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BioAssay: AID 624378

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

Name: Luminescence-based cell-based high throughput confirmation assay to identify agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3). ..more
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 Tested Compounds
 Tested Compounds
All(2313)
 
 
Active(1179)
 
 
Inactive(1134)
 
 
 Tested Substances
 Tested Substances
All(2315)
 
 
Active(1180)
 
 
Inactive(1135)
 
 
AID: 624378
Data Source: The Scripps Research Institute Molecular Screening Center (NR2E3-CELL_AG_LUMI_1536_3X%INH CRUN)
BioAssay Type: Primary, Primary Screening, Single Concentration Activity Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
Deposit Date: 2012-07-11

Data Table ( Complete ):           Active    All
Target
BioActive Compounds: 1179
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)
2379TR-FRET-based biochemical high throughput confirmation assay for agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3)screeningConfirmation screen (NR2E3 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)
2758TR-FRET-based biochemical high throughput dose response assay for agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3)confirmatoryDose response (NR2E3 agonists in triplicate)
2759Counterscreen for agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3): TR-FRET-based biochemical high throughput dose response assay to identify 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 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)
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
2325Summary of probe development efforts to identify agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3).summary
624394Luminescence-based cell-based high throughput dose response assay for agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3)confirmatory
624395Counterscreen for agonists of nuclear receptor subfamily 2, group E, member 3 (NR2E3):Luminescence-based cell-based high throughput dose response assay to identify inhibitors of the Herpes Virus Virion Protein 16 (VP16)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_3X%INH CRUN

Name: Luminescence-based cell-based high throughput confirmation assay to identify 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:

confirmation, 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 confirm NR2E3 agonist activity of available compounds identifeid as active in a set of previous experiemtns 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 at a nominal concentration of 4 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 meaasured 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.

PubChem Activity Outcome and Score:

The average percent inhibition and standard deviation of each compound tested were calculated. The sum of these two values was used as a hit cutoff parameter. Any compound that exhibited an average percent inhibition greater than the calculated hit cutoff was declared active.

The reported PubChem Activity Score has been normalized to 100% observed primary inhibition. Negative % inhibition values are reported as activity score zero.

The PubChem Activity Score range for active compounds is 100-69, for inactive 69-0.

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.
Result Definitions
TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1Average Inhibition at 3.98 uM (3.98μM**)Normalized percent inhibition of the confirmation screen at a compound concentration of 3.98 micromolar.Float%
2Standard DeviationStandard deviation of the confirmation assay derived from the normalized percent inhibition of the replicate data for each compound.Float
3Inhibition at 3.98 uM [1] (3.98μM**)Percent inhibition of the confirmation screen at a compound concentration of 3.98 micromolar.Float%
4Inhibition at 3.98 uM [2] (3.98μM**)Percent inhibition of the confirmation screen at a compound concentration of 3.98 micromolar.Float%
5Inhibition at 3.98 uM [3] (3.98μM**)Percent inhibition of the confirmation screen at a compound concentration of 3.98 micromolar.Float%
6Inhibition at 3.98 uM [4] (3.98μM**)Percent inhibition of the confirmation screen at a compound concentration of 3.98 micromolar.Float%

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

Data Table (Concise)
Classification
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