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BioAssay: AID 1450

SAR assay for compounds activating TNAP in the absence of phosphate acceptor performed in a luminescent assay

This TNAP dose response assay is developed and performed to confirm hits originally identified in the TNAP luminescent HTS assay (AID 1001) and to study the structure-activity relationship on analogs of the confirmed hits. Compounds are either acquired from commercial sources or synthesized internally. ..more
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 Tested Compounds
 Tested Compounds
All(39)
 
 
Active(36)
 
 
Inactive(3)
 
 
 Tested Substances
 Tested Substances
All(39)
 
 
Active(36)
 
 
Inactive(3)
 
 
AID: 1450
Data Source: Burnham Center for Chemical Genomics (BCCG-A127-TNAP-Dry-Powder)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: NIH Molecular Libraries Screening Center Network
BioAssay Version:
Deposit Date: 2008-12-18
Modify Date: 2011-01-19

Data Table ( Complete ):           View Active Data    View All Data
Target
BioActive Compounds: 36
Related Experiments
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AIDNameTypeProbeComment
518TNAP luminescent HTS assayConfirmatory depositor-specified cross reference
813HTS identification of compounds activating TNAP at intermediate concentration of phosphate acceptor detected in luminescent assayScreening depositor-specified cross reference
1001uHTS identification of compounds activating TNAP in the absence of phosphate acceptor performed in luminescent assayConfirmatory depositor-specified cross reference
1548Summary assay for compounds activating TNAP performed in a luminescent assaySummary2 depositor-specified cross reference
1659SAR assay for compounds activating TNAP in the presence of 100 mM DEA performed in a luminescence assayConfirmatory depositor-specified cross reference
1056SAR analysis of an In Vitro TNAP Dose Response Luminescent AssayConfirmatory same project related to Summary assay
1136uHTS identification of compounds activating TNAP at a high concentration of phosphate acceptor detected in a luminescent assayScreening same project related to Summary assay
1227GAPDH Dose Response Colorimetric AssayConfirmatory same project related to Summary assay
1941SAR assay for compounds inhibiting TNAP in the absence of phosphate acceptor performed in a luminescent assayConfirmatory same 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 Screening Centers Network (MLSCN)
Grant Proposal Number: 1R03 MH082385-01

This TNAP dose response assay is developed and performed to confirm hits originally identified in the TNAP luminescent HTS assay (AID 1001) and to study the structure-activity relationship on analogs of the confirmed hits. Compounds are either acquired from commercial sources or synthesized internally.

Alkaline phosphatases (EC 3.1.3.1) (APs) catalyze the hydrolysis of phosphomonoesters, releasing phosphate and alcohol. APs are dimeric enzymes found in the most organisms. In human, four isozymes of APs have been identified. Three isozymes are tissue-specific and the fourth one is tissue-non specific, named TNAP. TNAP deficiency is associated with defective bone mineralization in the form of rickets and osteomalacia. Therefore, there is therapeutic potential of modulating TNAP activity.

The goal of this HTS is to identify novel and specific activators of TNAP. The only known to date class of alkaline phosphatases activators are amino-containing alcohols, such as diethanolamine (DEA), that act as phosphoacceptor substrate and exhibit its effect in high-mM concentration range. Compounds with a similar mode of action are expected to demonstrate diminished stimulating potential if tested in the presence of DEA. Therefore, for detection of compounds with diverse mode of action, the HTS assay was optimized and HTS campaigns were performed in the presence and in the absence of DEA. The current AID reports a set of the data from screening in the absence of DEA or any other phosphate acceptor.

