External ID: CHEMBL1266185

Protocol: N/A

Comment: Journal: Nat Chem Biol
Year: 2007
Volume: 3
Issue: 5
First Page: 268
Last Page: 273
DOI: 10.1038/nchembio873

External ID: SNCA-p-activity-luciferase

Protocol: PROTOCOL TABLE
SEQUENCE No. (e.g., 1, 2, 3, etc.); PARAMETER (e.g., Cells, Incubation, Reagent, etc.); VALUE; DESCRIPTION

1; Cells; 4 uL; Dispense 1500 HEK-293-SNCA-luc cells/well into Greiner 1536-well white / solid bottom tissue culture treated plate. The plate was covered with metal lids with gas-exchange holes.
2; Incubate; 24 hours; Incubate at 37C, 5% CO2, 95% RH.
3; Compounds; 23 nL; Compounds and controls were transferred via a Kalypsys Pin Tool (Wako USA) equipped with a 1536-slotted pin array. The plate was covered with metal lids with gas-exchange holes.
4; Incubate; 24 hours; Incubate at 37C, 5% CO2, 95% RH.
5; Dispense; 1 uL; Dispense Gly-Phe-7-amino-4-trifluoromethylcoumarin (GF-AFC, prepared at 125 uM in PBS) was added. The plate was covered with metal lids with gas-exchange holes.
6; Incubate; 30 min; Incubate at 37C, 5% CO2.
7; Detector; Fluorescence; Measure fluorescence with ViewLux microplate reader (PerkinElmer) equipped with 405/10 excitation and 540/25 emission filters.
8; Dispense; 3 uL; Dispense ONE-Glo (PerkinElmer) lucifase detection reagent was added to each well. Plates were covered with metal lids with gas-exchange holes.
9; Incubate; 15 min; Incubate at room temperature.
10; Detector; Luminescence; Measure luminescence with ViewLux microplate reader (PerkinElmer) equipped with clear filters.

NOTES (numbers refer to sequence above)
1; HEK-293-SNCA-luc were cultured and suspended in phenol-red free DMEM (4.5 g/L glucose, 25 mM HEPES, cat #21063 (Thermo)).
3; Compounds were added to the assay plate in an 11-point intra plate dose response, 1:3 titration in DMSO with a final concentration range of xxx - yyy uM. Vehicle-only plates, with DMSO being pin-transferred to every well, were inserted at the beginning of screening runs to confirm expected assay performance. Activity was normalized to wells containing medium only (-100% activity, full inhibition) and SNCA-luc cells treated with DMSO vehicle control (0% activity), contained on the same plate as test samples.
10; Signals were analyzed, and dose-response curves were fit using the Hill equation. Compounds in curve classes -1.1, -1.2, -2.1, -2.2 in the SNCA-luc assay were considered active. Compounds were eliminated from further consideration if also active (curve class -1.1, -1.2, -1.3, -1.4, -2.1, -2.2, -2.3, -2.4) in the GF-AFC cytotoxicity assay.

Comment: Disclaimer:
Although all reasonable efforts have been made to ensure the accuracy and reliability of the data, caution should be exercised when interpreting the results as artifacts are possible from nonspecific effects such as assay signal interference. The curve fitting and activity calls presented here are based on the NCATS analysis methods.

Compound Ranking:
1. Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. For this assay, apparent inhibitors are ranked higher than compounds that showed apparent activation.
2. For all inactive compounds, with a ratio activity curve class of 4, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. For a ratio activity curve class = -1.1, score = 80+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == -1.2 && abs(ratio.max_response) > 6*10, score = 60+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == -2.1 || ( ratio.curve_class==-2.2 && abs(ratio.max_response) > 6*10), score = 40+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == -1.2 || ratio.curve_class == -2.2, score = 20+abs((log_ac50+4.5)*inf_activity/20). Inconclusive compounds, with a donor curve class other than 4, have PUBCHEM_ACTIVITY_SCORE of 10. Inconclusive compounds have PUBCHEM_ACTIVITY_SCORE between 1 and 39.

