External ID: MDAN535

Protocol: Please refer to other AIDs 743042 and 743041 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 AR antagonist mode assay (AID 743042) and cell viability counter screen (AID 743041). 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 (http://actor.epa.gov) and NTP (http://tools.niehs.nih.gov/cebs3/ui/).

External ID: TDP1100

Protocol: DT40-hTDP1 cells without 20 nM Camptothecin (add 20 microL of DMSO in 1 L of cell culture medium) were dispensed at 400 cells/5microL/well in tissue culture treated 1536-well white wall/solid bottom assay plates (Greiner Bio-One North America, NC, U.S.A.) using a Multidrop Combi 8 channel dispenser (Thermo Fisher, Waltham, MA, USA). 23 nL compounds and controls were transferred using the pin tool (Kalypsys, San Diego, CA, USA) to the assay plates. The assay plates were then incubated at 37 masculineC for a minimum 48 hr. Three microL of Cell Titer Glo solution was added to the plates and incubated at RT in dark for 30 min. Luminescence was read using ViewLux (Perkin Elmer) with 1 sec exposure slow speed, high gain and 2x binning.

Comment: 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: TDP1101

Protocol: DT40-hTDP1 cells with 20 nM Camptothecin (add 20 microL of 1 mM CPT stock in 1 L of cell culture medium) were dispensed at 400 cells/5microL/well in tissue culture treated 1536-well white wall/solid bottom assay plates (Greiner Bio-One North America, NC, U.S.A.) using a Multidrop Combi 8 channel dispenser (Thermo Fisher, Waltham, MA, USA). 23 nL compounds and controls were transferred using the pin tool (Kalypsys, San Diego, CA, USA) to the assay plates. The assay plates were then incubated at 37 masculineC for a minimum 48 hr. Three microL of Cell Titer Glo solution was added to the plates and incubated at RT in dark for 30 min. Luminescence was read using ViewLux (Perkin Elmer) with 1 sec exposure slow speed, high gain and 2x binning.

Comment: 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: MDAV150

Protocol: Tox21 Assay Protocol Summary:

MDA-kb2 AR-luc cells were dispensed at 3,000 cells/4 uL/well of culture medium into white wall/solid-bottom 1536-well plates using a Multidrop Combi (ThermoFisher Scientific, Waltham, MA) dispenser. After the assay plates were incubated at a 37C and 0% CO2 for 5 hr, 23 nL of compounds dissolved in DMSO, positive controls or DMSO only was transferred to the assay plate by a Pintool station (Kalypsys, San Diego, CA), followed by addition of 1 uL of agonist (R1881) in culture medium using a Bioraptr Flying Reagent Dispenser (FRD) workstation (Beckman Coulter, Indianapolis, IN, USA). The plates were incubated at a 37C and 0% CO2 for 16 h. After 15.5 h incubation, 1uL of CellTiter-Fluor reagent (Promega) was added using a Bioraptr FRD to each plate for measuring cytotoxicity. The fluorescence intensity was quantified on a ViewLux plate reader (PerkinElmer, Shelton, CT) following 30 min incubation at 37C and 0% CO2.

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: IucA Pilot Assay Spectrum Library

Protocol: A solution containing 55.6 mM HEPES pH 7.5, 0.11% Tween 20, 16.7 mM MgCl2, 55.6 mM hydroxylamine, 55.6 microM ATP, 55.6 microM citrate, and 0.28 U/mL IPP was dispensed (45 microL) into clear polystyrene microplates (Corning, Inc.) using a BioTek MicroFlo dispenser.

Next, 40 nL of test compounds (10 mM in DMSO, 8 microM final concentration) were transferred from deep-well blocks to the reaction solution using a stainless-steel pin tool operated by a robotic workstation (JANUS, PerkinElmer, Waltham, MA). The IucA-catalyzed reaction was initiated by adding 5 microL of 3 microM IucA in 25 mM HEPES, 75 mM NaCl, and 0.1 mM TCEP at pH 7.5.

The reactions were allowed to proceed for 30 min at room temperature before being quenched by dispensing (microFill, BioTek) 13 microL of MG developing solution, containing 1.0 mg/mL MG oxalate, 1.5% (w/v) ammonium molybdate, 0.15% (v/v) Tween 20, and 4.7 N sulfuric acid. After allowing the assay color to develop/stabilize for 30 min, the absorbance at 620 nm was measured (EnVision 2103 Multilabel Microplate Reader, PerkinElmer).

