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BioAssay: AID 2586

Luminescence Cell-Based Secondary HTS screen to identify cytotoxic compounds of NIH3T3 cells

Assay Overview: The assay detects compounds that are cytotoxic to NIH3T3 cells after approx. 90hrs in culture. After plating the NIH3T3 cells, compounds are added to the wells. After 90 hours culturing, all cells in the well are lysed and ATP is detected using Cell Titer Glo ..more
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 Tested Compounds
 Tested Compounds
All(27)
 
 
Active(3)
 
 
Inactive(21)
 
 
Inconclusive(3)
 
 
 Tested Substances
 Tested Substances
All(27)
 
 
Active(3)
 
 
Inactive(21)
 
 
Inconclusive(3)
 
 
 Related BioAssays
 Related BioAssays
AID: 2586
Data Source: Broad Institute (2017-02_INHIBITORS_DOSE-TITRATION_MLPCN-DRYPOWDER_TOXICITY)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
BioAssay Version:
Deposit Date: 2010-03-17
Hold-until Date: 2010-09-30
Modify Date: 2010-09-30

Data Table ( Complete ):           View Active Data    View All Data
BioActive Compounds: 3
Related Experiments
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AIDNameTypeProbeComment
1885Luminescence Cell-Based/Microorganism Primary HTS to Identify Inhibitors of T.Cruzi ReplicationScreening depositor-specified cross reference
1968Broad Institute MLPCN T. Cruzi Inhibition ProjectSummary3 depositor-specified cross reference
2010Luminescence Cell-Based Dose Response HTS Screen to Identify Cytotoxic Compounds of NIH3T3 cells.Confirmatory same project related to Summary assay
2044Luminescence Cell-Based/Microorganism Dose Confirmation HTS to Identify Inhibitors of T.Cruzi Replication.Confirmatory same project related to Summary assay
2294Luminescence Cell-Based/Microorganism Primary HTS to Identify Inhibitors of T.Cruzi InfectionConfirmatory same project related to Summary assay
2396Luminescence Cell-Based/Microorganism Confirmation at Dose of Inhibitors of T.Cruzi InfectionConfirmatory same project related to Summary assay
2630Luminescence Cell-Based/Microorganism Confirmation at dose of Inhibitors of T.Cruzi InfectionConfirmatory same project related to Summary assay
2632Fluorescence Cell-Based/Microorganism Screen to Determine Compound Effect on T. cruzi in NIH3T3 CellsScreening same project related to Summary assay
493197Intracellular Trypanosomes Measured in Cell-Based/Microorganism System Using Plate Reader - 2017-01_Inhibitor_Dose_DryPowder_Activity_Set3Confirmatory same project related to Summary assay
493247NIH/3T3(mouse embryonic fibroblast cell line) toxicity Measured in Cell-Based System Using Plate Reader - 2017-02_Inhibitor_Dose_DryPowder_Activity_Set2Confirmatory same project related to Summary assay
Description:
Keywords: NIH3T3, cytotoxic

Assay Overview: The assay detects compounds that are cytotoxic to NIH3T3 cells after approx. 90hrs in culture. After plating the NIH3T3 cells, compounds are added to the wells. After 90 hours culturing, all cells in the well are lysed and ATP is detected using Cell Titer Glo

Expected Outcome: Compounds significantly suppressing luminescence, and therefore cytotoxic to NIH3T3s will be resolved as hits. This is a counter screen to determine compounds that might yield false positive by killing host cell in T. Cruzi invasion assays.
Protocol
PROTOCOL HTS ASSAY in 384-well plate

A. Cells and parasite:
-NIH/3T3 cells (mouse embryonic fibroblast cell line)

B. Reagents, materials and culture media:
Reagents:
-DMEM with Phenol Red, high glucose, with L-glutamine and Sodium pyruvate (Cellgro, cat number: 10-013-CM)
-PSG or Penicillin-streptomycin-L-glutamine (Gibco-Invitrogen, cat number: 10378-016)
-FBS-Heat inactivated fetal bovine serum (Gibco-invitrogen, cat number: 16140-089)
-0.25% Trypsin-EDTA 1X (Gibco-Invitrogen, cat number: 25200-072)
-Sterile PBS (Phosphate Buffer Saline) 1X

-Materials:
-T175, T225 culture flasks with vented caps (BD Falcon, cat number: 353028)
-Corning Hyperflasks (Corning, cat number: 10024)
Culture medium:
-For cell propagation:
90% DMEM+Phenol red, 10% FBS, 1% PSG. Mix and filter through 0.2 microns membrane. Keep at 4#C. Warm up to 37#C in water bath before use.
-For Tc culture and assays:
98% DMEM+Phenol red, 2% FBS, 1% PSG. Mix and filter through 0.2 microns membrane. Keep at 4#C. Warm up to 37#C in water bath before use.

C. Cell Culture
NIH/3T3
Notes:
-NIH/3T3 cells are cultivated in DMEM supplemented with 10% FBS and 1% PSG in T175 or Corning Hyperflasks .
-Conditions can be adapted to other culture plate sizes.

