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BioAssay: AID 651579

Dose Response Confirmation of SKN-1 Inhibitor hits via a heat-shock counterscreen assay

Nematodes parasitize ~1/3 of humans world-wide. Helminth targeting drugs, or anthelmintics, have been used to control parasitic nematodes for decades and many species are evolving multidrug resistance. Indiverse organisms, multidrug resistance is mediated by increased expression and activity of enzymes that detoxify xenobiotics. Pharmacological compounds that target xenobiotic detoxification more ..
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 Tested Compounds
 Tested Compounds
All(127)
 
 
Active(39)
 
 
Inactive(88)
 
 
 Tested Substances
 Tested Substances
All(127)
 
 
Active(39)
 
 
Inactive(88)
 
 
AID: 651579
Data Source: Burnham Center for Chemical Genomics (SBCCG-A899-SKN1-Inh-CTR-DMSO-DR-Assay)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
BioAssay Version:
Deposit Date: 2012-09-12
Modify Date: 2013-03-15

Data Table ( Complete ):           View Active Data    View All Data
Target
BioActive Compounds: 39
Related Experiments
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AIDNameTypeComment
624304uHTS identification of SKN-1 Inhibitors in a fluoresence assayScreeningdepositor-specified cross reference
624318Summary assay for small molecule inhibitors of SKN-1Summarydepositor-specified cross reference
624474Dose Response Confirmation of SKN-1 Inhibitor hits in a fluorescence ratio assayConfirmatorysame project related to Summary assay
651563Dose ResponseConfirmation of SKN-1 Inhibitor hits in a fluorescence ratio assay - Set 2Confirmatorysame project related to Summary assay
651993SAR analysis of small molecule inhibitors of SKN-1 via a heat-shock counterscreen assayConfirmatorysame project related to Summary assay
651996SAR analysis of small molecule inhibitors of SKN-1 in a fluorescence ratio assayConfirmatorysame project related to Summary assay
652140SAR analysis to confirm small molecule inhibitors of SKN-1 in a fluorescence ratio assayConfirmatorysame project related to Summary assay
652155SAR analysis to confirm small molecule inhibitors of SKN-1 via a heat-shock counterscreen assayConfirmatorysame project related to Summary assay
652161SAR Confirmation of SKN-1 Inhibitors via an in vivo cytotoxicity scoringConfirmatorysame project related to Summary assay
652187SAR Confirmation of SKN-1 Inhibitors via an in vivo cytotoxicity scoring - round 1Confirmatorysame project related to Summary assay
652265SAR analysis to confirm small molecule inhibitors of SKN-1 in a fluorescence ratio assay , round 2Confirmatorysame project related to Summary assay
652273SAR analysis to confirm small molecule inhibitors of SKN-1 via a heat-shock counterscreen assay, round 2Confirmatorysame project related to Summary assay
652281SAR Confirmation of SKN-1 Inhibitors via an in vivo cytotoxicity scoring, round 2Confirmatorysame project related to Summary assay
743022SAR analysis to confirm small molecule inhibitors of SKN-1 in a fluorescence ratio assay, round 3Confirmatorysame project related to Summary assay
743023SAR analysis of small molecule inhibitors of SKN-1 via a heat-shock counterscreen assay, round 3Confirmatorysame project related to Summary assay
743062SAR Confirmation of SKN-1 Inhibitors via an in vivo cytotoxicity scoring, round 3Confirmatorysame project related to Summary assay
Description:
Data Source: Sanford-Burnham Center for Chemical Genomics (SBCCG)
Source Affiliation: Sanford-Burnham Medical Research Institute (SBMRI, San Diego, CA)
Network: NIH Molecular Libraries Production Centers Network (MLPCN)
Grant Number: 1R21NS067678-01
Assay Provider: Keith Choe, Ph.D., University of Florida, Fl

Nematodes parasitize ~1/3 of humans world-wide. Helminth targeting drugs, or anthelmintics, have been used to control parasitic nematodes for decades and many species are evolving multidrug resistance. Indiverse organisms, multidrug resistance is mediated by increased expression and activity of enzymes that detoxify xenobiotics. Pharmacological compounds that target xenobiotic detoxification pathways would provide much needed tools for studying multidrug resistance and could greatly increase the useful life of current and future anthelmintics. Few pharmacological compounds are available for studying and targetingmultidrug resistance and those that are available are not specific for nematodes and only target a single enzyme or class of enzymes.

The transcription factor SKN-1 activates the expression of ~100 genes predicted to promote drug modification, conjugation, or export (1-2). SKN-1 is also essential for the development of nematode embryos. Our recent studies have identified a major pathway regulating SKN-1 that is distinct from the major pathway regulating xenobiotic detoxification in mammals. SKN-1 also binds to target DNA by a unique monomeric mechanism relative to all other known basic leucine zipper factors (3,4). Therefore, SKN-1 is a promising target for the development of drugs that disrupt embryonic development, decrease stress resistance, and inhibit xenobiotic detoxification in nematodes without affecting homologous pathways in humans. The small size, simple culturing characteristics, and genetic tractability of C. elegans make it an ideal system to screen for inhibitors of xenobiotic detoxification genes.