Average positive controls from 24 wells with no test compound and average negative controls from 8 wells with no enzyme were calculated. Dynamic range was calculated by difference between Avg Pos Control and Avg Neg Control. Percent inhibition was calculated by the ratio of (Avg. Pos. Ctrl - Sample OD) to Dynamic Range.

Comment: Protein Target is
IucA

EMB09144
574 aa
G057_19877
Klebsiella pneumoniae hvKP1

Active compounds were defined by <80% activity at 8 microM screening concentration.

External ID: CF Folding

Protocol: A high throughput 384-well microplate based fluorescence assay was developed using HeLa cells engineered to express F508del-CFTR. Cells were maintained in cell culture media (High Glucose DMEM (Gibco) supplemented w/ 10% FBS (Gibco)). For the assay, cells were trypsinized (0.25% Trypsin-EDTA solution (Gibco)) and resuspended in assay media (cell culture media + 1% Pen/Strep (Gibco)) at a density of 320,000 cells per ml. Cells were dispensed to the assay plates (Corning 3712) in 25 ul using a Wellmate (Matrix/Thermo). Plates were incubated overnight at 37C, 5% CO2 and high humidity. The next day, compounds were prepared by making a dilution in assay media to a concentration of either 150 uM or 60 ug/ml (6x) depending on the library being screened. Then 5 ul of the diluted compound was transferred to the assay plate containing the cells. Assay plates were incubated for 24 hours 37C, 5% CO2 and high humidity. Following incubation with the compounds, relative cell number was determined by adding 3 ul of alamarBlue (TREK Diagnostics) and incubating the plates at 37C, 5% CO2 and high humidity, until cell control values reached ~4 million, as measured with a fluorescent intensity protocol on an Envision multimode plate reader (Perkin Elmer) (excitation 535 nm, emission 595 nm wavelengths) . Following the alamarBlue read, the media was removed and the cells were fixed with the addition of 13 ul of 4% paraformaldehyde in PBS (pH 7.4) and incubated for 10 minutes at room temperature. Plates were washed twice with PBS to remove the fixative. Cells were permeabilized with the addition of blocking solution (PBS, 0. 1% Triton X-100, 10 mg/ml BSA) and incubated at room temperature for 30 minutes. The blocking solution was removed and the primary antibody mixture was added in 13ul (Antibodies UNC570 and UNC596; CFF Therapeutics, Inc., Bedford, MA) at a 1/5000 dilution of each antibody in blocking solution. Plates were then incubated over night at 4oC. Primary antibody was removed by washing three times with 50 ul of wash solution (PBS, 0.1% Triton X-100) with at least 5 minutes between wash cycles. Secondary antibody (Alexa 488 anti-mouse IgG Invitrogen) was then added in a volume of 13 ul (1/1000 dilution in blocking solution) and incubated for two hours at room temperature in the dark. To remove excess secondary antibody, plates were washed three times with 50 ul of wash solution and one time with 50 ul of PBS. Plates were read from the bottom using a fluorescent intensity protocol on an Envision multimode plate reader (485 nm excitation and 535 nm emission).
To minimize the disruption of the cell monolayer during the numerous washes, the following process was used. The removal of media or other reagents for the wells of the microtiter plate was done using a Biomek FX (Beckman, Fullerton CA) with a 384 tip multichannel head. Aspiration was done at a slow rate following the liquid level with the tip positioned in the top right corner of the well. All solution additions, starting with the fixative, were done with a Matrix Wellmate. Again to avoid disturbing the cell monolayer, the plate offset was adjusted so that the liquid dispensed to the left wall of the well rather than directly on the cell monolayer.
For the screen, approximately ten thousand compounds from a mix of FDA and diverse libraries (MicroSource Pharmacon-1600 (FDA), Enzo (FDA), Selleck (FDA) and Enamine) were tested at a final concentration 25 uM (Enzo, Selleck & MS Pharmakon) or 10 ug/ml (Enamine 30K diversity set). The proteasome inhibitor ALLN was used as the positive control (50 uM) and 100 uM Hyamine was used as a viability control on all microtiter plates. All wells including the cell controls contained 0.5% DMSO. In-plate controls were used to normalize the data and results were reported as fold increase above the cell control and normalized to relative cell number derived from the alamarBlue data.
Ninety six compounds identified in the single dose screen were evaluated further in dose response. Compound high dose was twice the screening concentration and a ten point series of two fold dilutions were done for each compound. DMSO concentration was 1% for in all wells. Compounds were evaluated in both the immunostain assay and in the cell viability assay.