External ID: CYP273

Protocol: Tox21 Assay Protocol Summary:

Two ul of enzyme-substrate mix was dispensed into medium binding white/solid 1536-well plates (Greiner Bio-One North America Inc., Monroe, NC) using a BioRaptr Flying Reagent Dispenser (FRD, Beckman Coulter, Brea, CA). Compounds dissolved in DMSO and positive control (furafyllline) were transferred to the assay plates at 23 nl using a Pintool station (Wako, San Diego, CA). The assay plates were incubated at room temperature for 10 min. Then 2 ul of NADPH regeneration solution was added to each well of the assay plates using an FRD and incubated at room temperature for 1 h. The reaction was stopped by adding 4 ul of detection reagent using an FRD and after 20 min incubation at room temperature the luminescence signal was measured using a ViewLux plate reader (Perkin Elmer, Shelton, CT). Data were expressed as relative luminescence units.

Comment: Disclaimer:

Although all reasonable efforts have been made to ensure the accuracy and reliability of the data, caution should be exercised when interpreting the results as artifacts are possible from nonspecific effects such as assay signal interference. The curve fitting and activity calls presented here are based on the NCATS analysis methods. Alternative analysis methods and interpretations of the data are available at EPA (http://actor.epa.gov) and NTP (http://tools.niehs.nih.gov/cebs3/ui/).

Compound Ranking:

1. Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. See data field "Curve Description". For this assay, apparent inhibitors are ranked higher than compounds that showed apparent activation.
2. For all inactive compounds, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. Inconclusive compounds have PUBCHEM_ACTIVITY_SCORE between 1 and 39. Fit_LogAC50 was used for determining relative score and was scaled to each curve class' score range.

External ID: CHEMBL1664602

Protocol: N/A

Comment: Compounds with activity <= 10uM or explicitly reported as active by ChEMBL are flagged as active in this PubChem assay presentation.

Journal: J. Med. Chem.
Year: 2011
Volume: 54
Issue: 2
First Page: 534
Last Page: 547
DOI: 10.1021/jm1009082

Target ChEMBL ID: CHEMBL3356
ChEMBL Target Name: Cytochrome P450 1A2
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: HMS1625

Protocol: The fix-reporter plasmid was conjugated into this strain which the stably integrates into the chromosome using the mini-Tn7 system (PMID: 15908923). This plasmid consists of the fixK promoter, which is a target of the fixLJ pathway driving expression of GFP.
The day before screen an overnight culture of B. multivorans strain VC7102, with fix reporter, is set up in tryptic soy broth (TSB) at 37 degrees C with shaking. The day of the screen the overnight culture is diluted 1:100 in fresh tryptic soy broth.
The day of the screen, 30 microL of tryptic soy broth (TSB) is pipetted into columns 1-22 of a 384-well plate (Corning 3764) using the Combi multidrop dispenser. To column 24, 30 microL of TSB containing 78 microM of Benserazide TSB is added for a positive control. To column 23, 30 microL of TSB containing with DMSO (0.078% v/v in TSB) is added for a negative control. 300 nL of each compound are pin-transferred to each plate. For every compound plate 2 replicate assay plates are set up. 30 microL of the 1:100 diluted-B. multivorans strain VC7102 is added to each well using the Combi. Initial OD600 and GFP are measured using the PerkinElmer EnVision. Plates are stacked 5 high, covered with lids and incubated at 37 degrees C overnight (~18 h).
The following day, assay plates are read using a PerkinElmer EnVision (600 nm filter and GFP).
Positive control: Benserazide 39 microM in column 24 (No positive control was used for plates 2089 & 2090; Plates 2091-2093: columns 1 & 24)
Negative control: DMSO 300 nL/well in column 23 (For plates 2089 & 2090 negative controls were located in columns 2 & 24; plates 2091-2093: columns 2 & 23)

Comment: Analysis method:
For each compound well, the initial GFP value was subtracted from overnight GFP value to calculate the deltaGFP. The mean and standard deviation of the negative control wells deltaGFP (column 23) on both replicate plates was calculated. Wells with replicate average deltaGFP at least 3 standard deviations above the plate negative control deltaGFP average were scored as potential positives.

To determine activity scores, Z-scores were calculated for each replicate separately based on the replicate negative control deltaGFP plate average and standard deviation. The replicate average deltaGFP Z-scores were used for activity scores, with activity score of 100 set to Z-score = 4 and activity score = 0 (no activity) set to Z-score = 0. Z-scores > 4 were considered activity score = 100, and Z-scores < 0 were considered activity score = 0.