TNAP luminescent assay was developed and performed at the Burnham Center for Chemical Genomics (SBCCG), part of the Molecular Library Screening Center Network (MLSCN). RO3 submission, MH082385-01: Activators of the Pyrophosphatase Activity of Alkaline Phosphatase. Assay Providers: Drs. Jose Luis Millan and Eduard Sergienko, Sanford-Burnham Medical Research Institute, San Diego, CA
Protocol
TNAP assay materials:
1) TNAP protein was provided by Dr. Jose Luis Millan (Sanford-Burnham Medical Research Institute, San Diego, CA). The CDP-star was obtained from New England Biolabs.
2) Assay Buffer: 100 mM CAPS, pH 9.8, 2 mM MgCl2, and 0.04 mM ZnCl2.
3) TNAP working solution contained a 1/400 dilution in assay buffer.
4) CDP-star working solution contained 200 uM CDP-star in MQ water.
5) Negative Control (NC) solution - 5 mM levamisole.
6) Positive Control (PC) solution - 10% DMSO.
TNAP dose-response confirmation screening protocol:
1) Dose-response curves contained 10 concentrations of compounds obtained using 2-fold serial dilution. Compounds were serially diluted in 100% DMSO, and then diluted with water to 10% final DMSO concentration. 4 uL compounds in 10% DMSO were transferred into columns 3-22 of Greiner 384-well white small-volume plates (784075). Each curve was performed in duplicate.
2) Columns 1-2 and 23-24 contained 4 uL of NC and PC solutions, respectively.
3) 8 uL of TNAP working solution was added to the whole plate using WellMate bulk dispenser (Matrix).
4) 8 uL of CDP-star working solution was added to the whole plate using WellMate bulk dispenser (Matrix).
5) Plates were incubated for 30 mins at room temperature.
6) Luminescence was measured on the Envision plate reader (Perkin Elmer).
7) Data analysis was performed using CBIS software (ChemInnovations, Inc) using sigmoidal dose-response equation through non-linear regression
Comment
TNAP activation was calculated using the following formula:
Activation Factor (AF) = (Signal_Well - Mean_NC)/(Mean_PC - Mean_NC),
where Signal_Well corresponds to luminescence signal in the well with a compound, Mean_NC and Mean_PC correspond to mean values of corresponding controls in the plate.
Compounds were tested in one concentration range.
Range1 0-100 uM
For all samples in the range that resolved to an EC50 the results were averaged and reported as EC50_Range. Also the EC50 results for all of the ranges were averaged to produce EC50_Mean. Compounds with an EC50_Mean < 100 uM are considered to be active in this assay.
The EC50 and Max_value were calculated from fitting the AF vs [compound] curve according to the following equation:
AF = ((Max_Value*[compound]^nH)/EC50^nH + [compound]^nH) + 1
To simplify the distinction between the inactives of the primary screen (see AID 1001) and of the confirmatory screening stage, the Tiered Activity Scoring System was developed and implemented. Its utilization for the TNAP assay is described below.
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 TNAP assay is as follows:
1) First tier (0-40 range) is reserved for primary screening data and is not applicable to this assay
2) In this assay we tested resynthesized analogs, therefore, the second tier (41-80 range) that is reserved for dose-response confirmation data is not applicable.
3) Third tier (81-100 range) is reserved for resynthesized true positives and their analogues.
a. Inactive compounds of the confirmatory stage are assigned a score value equal 81.
b. The score is linearly correlated with a compound's activatory 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-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 TNAP activation 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 the items discussed above is
Score = 82 + 3*(pEC50-3)*QC,
where pEC50 is a negative log(10) of the EC50 value expressed in mole/L concentration units. This equation results in the Score values above 85 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. Compounds with a qualifier of < or > are calculated the Score based on their numerical part.
e. The Score of 100 was assigned to any compounds whose Score was calculated to be >100.
Categorized Comment - additional comments and annotations
From ChEMBL:
Assay Type: Binding
Result Definitions
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TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1EC50_Mean_QualifierThis qualifier is to be used with the next TID, EC50_Mean. If qualifier is "=", EC50 result equals to the value in that column;if qualifier is ">", EC50 result is greater than that value. if qualifier is "<", EC50 result is smaller than that value.String
2EC50_Mean*EC50value determined using sigmoidal dose response equationFloatμM
3EC50_Qualifier_1_Range1This qualifier is to be used with the next TID, EC50_1_Range1. If the qualifier is "=", the EC50 result equals the value in that column. If the qualifier is ">", the EC50 result is greater than that value. If the qualifier is "<", the EC50 result is smaller than that valueString
4EC50_1_Range1EC50 value determined using sigmoidal dose response equationFloatμM
5Std.Err(EC50)_1_Range1Standard Error of EC50 valueFloatμM
6nH_1_Range1Hill coefficient determined using sigmoidal dose response equationFloat
7Max_Value_1_Range1The AF value asymptotically approached by the dose response curve at saturating compound concentrationsFloat
8Excluded_Points_first_point_Range1Flags to indicate which of the first dose-response points were excluded from analysis. (1) means the titration point was (1) excluded and (0) means the point was not excluded, for the titration series going from low to high compound concentrations.String
9% inhibition at 100 uM_first_point_Range1 (100μM**)% inhibition at a given concentrationFloat%
10% inhibition at 50 uM_first_point_Range1 (50μM**)% inhibition at a given concentrationFloat%
11% inhibition at 25 uM_first_point_Range1 (25μM**)% inhibition at a given concentrationFloat%
12% inhibition at 12.5 uM_first_point_Range1 (12.5μM**)% inhibition at a given concentrationFloat%
13% inhibition at 6.25 uM_first_point_Range1 (6.25μM**)% inhibition at a given concentrationFloat%
14% inhibition at 3.125 uM_first_point_Range1 (3.125μM**)% inhibition at a given concentrationFloat%
15% inhibition at 1.5625 uM_first_point_Range1 (1.5625μM**)% inhibition at a given concentrationFloat%
16% inhibition at 0.78125 uM_first_point_Range1 (0.78125μM**)% inhibition at a given concentrationFloat%
17% inhibition at 0.390625 uM_first_point_Range1 (0.390625μM**)% inhibition at a given concentrationFloat%
18% inhibition at 0.1953125 uM_first_point_Range1 (0.195312μM**)% inhibition at a given concentrationFloat%
19Excluded_Points_second_point_Range1Flags to indicate which of the second dose-response points were excluded from analysis. (1) means the titration point was (1) excluded and (0) means the point was not excluded, for the titration series going from low to high compound concentrations.String
20% inhibition at 100 uM_second_point_Range1 (100μM**)% inhibition at a given concentrationFloat%
21% inhibition at 50 uM_second_point_Range1 (50μM**)% inhibition at a given concentrationFloat%
22% inhibition at 25 uM_second_point_Range1 (25μM**)% inhibition at a given concentrationFloat%
23% inhibition at 12.5 uM_second_point_Range1 (12.5μM**)% inhibition at a given concentrationFloat%
24% inhibition at 6.25 uM_second_point_Range1 (6.25μM**)% inhibition at a given concentrationFloat%
25% inhibition at 3.125 uM_second_point_Range1 (3.125μM**)% inhibition at a given concentrationFloat%
26% inhibition at 1.5625 uM_second_point_Range1 (1.5625μM**)% inhibition at a given concentrationFloat%
27% inhibition at 0.78125 uM_second_point_Range1 (0.78125μM**)% inhibition at a given concentrationFloat%
28% inhibition at 0.390625 uM_second_point_Range1 (0.390625μM**)% inhibition at a given concentrationFloat%
29% inhibition at 0.1953125 uM_second_point_Range1 (0.195312μM**)% inhibition at a given concentrationFloat%

* Activity Concentration. ** Test Concentration.
Additional Information
Grant Number: 1R03 MH082385-01

Data Table (Concise)
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Classification
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