Data Analysis: Thirty two control wells containing cells only, 24 wells containing Hyamine and 8 wells containing ALLN were included on each assay plate and used to calculate Z' value for each plate and to normalize the data on a per plate basis. Data were analyzed using the IDBS Activity Base software. Results were expressed as Fold Increase (FI) for the immunostain assay and cell viability (V) for the alamarBlue assay. Final data was reported as Normalized fold increase (NFI). Data was analyzed as follows FI=DataValue/Median cell control, V= (DataValue-median Hyamine control)/(median cell control -median Hyamine control) and NFI=FI/V.

For the immunostain dose response assay, IC50 values were calculated for active compounds by plotting the FI for each concentration, and using a 4 parameter Levenburg-Marquardt algorithm with the minimum limit set at 0. Similarly, EC50 values were calculated for the cell viability dose response assay, plotting the % Viability at each concentration and also using a 4 parameter Levenburg-Marquardt algorithm with the minimum limit set at 0 and the maximum limit set at 100.

Outcome- From the primary screen, compounds selected as Active were those that met one of the following two criteria: (1) Fold Induction >/= 1.5, Cell Viability >/= 50% and the ratio of Fold Induction to Cell Viability >/= 1.5; or (2) Fold Induction >/= 1, Cell Viability >/= 50% and the ratio of Fold Induction to Cell Viability >/=1.75. While 101 compounds met this criteria, 96 were ultimately selected for confirmatory screening. For the dose response screen, compounds were labeled as "Active" if they showed at least 8 fold increase over the ALLN control at any concentration.

Comment: Possible Artifacts: Possible artifacts in this assay include, but are not limited to, compounds that are fluorescent, absorb at the excitation or emission wavelengths, or non-specifically upregulate protein expression

External ID: CGM data for Cell Systems paper Dec 2015

Protocol: Yeast strains and Media:
All S. cerevisiae deletion strains were obtained from the Euroscarf deletion collection. The wild type parental strain for this collection is BY 4741 MATa his31 leu20 met150 ura30. An isogenic pdr1pdr3 strain (MT2481) was created using PDR1::nat and PDR::URA3 deletion cassettes. All strains were grown and screened in synthetic complete (SC) medium with 2% glucose.

Handling:
Strains were seeded at 50,000 cells per well in a volume of 100 L in 96 well plates followed by addition of 2 L of 1 mM compound stock for final concentration of 20 M. Screens were conducted in technical duplicate using a Biomek FX liquid handling workstation with an integrated stacker carousel. DMSO solvent only controls and 10 uM cycloheximide positive controls were seeded in columns 1 and 12 of each assay plate. Plates were incubated at 30 C without shaking for approximately 18 h or until culture saturation was achieved for the solvent controls. Cultures were resuspended by shaking on the robotic platform prior to reading OD600 values on either Tecan M1000 or Tecan Sunrise plate readers.

Analysis procedure:
All data was subjected to the following workflow:
1. Consistent spatial effects on growth across plates were corrected by Lowess regression using an empirically estimated sliding window of 1/3 and normalized based on plate median.
2. If more than 30% of compounds were active within a plate, data was normalized to DMSO controls.
3. Median normalization was applied to all plates and experiments.
4. Z-factors for growth inhibition were calculated using the median and the interquartile range (IQR) by fitting a normal distribution with N(1,IQR) to the experimental data. In addition, we calculated the Z-factor, percent inhibition and normalized OD values for manual validation.
5. Data points with high variation between replicates (> 3 MAD) were removed as inconsistent outliers.

BioAssay submission file header:

Pubchem_ext_datasource_regid: compound identifier used in on chemgrid.org/cgm
Orf yeast gene deletion (open reading frame)
Sym# yeast gene deletion gene symbol
Raw OD read 1 first replicate
Raw OD read 2 second replicate
Normalized OD average normalized read based on workflow described above
Z_score Z-Score calculated based on kernel density distribution from normalized average reads per screen
P_value p-value calculated based on kernel density distribution calculated from average reads per screen
Non replicate test for non-replicates between first and second replicate
Pubchem_activity_outcome pubchem activity outcome
Cryptagen if compound identifier fulfilled cryptagen rule of activity in at least 4 and not more than 2/3rds of screens per library
Bioactivity sensitive if compound decreases fitness or resistant if compound increases fitness compared to negative control

Comment:

External ID: ELG271

Protocol: Please refer to other AIDs 651632 and 651634 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 ATAD5 assay (AID 651632) and cell viability counter screen (AID 651634). 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 (http://actor.epa.gov) and NTP (http://tools.niehs.nih.gov/cebs3/ui/).