External ID: TargetID_659_CEMA

Protocol: Black, standard capacity streptavidin-coated 384-well plates (Pierce 15407) were first washed with 50 L of phosphate buffer (100 mM, pH 7.0; PB7) three times using a Biotek 405 ELX plate washer. Subsequently, 5 L of biotinylated pre-miRNA substrate (500 nM final) was dispensed into the plate using a Multidrop Combi Reagent Dispenser (Thermo Scientific). Plates were then centrifuged for 1 min at 1,000 RPM (223 g), sealed with plate tape, and incubated overnight at 4 C. The following morning, plates were washed three times with 50 L of PB7, followed by the addition of 5 L of Dicer digest buffer (20 mM Tris, 12 mM NaCl, 2.5 mM MgCl2, 1 mM fresh DTT, and 4.5% DMSO) and centrifugation. Compounds (50 nL of 5 mM DMSO stock, 25 M final) were then added into the sample wells using a Sciclone (Caliper) liquid handler with V&P pintool; the same volume of DMSO was added to the control wells. The plates were incubated at 25 C for 15 min before addition of 5 L of digest buffer containing 217 g/nL Dicer (108 g/mL Dicer, 5% glycerol and 0.01% Triton X-100 final, excess with respect to pre-miRNA). For the positive control wells, digest buffer without Dicer was added. The plates were centrifuged again and resealed before being placed in a 37 C incubator for 5 h. After Dicer cleavage, plates were washed three times with 50 L of PB7. mTet-HRP in PB7 (10 L, 750 nM final) was then dispensed into each well. The plates were subsequently centrifuged, sealed, and incubated at 25 C for 2 h. Plates were then washed three times with 50 L of wash buffer (2 mM imidazole, 260 mM NaCl, 0.5 mM EDTA, 0.1% Tween-20, pH 7.0), followed by washing three additional times with 50 L of PB7. Finally, SuperSignal West Pico (25 L; Pierce) was added, the plates were incubated at 25 C for 5 min, and chemiluminescence signal was detected using a PHERAstar plate reader using LUM plus module (BMG Labtech).

Comment: The activity outcome is based on a Z-score (number of standard deviations from the negative control mean) of 3 or higher on at least 50% times that the sample was screened.

For instance, if the sample was screened in n=4 runs, it would be considered active only if it had a Z-score of 3 or above in at least 2 runs.

External ID: P53600

Protocol: Tox21 Assay Protocol Summary:

The p53RE-bla cells were dispensed at 4,000 cells/5 ul/well in 1536-well black wall/clear bottom plates using a Multidrop dispenser. After the assay plates were incubated at a 37 C/5% CO2 incubator for 5 hours, 23 nL of compounds dissolved in DMSO, positive controls or DMSO only was transferred to the assay plate by a pin tool. The plates were incubated at 37 C for 16 hours. After 1 uL of LiveBLAzerTM B/G FRET substrate was added using a Flying Reagent Dispenser, the plates were incubated at room temperature for 2 hours, and fluorescence intensity was measured by an Envision plate reader. For cell viability readout that measures cytotoxicity, 4 ul/well of CellTiter-Glo reagent was added into the assay plates using a Flying Reagent Dispenser. After 30 min incubation at room temperature, the luminescence intensity in the plates was measured using a ViewLux plate reader.

Comment: Disclaimer:

Although all reasonable efforts have been made to ensure the accuracy and reliability of the data, caution should be exercised when interpreting the results as artifacts are possible from nonspecific effects such as assay signal interference. The curve fitting and activity calls presented here are based on the NCATS analysis methods. Alternative analysis methods and interpretations of the data are available at EPA (https://www.epa.gov/comptox-tools/comptox-chemicals-dashboard) and NTP (https://cebs.niehs.nih.gov/cebs/).
Compound Ranking:

1. Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. See data field "Curve Description". For this assay, apparent inhibitors are ranked higher than compounds that showed apparent activation.
2. For all inactive compounds, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. Inconclusive compounds have PUBCHEM_ACTIVITY_SCORE between 1 and 39. Fit_LogAC50 was used for determining relative score and was scaled to each curve class' score range.

