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BioAssay: AID 687028

Mammalian cell toxicity in A549 cells Measured in Cell-Based System Using Plate Reader - 2149-02_Inhibitor_Dose_CherryPick_Activity

Assay Overview: The assay uses A549 cells to counter screen in a concentration dependent manner for cytotoxicity of active compounds identified in the primary cytopathic effect assay. Cells were plated in assay ready plates (ARPs) with active compounds from the primary screen arrayed at dose, grown from 72 hours, and then assayed for cytotoxicity using CellTiter-Glo (Promega), which detects decreases to cellular ATP due to cell death. ..more
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 Tested Compounds
 Tested Compounds
All(1403)
 
 
Active(53)
 
 
Inactive(1348)
 
 
Inconclusive(2)
 
 
 Tested Substances
 Tested Substances
All(1403)
 
 
Active(53)
 
 
Inactive(1348)
 
 
Inconclusive(2)
 
 
 Related BioAssays
 Related BioAssays
AID: 687028
Data Source: Broad Institute (2149-02_Inhibitor_Dose_CherryPick_Activity)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
Deposit Date: 2013-06-15

Data Table ( Complete ):           Active    All
BioActive Compounds: 53
Depositor Specified Assays
AIDNameTypeComment
651637Broad Institute A CPE-Based HTS Assay for Antiviral Drug Screening Against Dengue Virus Inhibitor Probe ProjectsummarySummary assay
Description:
Keywords: Cytotoxicity assay, A549 cells

Assay Overview: The assay uses A549 cells to counter screen in a concentration dependent manner for cytotoxicity of active compounds identified in the primary cytopathic effect assay. Cells were plated in assay ready plates (ARPs) with active compounds from the primary screen arrayed at dose, grown from 72 hours, and then assayed for cytotoxicity using CellTiter-Glo (Promega), which detects decreases to cellular ATP due to cell death.

Expected Outcome: Compounds exhibiting a CC50 <50uM will be considered as active in this counterassay. The active compounds are considered cytotoxic, and removed from consideration as possible probe candidates. Inactive compounds will be prioritized for additional studies.
Protocol
Cytotoxicity Assay in A549 Cells

Cell Line: A549 (ATCC CCL-185)
Materials:
Propagation media: DMEM (Invitrogen, 11960), 10% FBS, 1%PSG
CellTiter-Glo: CellTiter-Glo (Promega)

Procedures:
1.1536-well assay ready plates (ARPs) were previously prepared by acoustic transfer (Echo555, LabCyte) with the addition of 10nl of compound to each well. One day before the initiation of the assay, the evaporation barriers of the ARPs were filled with MEM + 1% PSG.
2.Six to seven days prior to starting the assay, A549 cells were thawed into Propagation media and grown for 3 days. Cells were then split so as to be close to full confluency after 3-4 days.
3.A549 cells were harvested, counted, and resuspended to 75,000 cells/ml. Cells were plated into the ARPs at 375 cells/well in 5ul. The final concentration of compound ranged in concentration from 20uM to 0.15uM in the retest at dose. Plates were incubated at 37 degrees C, 5%CO2, 95% relative humidity for 72 hours.
5.After 3 days of incubation, plates were removed from the incubator to cool to room temperature for 10 minutes. Following the cooling, 1.5ul of CellTiter-Glo was added and the plates were set to incubate for 10 minutes at room temperature. At the conclusion of the incubation, plates were read with a plate reader for luminescence (0.1 sec. standard luminescence).
Comment
PRESENCE OF CONTROLS: Neutral control wells (NC; n=128) and positive control wells (PC; n=128) were included on every plate.

EXPECTED OUTCOME: Active compounds result in decreasing readout signal.
The compounds were assayed in multiple independent instances using an identical protocol; each instance is called a 'test'. For each test, the following analysis was applied:

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 (v10.0.2):
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.10.0.2) 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.

DATA AGGREGATION:
Once the data for each test was processed, the test number was appended to all column headers in that test's data set. The individual test results were then aggregated as follows:

1. The final PUBCHEM_ACTIVITY_OUTCOME was set to:
a. '2' (active) when all test outcomes were '2' (active), or
b. '1' (inactive) when all test outcomes were '1' (inactive), or
c. '3' (inconclusive) when the test outcomes were mixed.

2. The final ACTIVE_CONCENTRATION (AC) was set as follows:
a. If the final PUBCHEM_ACTIVITY_OUTCOME = 2, AC was set as the mean of the constituent test active concentrations;
b. If the final PUBCHEM_ACTIVITY_OUTCOME = 1 or 3, AC was left empty.

3. The final PUBCHEM_ACTIVITY_SCORE was calculated based on the aggregated ACTIVE_CONCENTRATION, using the same logic described above for individual test scores.