External ID: Sarm1 Tir NADase inhibitors screen

Protocol: NRK1-HEK293T cells were seeded onto 150 cm2 plates at 20 x 106 cells per plate. The next day, the cells were transfected with 15 microg FCIV-SST (SAM-TIR expression plasmid) using X-tremeGENE 9 DNA Transfection Reagent (Roche product #06365787001). The cultures were supplemented with 1 mM nicotinamide riboside at time of transfection to minimize toxicity from SAM-TIR overexpression. Forty-eight hours after transfection, cells were harvested, pelleted by centrifugation at 1,000 rpm (Sorvall ST 16R centrifuge, Thermo Fisher), and washed once with cold PBS (0.01 M phosphate buffered saline NaCl 0.138 M; KCl 0.0027 M; pH 7.4). The cells were resuspended in PBS with protease inhibitors (Complete protease inhibitor cocktail, Roche product # 11873580001) and cell lysates were prepared by sonication (Branson Sonifer 450, output = 3, 20 episodes of stroke). The lysates were centrifuged (12,000xg for 10 min at 4 degrees C) to remove cell debris and the supernatants (containing SARM1 SAM-TIR protein) were stored at -80 degrees C for later use in the in vitro SARM1 SAM-TIR NADase assay (see below). Protein concentration was determined by the Bicinchoninic (BCA) method.

This screen is an adaptation of the NAD/NADH Glo assay (Promega G9071). In this assay, NAD cycling enzymes convert NAD into NADH. In the presence of NADH, the reductase enzymatically converts a proluciferin reductase substrate into luciferin. Luciferin is detected using Ultra-GloTM rLuciferase, and the chemiluminescence intensity is proportional to the amount of NAD and NADH in the sample. In our diluted lysate alone, the amount of NAD and NADH is undetectable with this assay precluding any endogenous contribution to the final NAD detected. The assay was set up as follows: 2 microl candidate inhibitor (final concentration 1 microM, 2% DMSO), 0.07 microg lysate (2 microl), and 2 microl of 400 nM NAD. The reaction was incubated at 37 degrees C for 60 min, then 6 microl NAD/NADH Glo detection reagent was added. After 30 min at room temperature, the luminescent signals were quantified using a Cytation5 imaging reader (BioTek). The SARM1 SAM-TIR lysate catalyzed a dose-dependent depletion of NAD, whereas NAD levels did not decline when reactions were performed with lysate prepared from control NRK1-HEK293T cells.

Comment:

External ID: TRN186

Protocol: Tox21 Assay Protocol Summary:

GH3.TRE-Luc cells were dispensed at 1500 cells/4 uL/well into 1536-well white solid bottom plates using a Multidrop Combi dispenser (Thermo Fisher Scientific Inc., Waltham, MA). After the assay plates were incubated at 37 C for 4 hours, 23 nL of library compound or DMSO controls was transferred to the assay plates by a pintool station (Kalypsys, San Diego, CA), followed by addition of 1 ul of T3 (1 nM, final concentration in the wells) to stimulate TR transactivation. The assay plates were incubated at 37 C for 23.5 h, and then 1 uL of CellTiter-Fluor reagent (Promega, Madision, WI) of measuring cytotoxicity was added to each well using a Bioraptr Flying Reagent Dispenser (FRD) workstation (Beckman Coulter, Indianapolis, IN, USA). The plates were incubated at 37 C and 5% CO2 for additional 30 min, and fluorescence intensity was measured by a ViewLux plate reader (PerkinElmer, Shelton, CT). For measuring luciferase reporter gene activity, 4 uL of ONE-Glo Luciferase Assay reagent (Promega) was added to each well using a Bioraptr FRD (Beckman Coulter), followed by 30 min incubation at room temperature. The luminescence intensity of plates was recorded by a ViewLux plate reader (PerkinElmer, Shelton, CT).