Protocol:
-Aspirate medium.
-Rinse cells with 10 ml PBS/plate.
-Aspirate PBS.
-Add 4 ml of pre-warmed trypsin-EDTA, swirl the dish to make sure the trypsin covers all the cells.
-Leave the dish a few minutes at room temperature (usually not more than 5).
-Check that the cells are detaching.
-Add 21 ml of medium, pipet up and down to detach all the cells.
-Take 75 ul of media and add to Cellometer cassette (Nexcelom Biosciences). Using the Cellometer Auto T4 (Nexcelom Biosciences), focus so cell bodies have dark edges and clear/white centers. Select NIH3T3 preset menu, dilution 1x, display image, and count. Using this number dilute in either 2% FBS/DMEM for assays or 10% FBS/DMEM for propagation

D. Growth inhibition assay for HTS in 384 well plates:

Notes:
-Final volume per well for cells+compound is 50 ul.
-Final volume after adding substrate is ~65 ml. (evaporation of 50ul to 35 ul after 90 hrs, and then 30ul Cell titer glo)
-The assay is performed in DMEM+ 2% FBS and 1% PSG .
-Experiment set up is usually done ~12pm. Assay has to be incubated 90 hrs or a bit more.

Protocol:
-warm up medium 2% FBS/DMEM
-Trypsinize NIH/3T3 cells as described in cell culture protocol
-When NIH3T3 are detached, harvest them in DMEM- 2% FBS and 1% PSG and count using the NIH3T3 program using Cellometer Auto T4 (Nexcelom Biosciences).
-Dilute cells to 166,667 cells /ml and add to flask.
-plate 5,000 cells/50ul per well using a Thermo MultiDrop Combi liquid dispenser and a sterilized standard sized dispensing cassette adding at a fast speed in a tissue culture hood.
-Put back in incubator for 3 hours to allow cells to attach.
-Pin 50 nl compounds/DMSO to each well
-Incubate for 4 days (or minimum 90 hours).
-On day of substrate addition, prepare CELL TITER GLO
-Add 30 ul per well of 384 well plate using a Thermo MultiDrop Combi liquid dispenser and a sterilized standard sized dispensing cassette adding at a fast speed.
-Incubate for 10 minutes
-Read using the ultrasensitive luminescence program on the Envision (Perkin Elmer).
Comment
Dose Data Analysis

Neutral control (NC) wells and positive control (PC) wells were included on every plate.
Active inhibitor compounds result in decreased signal.

The raw signals of the plate wells were normalized using the 'Neutral Controls' method in Genedata Assay Analyzer (v7.0.3):
The median raw signal of the intraplate NC wells was set to a normalized activity value of 0.
2X the median raw signal of the intraplate NC wells was set to a normalized activity value of +100.
0.5X the median raw signal of the intraplate NC wells was set to a normalized activity value of -50.
Experimental wells were scaled to this range, giving an activity score as percent change in signal relative to the neutral controls.

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

IC50 values were calculated using the curve fitting strategies in Genedata
Screener Condoseo (7.0.3). IC50 values were extrapolated up to 1 log
over the highest tested concentration.


PubChem Activity Score and Outcome

PUBCHEM_ACTIVITY_SCORE:

Inactive compounds = 0
Active compounds = -10*Log(IC50)

PUBCHEM_ACTIVITY_OUTCOME:

Activity_Outcome = 1 (inactive)
IC50 > 1 log over the highest tested concentration

Activity_Outcome = 2 (active)
IC50 <= 1 log over the highest tested concentration

Activity_Outcome = 3 (inconclusive)
Curve fitting strategy resulted in a constant fit with activity >30% but <70%
or
The fit was not valid due to poor fit quality.
Categorized Comment - additional comments and annotations
From ChEMBL:
Assay Format: Cell-based
Assay Type: Functional
Assay Cell Type: NIH3T3
Result Definitions
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TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1EC50 Qualifier'<', '=', '>'String
2EC50*the concentration whereupon perceived activity reaches 50% of the maximumFloatμM
3EC50 Standard Errorthe standard error for the calculated EC50 valueFloatμM
4S0the fitted activity level at zero concentrationFloat%
5SInfthe fitted activity level at infinite concentrationFloat%
6Hill Slopethe slope at EC50Float
7Num. Pointsthe number of data points included in the plotInteger
8Max. Activitythe maximum activity value observedFloat%
9Activity at 0.000110uM (0.00011μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
10Activity at 0.000350uM (0.00035μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
11Activity at 0.00100uM (0.001μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
12Activity at 0.00300uM (0.003μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
13Activity at 0.00900uM (0.009μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
14Activity at 0.0285uM (0.03μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
15Activity at 0.0800uM (0.08μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
16Activity at 0.235uM (0.24μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
17Activity at 0.750uM (0.75μM**)The average measured activity of all accepted replicates at the specified concentrationFloat
18Activity at 2.10uM (2.1μM**)The average measured activity of all accepted replicates at the specified concentrationFloat
19Activity at 6.80uM (6.8μM**)The average measured activity of all accepted replicates at the specified concentrationFloat
20Activity at 19.5uM (19.5μM**)The average measured activity of all accepted replicates at the specified concentrationFloat

* Activity Concentration. ** Test Concentration.
Additional Information
Grant Number: MH085673-01

Data Table (Concise)
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