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
4ACTIVITY_OUTCOME_TEST1The PubChem Activity Outcome for the subset of data included in the indicated Test number.Integer
5ACTIVITY_SCORE_TEST1The PubChem Activity Score for the subset of data included in the indicated Test number.Integer
6ASSAYDATA_COMMENT_TEST1Comments relevant to the subset of data included in the indicated Test number.String
7AC50_Qualifier_TEST1'>','=', or '<'String
8AC50_uM_TEST1The concentration at which activity reaches 50% of the maximumFloatμM
9pAC50_M_TEST1Equal to -1*log10(AC50)String
10Hill_Slope_TEST1The slope at AC50Float
11S0_(%)_TEST1The fitted activity value at zero concentrationFloat%
12Sinf_(%)_TEST1The fitted activity value at infinite concentrationFloat%
13Num_Points_TEST1The number of data points used to generate the plotInteger
14Max_Activity_(%)_TEST1The maximum activity value observed, based on mean of replicates per concentrationFloat%
15Max_Activity_Conc_uM_TEST1The concentration at which the maximum activity is observedFloatμM
16Max_Concentration_uM_TEST1Maximum valid test concentrationFloatμM
17Activity_at_0.12uM_(%)_TEST1 (0.12μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
18Activity_at_0.135uM_(%)_TEST1 (0.135μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
19Activity_at_0.15uM_(%)_TEST1 (0.15μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
20Activity_at_0.16uM_(%)_TEST1 (0.16μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
21Activity_at_0.18uM_(%)_TEST1 (0.18μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
22Activity_at_0.26uM_(%)_TEST1 (0.26μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
23Activity_at_0.285uM_(%)_TEST1 (0.285μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
24Activity_at_0.3uM_(%)_TEST1 (0.3μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
25Activity_at_0.35uM_(%)_TEST1 (0.35μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
26Activity_at_0.5uM_(%)_TEST1 (0.5μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
27Activity_at_0.56uM_(%)_TEST1 (0.56μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
28Activity_at_0.6uM_(%)_TEST1 (0.6μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
29Activity_at_0.68uM_(%)_TEST1 (0.68μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
30Activity_at_1uM_(%)_TEST1 (1μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
31Activity_at_1.1uM_(%)_TEST1 (1.1μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
32Activity_at_1.2uM_(%)_TEST1 (1.2μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
33Activity_at_1.35uM_(%)_TEST1 (1.35μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
34Activity_at_1.95uM_(%)_TEST1 (1.95μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
35Activity_at_2.1uM_(%)_TEST1 (2.1μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
36Activity_at_2.35uM_(%)_TEST1 (2.35μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
37Activity_at_2.6uM_(%)_TEST1 (2.6μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
38Activity_at_2.85uM_(%)_TEST1 (2.85μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
39Activity_at_4.2uM_(%)_TEST1 (4.2μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
40Activity_at_4.6uM_(%)_TEST1 (4.6μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
41Activity_at_5uM_(%)_TEST1 (5μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
42Activity_at_5.6uM_(%)_TEST1 (5.6μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
43Activity_at_8uM_(%)_TEST1 (8μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
44Activity_at_9uM_(%)_TEST1 (9μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
45Activity_at_10uM_(%)_TEST1 (10μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
46Activity_at_11uM_(%)_TEST1 (11μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
47Activity_at_16uM_(%)_TEST1 (16μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
48Activity_at_18uM_(%)_TEST1 (18μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
49Activity_at_19.5uM_(%)_TEST1 (19.5μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
50Activity_at_21uM_(%)_TEST1 (21μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
51Activity_at_23.5uM_(%)_TEST1 (23.5μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
52ACTIVITY_OUTCOME_TEST2The PubChem Activity Outcome for the subset of data included in the indicated Test number.Integer
53ACTIVITY_SCORE_TEST2The PubChem Activity Score for the subset of data included in the indicated Test number.Integer
54ASSAYDATA_COMMENT_TEST2Comments relevant to the subset of data included in the indicated Test number.String
55AC50_Qualifier_TEST2'>','=', or '<'String
56AC50_uM_TEST2The concentration at which activity reaches 50% of the maximumFloatμM
57pAC50_M_TEST2Equal to -1*log10(AC50)String
58Hill_Slope_TEST2The slope at AC50Float
59S0_(%)_TEST2The fitted activity value at zero concentrationFloat%
60Sinf_(%)_TEST2The fitted activity value at infinite concentrationFloat%
61Num_Points_TEST2The number of data points used to generate the plotInteger
62Max_Activity_(%)_TEST2The maximum activity value observed, based on mean of replicates per concentrationFloat%
63Max_Activity_Conc_uM_TEST2The concentration at which the maximum activity is observedFloatμM
64Max_Concentration_uM_TEST2Maximum valid test concentrationFloatμM
65Activity_at_0.16uM_(%)_TEST2 (0.16μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
66Activity_at_0.3uM_(%)_TEST2 (0.3μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
67Activity_at_0.6uM_(%)_TEST2 (0.6μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
68Activity_at_1.2uM_(%)_TEST2 (1.2μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
69Activity_at_2.6uM_(%)_TEST2 (2.6μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
70Activity_at_5uM_(%)_TEST2 (5μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
71Activity_at_10uM_(%)_TEST2 (10μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%
72Activity_at_19.5uM_(%)_TEST2 (19.5μM**)The average measured activity of all accepted replicates at the specified concentrationFloat%

* Activity Concentration. ** Test Concentration.
Additional Information
Grant Number: 1 RO3 MH090816-01A1

Data Table (Concise)
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