External ID: P53MS958

Protocol: Tox21 Assay Protocol Summary:

The p53RE-bla cells were dispensed at 4,000cells/3ul/well in 1536-well black-clear bottom plates. After the assay plates were incubated at 37 C, 5% CO2 incubator for 5 hours, 23 nL of compounds dissolved in DMSO, positive controls or DMSO only was transferred to the assay plate. Following compound addition, 3 uL of rat liver microsomes (Molecular Toxicology, Boone, NC) at final concentration of 0.5 mg/mL and 1uL of B-Nicotinamide adenine dinucleotide 2'-phosphate (NADPH) at final concentration of 0.5 mg/mL were transferred to the assay plate. The plates were incubated at 37 C for 16 hours. 1 uL of LiveBLAzer detection mixture was added to each well and the plates were incubated at room temperature in the dark for 2 h. Fluorescence intensity at 460 and 530 nm emission and 405 nm excitation were measured by an Envision plate reader. For cell viability readout that measures cytotoxicity, 4 ul/well of CellTiter-Glo reagent was added into the assay plates using a Flying Reagent Dispenser. After 30 min incubation at room temperature, the luminescence intensity in the plates was measured using a ViewLux plate reader.

Comment: Disclaimer:

Although all reasonable efforts have been made to ensure the accuracy and reliability of the data, caution should be exercised when interpreting the results as artifacts are possible from nonspecific effects such as assay signal interference. The curve fitting and activity calls presented here are based on the NCATS analysis methods. Alternative analysis methods and interpretations of the data are available at EPA (https://www.epa.gov/comptox-tools/comptox-chemicals-dashboard) and NTP (https://cebs.niehs.nih.gov/cebs/).

Compound Ranking:

1. Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. See data field "Curve Description". For this assay, apparent inhibitors are ranked higher than compounds that showed apparent activation.
2. For all inactive compounds, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. Inconclusive compounds have PUBCHEM_ACTIVITY_SCORE between 1 and 39. Fit_LogAC50 was used for determining relative score and was scaled to each curve class' score range.

External ID: P53MS482

Protocol: Please refer to other AIDs 1963578, 1963580, 720687, 720685, 720678 and 720681 for detailed assay protocols.

Comment: This summary is written for the purposes of summarizing the compound activities from the project combining the results from both the p53 with rat microsomes agonist mode assay (AID 1963578), cell viability counter screen (AID 1963580), and auto fluorescence counter screens (AID 720687, 720685, 720678, and 720681). For all inactive compounds, PUBCHEM_ACTIVITY_SCORE is 0. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. Potency and efficacy were used for determining relative score. Inconclusive compounds have PUBCHEM_ACTIVITY_SCORE between 5 and 30 determined by phenotype.

Disclaimer:

Although all reasonable efforts have been made to ensure the accuracy and reliability of the data, caution should be exercised when interpreting the results as artifacts are possible from nonspecific effects such as assay signal interference. The curve fitting and activity calls presented here are based on the NCATS analysis methods. Alternative analysis methods and interpretations of the data are available at EPA (https://www.epa.gov/comptox-tools/comptox-chemicals-dashboard) and NTP (https://cebs.niehs.nih.gov/cebs/).

External ID: P53344

Protocol: Tox21 Assay Protocol Summary:

The p53RE-bla cells were dispensed at 4,000 cells/5 ul/well in 1536-well black wall/clear bottom plates using a Multidrop dispenser. After the assay plates were incubated at a 37 C/5% CO2 incubator for 5 hours, 23 nL of compounds dissolved in DMSO, positive controls or DMSO only was transferred to the assay plate by a pin tool. The plates were incubated at 37 C for 16 hours. After 1 uL of LiveBLAzerTM B/G FRET substrate was added using a Flying Reagent Dispenser, the plates were incubated at room temperature for 2 hours, and fluorescence intensity was measured by an Envision plate reader.

Comment: Disclaimer:

Although all reasonable efforts have been made to ensure the accuracy and reliability of the data, caution should be exercised when interpreting the results as artifacts are possible from nonspecific effects such as assay signal interference. The curve fitting and activity calls presented here are based on the NCATS analysis methods. Alternative analysis methods and interpretations of the data are available at EPA (https://www.epa.gov/comptox-tools/comptox-chemicals-dashboard) and NTP (https://cebs.niehs.nih.gov/cebs/).