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: TRV455

Protocol: Tox21 Assay Protocol Summary:

GH3.TRE-Luc cells were dispensed at 1500 cells/4 uL/well into 1536-well white solid bottom plates using a Multidrop Combi dispenser (Thermo Fisher Scientific Inc., Waltham, MA). After the assay plates were incubated at 37 C for 4 hours, 23 nL of library compound or DMSO controls was transferred to the assay plates by a pintool station (Kalypsys, San Diego, CA), followed by addition of 1 ul of T3 (1 nM, final concentration in the wells) to stimulate TR transactivation. The assay plates were incubated at 37 C for 23.5 h, and then 1 uL of CellTiter-Fluor reagent (Promega, Madision, WI) of measuring cytotoxicity was added to each well using a Bioraptr Flying Reagent Dispenser (FRD) workstation (Beckman Coulter, Indianapolis, IN, USA). The plates were incubated at 37C and 5% CO2 for additional 30 min, and fluorescence intensity was measured by a ViewLux plate reader (PerkinElmer, Shelton, CT).

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: 7124-01_Inhibitor_SinglePoint_HTS_Activity

Protocol:
Protocol:
1) Plate 10 uL BL2-NFkB-luc cells at 12.5K cells/well, using a Multidrop Combi reagent dispenser (1,250 cells/uL).
2) Add 25 nL compound or positive control, by pin transfer; IKK inhibitor VII will be used at 50 uM.
3) Incubate at 37 masculineC for 1 hour (allowing compounds to enter cells for action).
4) Add 5 uL 192 ng/mL tCD40L per well for a final concentration of 64 ng/ml using a Thermo Multidrop Combi.
5) Incubate at 37 masculineC for 4 hrs, then leave plate at RT for 30 minutes.
6) Add 15 uL SteadyGlo luciferase substrate (Promega) per well using a Thermo Multidrop Combi.
7) Incubate at RT for 5min, then read Luminescence using LJL Analyst HT plate reader.

Comment: PRESENCE OF CONTROLS: Neutral control wells (NC) and positive control wells (PC) were included on every plate.

EXPECTED OUTCOME: Active compounds result in decreasing readout signal.

NORMALIZATION:
The raw signals of the plate wells were normalized using the 'Neutral Controls Minus Inhibitors' method in Genedata Assay Analyzer (v10.0.2):
The median raw signal of the intraplate neutral control wells was set to a normalized activity value of 0.
The median raw signal of the intraplate positive control wells was set to a normalized activity value of -100.
Experimental wells values were scaled to this range.

PATTERN CORRECTION: No plate pattern correction algorithm from Genedata Condoseo (v.10.0.2) was applied.

PUBCHEM_ACTIVITY_SCORE:
This was set as equal to the mean of the normalized sample replicate activities, rounded to the nearest integer .
The minimum PUBCHEM_ACTIVITY_SCORE required for a compound to be called a hit (the activity threshold, or AT) was set at -50.

PERCENTAGE OF ACTIVE REPLICATES:
For each sample, the percentage of replicates (PCT_ACTIVE_REP) which had activity scores >= AT was determined.
The minimum percentage of replicates required for a compound to be called a hit (PAR_T) was set at 55.

PUBCHEM_ACTIVITY_OUTCOME:
Samples passing BOTH threshold criteria were assigned an outcome of 2 (active):
PUBCHEM_ACTIVITY_SCORE >= AT, and PCT_ACTIVE_REP >= PAR_T

Samples passing NEITHER threshold criteria were assigned an outcome of 1 (inactive):
PUBCHEM_ACTIVITY_SCORE < AT, and PCT_ACTIVE_REP < PAR_T

Samples passing AT only were assigned an outcome of 1 (inactive) :
PUBCHEM_ACTIVITY_SCORE >= AT, and PCT_ACTIVE_REP < PAR_T

Samples passing PAR_T only were assigned an outcome of 1 (inactive) :
PUBCHEM_ACTIVITY_SCORE < AT, and PCT_ACTIVE_REP >= PAR_T

External ID: 2125-01_Inhibitor_SinglePoint_HTS_Activity

Protocol: Protocol:
PRC2 activity was measured using Dissociation-Enhanced Lanthanide Fluoro-ImmunoAssays (DELFIA) performed on 384-well, white, streptavidin-coated plates (PerkinElmer). In short, PRC2 was diluted to 30 ng and 3 ng per well in 20 uL 2X Enzyme Buffer (50mM Tris HCl pH 8.5, 10 mM DTT, 5 mM MgCl). Compounds were pinned at 100 nL per well and reactions were initiated with 20 uL of a 5 uM SAM (NEB) solution containing 600 nM H3[21-44]-GK-biotin (AnaSpec; PRC2).

Plates were incubated at room temperature for 1 hr and then washed three times with 100 uL of Wash Buffer (50mM Tris pH 7.4, 150 mM NaCl, 0.05% Tween 20, 0.2% BSA). 50 ul of Fluoroimmunoassay (FI) Buffer (50 mM Tris HCl pH 7.8, 150 mM NaCl, 0.05% Tween 40, 25 iM DTPA, 0.2% BSA, 0.05% BGG)containing a 1:4000 dilution of anti-H3K27me2 rabbit IgG (Cell Signaling, #9728) with 691 ng/mL Eu-N1-anti-rabbit IgG (PerkinElmer)was added to each well for PRC2 reactions.

Following 1 hr incubation at room temperature, the plates were washed three times with Wash Buffer and 50 uL of Enhancement Solution (PerkinElmer) was added to each well. Plates were incubated for 30 min at room temperature and time-resolved fluorescence (TRF) was measured on Wallac Envision 2104 Multilabel Reader (400 us window, 400 us delay, 320 excitation, 615 emission).

Comment: PRESENCE OF CONTROLS: Neutral control wells (NC) and positive control wells (PC) were included on every plate.

EXPECTED OUTCOME: Active compounds result in decreasing readout signal.

NORMALIZATION:
The raw signals of the plate wells were normalized using the 'Neutral Controls Minus Inhibitors' method in Genedata Assay Analyzer (v7.0.3):
The median raw signal of the intraplate neutral control wells was set to a normalized activity value of 0.
The median raw signal of the intraplate positive control wells was set to a normalized activity value of -100.
Experimental wells values were scaled to this range.
All well activities were then multiplied by -1 to create a positive activity readout value range, to match Pubchem convention.

PATTERN CORRECTION: No plate pattern correction algorithm from Genedata Condoseo (v.7.0.3) was applied.

PUBCHEM_ACTIVITY_SCORE:
This was set as equal to the mean of the normalized sample replicate activities, rounded to the nearest integer .
The minimum PUBCHEM_ACTIVITY_SCORE required for a compound to be called a hit (the activity threshold, or AT) was set at 50.

PERCENTAGE OF ACTIVE REPLICATES:
For each sample, the percentage of replicates (PCT_ACTIVE_REP) which had activity scores >= AT was determined.
The minimum percentage of replicates required for a compound to be called a hit (PAR_T) was set at 100.

PUBCHEM_ACTIVITY_OUTCOME:
Samples passing BOTH threshold criteria were assigned an outcome of 2 (active):
PUBCHEM_ACTIVITY_SCORE >= AT, and PCT_ACTIVE_REP >= PAR_T

Samples passing NEITHER threshold criteria were assigned an outcome of 1 (inactive):
PUBCHEM_ACTIVITY_SCORE < AT, and PCT_ACTIVE_REP < PAR_T

Samples passing AT only were assigned an outcome of 3 (inconclusive) :
PUBCHEM_ACTIVITY_SCORE >= AT, and PCT_ACTIVE_REP < PAR_T

Samples passing PAR_T only were assigned an outcome of 1 (inactive) :
PUBCHEM_ACTIVITY_SCORE < AT, and PCT_ACTIVE_REP >= PAR_T

External ID: cmt-p4-fda-celltiter_regid

Protocol: Native S16 cells were seeded in white solid-bottom 1536 well plates at between 500-750 cells/6uL in DMEM medium containing 10% FBS, w/o phenol red. After overnight incubation at 37 degree Celsius/5% C02, 23 nL of compounds or DMSO were delivered to each well using a pin tool, followed by 24h-incubation at 37 degree Celsius/5% C02. Then one volume of CellTiter-Glo assay reagent (Promega) was added to each well for cell viability measured by a ViewLux plate reader (PerkinElmer). The % activity was determined by normalizing to the average readings from wells containing no cells relative to DMSO-treated cells (0% Activity). The concentration-effect curves were then classified based on curve quality (r2), response magnitude and degree of measured activity.

Comment: 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, toxic compounds are ranked higher than non-toxic compounds.
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. Toxic 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.