataPointsOverall number of data points of normalized percent activation that was used for calculations (includes all concentration points); in some cases a data point can be excluded as outlier.Integer
13Inhibition at 0.002 uM [1] (0.002μM**)Value of % inhibition at 0.002 uM inhibitor concentration; replicate [1]Float%
14Inhibition at 0.002 uM [2] (0.002μM**)Value of % inhibition at 0.002 uM inhibitor concentration; replicate [2]Float%
15Inhibition at 0.002 uM [3] (0.002μM**)Value of % inhibition at 0.002 uM inhibitor concentration; replicate [3]Float%
16Inhibition at 0.006 uM [1] (0.006μM**)Value of % inhibition at 0.006 uM inhibitor concentration; replicate [1]Float%
17Inhibition at 0.006 uM [2] (0.006μM**)Value of % inhibition at 0.006 uM inhibitor concentration; replicate [2]Float%
18Inhibition at 0.006 uM [3] (0.006μM**)Value of % inhibition at 0.006 uM inhibitor concentration; replicate [3]Float%
19Inhibition at 0.018 uM [1] (0.018μM**)Value of % inhibition at 0.018 uM inhibitor concentration; replicate [1]Float%
20Inhibition at 0.018 uM [2] (0.018μM**)Value of % inhibition at 0.018 uM inhibitor concentration; replicate [2]Float%
21Inhibition at 0.018 uM [3] (0.018μM**)Value of % inhibition at 0.018 uM inhibitor concentration; replicate [3]Float%
22Inhibition at 0.054 uM [1] (0.054μM**)Value of % inhibition at 0.054 uM inhibitor concentration; replicate [1]Float%
23Inhibition at 0.054 uM [2] (0.054μM**)Value of % inhibition at 0.054 uM inhibitor concentration; replicate [2]Float%
24Inhibition at 0.054 uM [3] (0.054μM**)Value of % inhibition at 0.054 uM inhibitor concentration; replicate [3]Float%
25Inhibition at 0.163 uM [1] (0.163μM**)Value of % inhibition at 0.163 uM inhibitor concentration; replicate [1]Float%
26Inhibition at 0.163 uM [2] (0.163μM**)Value of % inhibition at 0.163 uM inhibitor concentration; replicate [2]Float%
27Inhibition at 0.163 uM [3] (0.163μM**)Value of % inhibition at 0.163 uM inhibitor concentration; replicate [3]Float%
28Inhibition at 0.490 uM [1] (0.49μM**)Value of % inhibition at 0.490 uM inhibitor concentration; replicate [1]Float%
29Inhibition at 0.490 uM [2] (0.49μM**)Value of % inhibition at 0.490 uM inhibitor concentration; replicate [2]Float%
30Inhibition at 0.490 uM [3] (0.49μM**)Value of % inhibition at 0.490 uM inhibitor concentration; replicate [3]Float%
31Inhibition at 1.5 uM [1] (1.5μM**)Value of % inhibition at 1.5 uM inhibitor concentration; replicate [1]Float%
32Inhibition at 1.5 uM [2] (1.5μM**)Value of % inhibition at 1.5 uM inhibitor concentration; replicate [2]Float%
33Inhibition at 1.5 uM [3] (1.5μM**)Value of % inhibition at 1.5 uM inhibitor concentration; replicate [3]Float%
34Inhibition at 4.4 uM [1] (4.4μM**)Value of % inhibition at 4.4 uM inhibitor concentration; replicate [1]Float%
35Inhibition at 4.4 uM [2] (4.4μM**)Value of % inhibition at 4.4 uM inhibitor concentration; replicate [2]Float%
36Inhibition at 4.4 uM [3] (4.4μM**)Value of % inhibition at 4.4 uM inhibitor concentration; replicate [3]Float%
37Inhibition at 13.2 uM [1] (13.2μM**)Value of % inhibition at 13.2 uM inhibitor concentration; replicate [1]Float%
38Inhibition at 13.2 uM [2] (13.2μM**)Value of % inhibition at 13.2 uM inhibitor concentration; replicate [2]Float%
39Inhibition at 13.2 uM [3] (13.2μM**)Value of % inhibition at 13.2 uM inhibitor concentration; replicate [3]Float%
40Inhibition at 39.7 uM [1] (39.7μM**)Value of % inhibition at 39.7 uM inhibitor concentration; replicate [1]Float%
41Inhibition at 39.7 uM [2] (39.7μM**)Value of % inhibition at 39.7 uM inhibitor concentration; replicate [2]Float%
42Inhibition at 39.7 uM [3] (39.7μM**)Value of % inhibition at 39.7 uM inhibitor concentration; replicate [3]Float%

* Activity Concentration. ** Test Concentration.
Additional Information
Grant Number: 1 R21 NS061718-01

Data Table (Concise)
Classification
PageFrom: