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BioAssay: AID 623950

Counterscreen measuring mammalian cell toxicity screen in HeLa cells of pyoverdine inhibitors Measured in Cell-Based System Using Plate Reader - 2091-03_Inhibitor_Dose_DryPowder_Activity

Retest at dose using human epithelial adenocarcinoma HeLa cells to identify small molecules toxic to living cells. The toxicity of the small molecules will be measured by the conversion of luciferin to oxyluciferin and light (luminescence) mediated by the luciferase and the ATP present in cells. Toxic compounds will diminish intracellular ATP level in the cells and this will result in a decrease of luminescent signal. ..more
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 Tested Compounds
 Tested Compounds
All(41)
 
 
Active(7)
 
 
Inactive(34)
 
 
 Tested Substances
 Tested Substances
All(41)
 
 
Active(7)
 
 
Inactive(34)
 
 
AID: 623950
Data Source: Broad Institute (2091-03_Inhibitor_Dose_DryPowder_Activity)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
Deposit Date: 2012-03-29
Hold-until Date: 2013-03-29
Modify Date: 2013-03-29

Data Table ( Complete ):           Active    All
Target
BioActive Compounds: 7
Depositor Specified Assays
AIDNameTypeComment
488968Broad Institute Inhibitors of Pyoverdine Production ProjectsummarySummary assay
Description:
Keywords: Pyoverdine, cell toxicity and metal transport

Assay Overview:
Luciferase assay (Celltiter-Glo, Promega).
Retest at dose using human epithelial adenocarcinoma HeLa cells to identify small molecules toxic to living cells. The toxicity of the small molecules will be measured by the conversion of luciferin to oxyluciferin and light (luminescence) mediated by the luciferase and the ATP present in cells. Toxic compounds will diminish intracellular ATP level in the cells and this will result in a decrease of luminescent signal.

Expected Outcome: Compounds with an IC50 below 20 uM will be considered toxic and will be discarded for further analysis.
Protocol
Protocol: Cell toxicity assay (Hela cells)

HeLa cell line (ATCC, CCL-2trade mark) is propagated in DMEM media (Lonza, 12-614Q) supplemented with 10% heat inactivated fetal bovine serum (HyClone (Thermo Scientific, Cat# SH30071.03), 1% penicillin/streptomycin/glutamine (Invitrogen, 10378-016)) 37degrees C in CO2 incubators (Thermo Scientific) with 5% CO2, 21% O2, and 95% humidity. Cells are grown in T175 flask (BD Falcon, Ref# 353112) harvested at more than 80% confluence using 7 ml Trypsin-EDTA 0.25% (Cellgro, Cat# 25-053-CL) for 5 minutes and then the trypsin is inactivated with 7 ml of complete medium respectively. Cells are centrifuged at 1000rpm/5min and resuspended in fresh complete DMEM media with phenol red (Invitrogen, SKU# 11995) as mentioned above (for normal cell propagation) or DMEM medium without phenol red (Lonza 12-917F with 10% Heat inactivated fetal bovine serum (Invitrogen, Cat# 16140089), 1% penicillin/streptomycin/glutamine (Invitrogen, 10378-016) for compound screening. Cell number is counted using a Nexelcom Bioscience cell counter (Cellometer Auto M10) and viability is measured by mixing one volume of cells with one same volume of Trypan Blue solution (0.4%)(dilution 1/2). Only cultures of >94% viability are utilized for HTS.

Compound Screening is carried out on the Broad Institute/Chemical Biology Platform Walkup unit:

Day 1 (Cell plating):
1. HeLa cells are harvested and resuspended in DMEM without phenol red (Lonza, 12-917F) with 10% Heat inactivated fetal bovine serum (HyClone (Thermo Scientific, Cat# SH30071.03) and 1% penicillin/streptomycin/glutamine (Invitrogen, Cat#10378-016). HeLa cells (from an initial cell suspension of 50,000 cells/ml) are dispensed using a MultiDrop Combi/Standard tube dispensing cassette (Thermo Scientific) in white bottom 384 well assay plates (Corning, Cat.No. 8867BC) at a final density of 2,500 cells per well in final volume of 50 uL. The cells are kept in suspension using a magnetic bar and a stirrer during the dispensing.

2. The assay plate (cell plate) are placed in Liconic Instruments cassettes (22 plates/cassette) and incubated for 24 hours at 37 degrees C in the Liconic CO2 incubator (Liconic Instruments) calibrated at 5% CO2, 21% O2, and 95% humidity.

Day 2 (Compound pinning into assay plate):
3. The dose response compound plate (8 concentrations, 3 fold dilution, starting concentration 10 mM) are pinned twice using 384 well pin tool (100 nl) on pin table (Walkup Cybi Well) and transferred to assay plate. Pins are washed with methanol and DMSO between each pinning.
4. The assay plates treated with compounds are moving back to Liconic CO2 incubator to be incubated for an additional 48 hours.

Day 4 (Reading luminescence from assay plates with Envision):
5. Each assay plate is pulled out of the incubator and cooled down at room temperature for 30 minutes. 30 uL/well (384 well) of Celltiter-Glo luciferase reagent 0.5X (diluted in H2O) (Promega, G7573) is dispensed using the the MultiDrop Combi dispensing cassette from Thermo Scientific. The assay plate returned to room temperature for 30 minutes to allow a complete cellular lysis.

6. Luminescence is measured (0.2 second/well) using luminescence detector (384-well) in each well using the Envision plate reader (Perkin Elmer)(Corning plate setting).
Comment
PRESENCE OF CONTROLS: Neutral control wells (NC; n=150) were included on every plate.

EXPECTED OUTCOME: Active compounds result in decreasing readout signal.

ACTIVE CONCENTRATION LIMIT:
For each sample, the highest valid tested concentration (Max_Concentration) was determined and the active concentration limit (AC_limit) was set to equal (2)(Max_Concentration).

NORMALIZATION:
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 neutral controls (NC) is set to a normalized activity value of 0.
A normalized activity value of 100 is defined as (2)(NC).
A normalized activity value of -50 is defined as (0.5)(NC).
Experimental wells values were scaled to this range.

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

MEASUREMENT USED TO DETERMINE ACTIVE CONCENTRATION (AC): AC50
AC values were calculated using the curve fitting strategies in Genedata Screener Condoseo (7.0.3).
AC values were calculated up to the active concentration limit described for each sample.
pAC was set to equal -1*log10(AC)

PUBCHEM_ACTIVITY_OUTCOME:
Activity_Outcome = 1 (inactive) when:
a) compound shows activity but in a direction opposite to the expected outcome
in these cases, values describing curve fitting parameters (Sinf, S0, Hill Slope, log_AC50, log_AC50_SE) are set to null
b) curve fit is constant where activity is > -30% and < 30% at all tested concentrations, or
c) AC > AC_limit
Activity_Outcome = 2 (active) when:
AC <= AC_limit
Activity_Outcome = 3 (inconclusive) when:
a) Curve fitting strategy resulted in a constant fit with activity >= -70% but <= -30%, or
b) The fit was deemed not valid due to poor fit quality.

PUBCHEM_ACTIVITY_SCORE:
If PUBCHEM_ACTIVITY_OUTCOME = 1 (inactive) or 3 (inconclusive),
then PUBCHEM_ACTIVITY_SCORE = 0
If PUBCHEM_ACTIVITY_OUTCOME = 2 (active)
then PUBCHEM_ACTIVITY_SCORE = (10)(pAC)
Scores relate to AC in this manner:
120 = 1 pM
90 = 1 nM
60 = 1 uM
30 = 1 mM
0 = 1 M
When the active concentration (AC) is calculated to be greater than the highest valid tested concentration (Max_Concentration), the PUBCHEM_ACTIVITY_SCORE is calculated using Max_Concentration as the basis.
When the active concentration (AC) is calculated to be less than the lowest tested concentration, the PUBCHEM_ACTIVITY_SCORE is calculated using the lowest tested concentration as the basis.

Note:
The individual dose data point columns ('Activity_at_xxuM') reported here represent the median of valid (unmasked) replicate observations at each concentration. These values are the inputs to a curve fitting algorithm.
All other data columns represent values which are derived during the curve fitting algorithm; this may sometimes include automatic further masking of some replicate data points.
Occasionally this results in perceived inconsistencies: for example, between the derived 'Maximal_Activity' and the apparent most active data point.
Result Definitions
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TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1AC50_Qualifier'>','=', or '<'String
2AC50_uM*The concentration at which activity reaches 50% of the maximumFloatμM
3pAC50_MEqual to -1*log10(AC50)String
4Hill_SlopeThe slope at AC50Float
5S0_(%)The fitted activity value at zero concentrationFloat%
6Sinf_(%)The fitted activity value at infinite concentrationFloat%
7Num_PointsThe number of data points used to generate the plotInteger
8Max_Activity_(%)The maximum activity value observed, based on mean of replicates per concentrationFloat%
9Max_Activity_Conc_uMThe concentration at which the maximum activity is observedFloatμM
10Max_Concentration_uMMaximum valid test concentrationFloatμM
11Activity_at_0.0075uM_(%) (0.0075μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
12Activity_at_0.0235uM_(%) (0.0235μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
13Activity_at_0.068uM_(%) (0.068μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
14Activity_at_0.21uM_(%) (0.21μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
15Activity_at_0.6uM_(%) (0.6μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
16Activity_at_1.8uM_(%) (1.8μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
17Activity_at_5.6uM_(%) (5.6μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
18Activity_at_16uM_(%) (16μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
19Activity_at_50uM_(%) (50μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%

* Activity Concentration. ** Test Concentration.
Additional Information
Grant Number: 1 R03 MH092076-01

Data Table (Concise)
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