The goal of this assay is to confirm hits in "uHTS identification of SKN-1 inhibitors in a fluorescence assay" AID 624304. Gene induction by heat in this assay is via a pathway independent of SKN-1. Therefore, compounds active in this assay are artifacts of the assay and not desired.

REFERENCES
1. Oliveira RP, Abate JP, Dilks K, Landis J, Ashraf J, Murphy CT, and Blackwell TK. Condition-adapted stress and longevity gene regulation by Caenorhabditis elegans SKN-1/Nrf. Aging Cell 8:524-541, 2009.
2. Park S-K, Tedesco PM, and Johnson TE. Oxidative stress and longevity in Caenorhabditis elegans as mediated by SKN-1. Aging Cell 8: 258-269, 2009.
3.Blackwell TK, Bowerman B, Priess JR, and Weintraub H. Formation of a monomeric DNA binding domain by SKN-1 bZIP and homeodomain elements. Science 266: 621-628, 1994.
4.Hasegawa K, and Miwa J. Genetic and cellular characterization of Caenorhabditis elegans mutants
abnormal in the regulation of many phase II enzymes. PLoS ONE 5: e11194, 2010.
Protocol
Assay Materials:
Worm strain VP596 (Phsp-16.2GFP;Pdop-3RFP) (Assay Provider)
LB Broth (Research Products L24066-1000)
Terrific Broth (Research Products T15100-5000)
Sealing Tape (Fisher Scientific 1256705)
Greiner Black 384-well plates
I. Compound Addition:
1- Transfer test compounds to columns 3-22 and DMSO to columns 1-2 and 23-24 using the Labcyte ECHO 555. Transfer volume of test compound is 320-2.5 nl of 10mM stock and 40nl - 20nl from 0.3125 mM stock for 10pt dose-response curves with concentration range 64 - 0.125 M. Wells are backfilled with DMSO to 320nl (0.64% DMSO).
II. Worm Suspension
2- Dispense 50 uL/well of worm suspension (~60 worms/well)
3- Spin down plates on Eppendorf centrifuge 5810 at 500 rpm for 1 minute.
III Heat Shock
4- Seal plates with breathable tape and Incubate plates for 1.5h and room temperature
5- Heat plates at 35 degrees C for 1h; maintain a DMSO only plate at 20 degrees C for a non-heat shock control
6- Cool plates at 20 degrees C for 4h.
IV. Reading plates:
8-Spin plates at 800 rpm for 1 min. Remove seals.
9-Read on envision for GFP/RFP ratio fluorescence.
Comment
Compounds that have IC50 <= 50 uM are confirmed as inhibitors of the reaction.
To simplify the distinction between the inactives of the primary screen and of the confirmatory screening stage, the Tiered Activity Scoring System was developed and implemented.
Activity Scoring
Activity scoring rules were devised to take into consideration compound efficacy, its potential interference with the assay and the screening stage that the data was obtained. Details of the Scoring System will be published elsewhere. Briefly, the outline of the scoring system utilized for the assay is as follows:
1) First tier (0-40 range) is reserved for primary screening data and is not applicable in this assay
2) Second tier (41-80 range) is reserved for dose-response confirmation data
a. Inactive compounds of the confirmatory stage are assigned a score value equal 41.
b. The score is linearly correlated with a compound's potency and, in addition, provides a measure of the likelihood that the compound is not an artifact based on the available information.
c. The Hill coefficient is taken as a measure of compound behavior in the assay via an additional scaling factor QC:
QC = 2.6*[exp(-0.5*nH;2) - exp(-1.5*nH;2)]
This empirical factor prorates the likelihood of target- or pathway-specific compound effect vs. its non-specific behavior in the assay. This factor is based on expectation that a compound with a single mode of action that achieved equilibrium in the assay demonstrates the Hill coefficient value of 1. Compounds deviating from that behavior are penalized proportionally to the degree of their deviation.
d. Summary equation that takes into account all the items discussed above is
Score = 44 + 6*(pIC50-3)*QC,
Where pIC50 is a negative log(10) of the IC50 value expressed in mole/L concentration units. This equation results in the Score values above 50 for compounds that demonstrate high potency and predictable behavior. Compounds that are inactive in the assay or whose concentration-dependent behavior are likely to be an artifact of that assay will generally have lower Score values.
3) Third tier (81-100 range) is reserved for resynthesized true positives and their analogues and is not applicable in this assay
Categorized Comment - additional comments and annotations
From ChEMBL:
Assay Type: Functional
Result Definitions
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TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1IC50_Mean_QualifierThis qualifier is to be used with the next TID, IC50_Mean. If the qualifier is "=", the IC50 result equals the value in that column. If the qualifier is "">"", the IC50 result is greater than that value. If the qualifier is ""<"", the IC50 result is smaller than that valueString
2IC50_Mean*IC50 value determined using a sigmoidal dose response equationFloatμM