Compound Ranking:

1. Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. See data field "Curve Description". For this assay, apparent activators are ranked higher than compounds that showed apparent inhibition.
2. For all inactive compounds, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. Inconclusive compounds have PUBCHEM_ACTIVITY_SCORE between 1 and 39. Fit_LogAC50 was used for determining relative score and was scaled to each curve class' score range.

External ID: P53MS233

Protocol: Tox21 Assay Protocol Summary:

The p53RE-bla cells were dispensed at 4,000cells/3ul/well in 1536-well black-clear bottom plates. After the assay plates were incubated at 37 C, 5% CO2 incubator for 5 hours, 23 nL of compounds dissolved in DMSO, positive controls or DMSO only was transferred to the assay plate. Following compound addition, 3 uL of human liver microsomes (XenoTech, Kansas City, KS) at final concentration of 0.5 mg/mL and 1uL of Beta-Nicotinamide adenine dinucleotide 2-phosphate (NADPH) at final concentration of 0.5 mg/mL were transferred to the assay plate. The plates were incubated at 37 C for 16 hours. 1 uL of LiveBLAzer detection mixture was added to each well and the plates were incubated at room temperature in the dark for 2 h. Fluorescence intensity at 460 and 530 nm emission and 405 nm excitation were measured by an Envision plate reader.

Comment: Disclaimer:

Although all reasonable efforts have been made to ensure the accuracy and reliability of the data, caution should be exercised when interpreting the results as artifacts are possible from nonspecific effects such as assay signal interference. The curve fitting and activity calls presented here are based on the NCATS analysis methods. Alternative analysis methods and interpretations of the data are available at EPA (https://www.epa.gov/comptox-tools/comptox-chemicals-dashboard) and NTP (https://cebs.niehs.nih.gov/cebs/).

Compound Ranking:

1. Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. See data field "Curve Description". For this assay, apparent activators are ranked higher than compounds that showed apparent inhibition.
2. For all inactive compounds, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. Inconclusive compounds have PUBCHEM_ACTIVITY_SCORE between 1 and 39. Fit_LogAC50 was used for determining relative score and was scaled to each curve class' score range.

External ID: P53MS837

Protocol: Tox21 Assay Protocol Summary:

The p53RE-bla cells were dispensed at 4,000cells/3ul/well in 1536-well black-clear bottom plates. After the assay plates were incubated at 37 C, 5% CO2 incubator for 5 hours, 23 nL of compounds dissolved in DMSO, positive controls or DMSO only was transferred to the assay plate. Following compound addition, 3 uL of human liver microsomes (XenoTech, Kansas City, KS) at final concentration of 0.5 mg/mL and 1uL of B-Nicotinamide adenine dinucleotide 2'-phosphate (NADPH) at final concentration of 0.5 mg/mL were transferred to the assay plate. The plates were incubated at 37 C for 16 hours. 1 uL of LiveBLAzer detection mixture was added to each well and the plates were incubated at room temperature in the dark for 2 h. Fluorescence intensity at 460 and 530 nm emission and 405 nm excitation were measured by an Envision plate reader. For cell viability readout that measures cytotoxicity, 4 ul/well of CellTiter-Glo reagent was added into the assay plates using a Flying Reagent Dispenser. After 30 min incubation at room temperature, the luminescence intensity in the plates was measured using a ViewLux plate reader.

Comment: Disclaimer:

Although all reasonable efforts have been made to ensure the accuracy and reliability of the data, caution should be exercised when interpreting the results as artifacts are possible from nonspecific effects such as assay signal interference. The curve fitting and activity calls presented here are based on the NCATS analysis methods. Alternative analysis methods and interpretations of the data are available at EPA (https://www.epa.gov/comptox-tools/comptox-chemicals-dashboard) and NTP (https://cebs.niehs.nih.gov/cebs/).
Compound Ranking:

1. Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. See data field "Curve Description". For this assay, apparent inhibitors are ranked higher than compounds that showed apparent activation.
2. For all inactive compounds, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. Inconclusive compounds have PUBCHEM_ACTIVITY_SCORE between 1 and 39. Fit_LogAC50 was used for determining relative score and was scaled to each curve class' score range.