3IC50_Qualifier_1This qualifier is to be used with the next TID, IC50_1. If the qualifier is "=", the IC50 result equals the value in that column. If the qualifier is ">", the IC50 result is greater than that value. If the qualifier is "<", the IC50 result is smaller than that valueString
4IC50_1IC50 value determined using a sigmoidal dose response equationFloatμM
5Std.Err(IC50)_1Standard Error of the IC50 valueFloatμM
6nH_1Hill coefficient determined using sigmoidal dose response equationFloat
7Excluded_Points_first_pointFlags to indicate which of the first dose-response points were excluded from analysis. (1) means the titration point was excluded and (0) means the point was not excluded.String
8% Activity at 64 uM_first_point (64μM**)% Activity at the test concentrationFloat%
9% Activity at 32 uM_first_point (32μM**)% Activity at the test concentrationFloat%
10% Activity at 16 uM_first_point (16μM**)% Activity at the test concentrationFloat%
11% Activity at 8 uM_first_point (8μM**)% Activity at the test concentrationFloat%
12% Activity at 4 uM_first_point (4μM**)% Activity at the test concentrationFloat%
13% Activity at 2 uM_first_point (2μM**)% Activity at the test concentrationFloat%
14% Activity at 1 uM_first_point (1μM**)% Activity at the test concentrationFloat%
15% Activity at 0.5 uM_first_point (0.5μM**)% Activity at the test concentrationFloat%
16% Activity at 0.25 uM_first_point (0.25μM**)% Activity at the test concentrationFloat%
17% Activity at 0.125 uM_first_point (0.125μM**)% Activity at the test concentrationFloat%
18IC50_Qualifier_2This qualifier is to be used with the next TID, IC50_2. If the qualifier is "=", the IC50 result equals the value in that column. If the qualifier is ">", the IC50 result is greater than that value. If the qualifier is "<", the IC50 result is smaller than that valueString
19IC50_2IC50 value determined using a sigmoidal dose response equationFloatμM
20Std.Err(IC50)_2Standard Error of the IC50 valueFloatμM
21nH_2Hill coefficient determined using sigmoidal dose response equationFloat
22Excluded_Points_second_pointFlags to indicate which of the second dose-response points were excluded from analysis. (1) means the titration point was excluded and (0) means the point was not excluded.String
23% Activity at 64 uM_second_point (64μM**)% Activity at the test concentrationFloat%
24% Activity at 32 uM_second_point (32μM**)% Activity at the test concentrationFloat%
25% Activity at 16 uM_second_point (16μM**)% Activity at the test concentrationFloat%
26% Activity at 8 uM_second_point (8μM**)% Activity at the test concentrationFloat%
27% Activity at 4 uM_second_point (4μM**)% Activity at the test concentrationFloat%
28% Activity at 2 uM_second_point (2μM**)% Activity at the test concentrationFloat%
29% Activity at 1 uM_second_point (1μM**)% Activity at the test concentrationFloat%
30% Activity at 0.5 uM_second_point (0.5μM**)% Activity at the test concentrationFloat%
31% Activity at 0.25 uM_second_point (0.25μM**)% Activity at the test concentrationFloat%
32% Activity at 0.125 uM_second_point (0.125μM**)% Activity at the test concentrationFloat%
33IC50_Qualifier_3This qualifier is to be used with the next TID, IC50_3. If the qualifier is "=", the IC50 result equals the value in that column. If the qualifier is ">", the IC50 result is greater than that value. If the qualifier is "<", the IC50 result is smaller than that valueString
34IC50_3IC50 value determined using a sigmoidal dose response equationFloatμM
35Std.Err(IC50)_3Standard Error of the IC50 valueFloatμM
36nH_3Hill coefficient determined using sigmoidal dose response equationFloat
37Excluded_Points_third_pointFlags to indicate which of the third dose-response points were excluded from analysis. (1) means the titration point was excluded and (0) means the point was not excluded.String
38% Activity at 64 uM_third_point (64μM**)% Activity at the test concentrationFloat%
39% Activity at 32 uM_third_point (32μM**)% Activity at the test concentrationFloat%
40% Activity at 16 uM_third_point (16μM**)% Activity at the test concentrationFloat%
41% Activity at 8 uM_third_point (8μM**)% Activity at the test concentrationFloat%
42% Activity at 4 uM_third_point (4μM**)% Activity at the test concentrationFloat%
43% Activity at 2 uM_third_point (2μM**)% Activity at the test concentrationFloat%
44% Activity at 1 uM_third_point (1μM**)% Activity at the test concentrationFloat%
45% Activity at 0.5 uM_third_point (0.5μM**)% Activity at the test concentrationFloat%
46% Activity at 0.25 uM_third_point (0.25μM**)% Activity at the test concentrationFloat%
47% Activity at 0.125 uM_third_point (0.125μM**)% Activity at the test concentrationFloat%

* Activity Concentration. ** Test Concentration.
Additional Information
Grant Number: 1R21NS067678-01

Data Table (Concise)
Data Table ( Complete ):     View Active Data    View All Data
Classification
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