Bookmark and Share
BioAssay: AID 540280

Inhibitors of DNA Polymerase Beta: Hit validation

The base excision repair system in human cells is a target for therapeutic modulation of the response to irradiation treatment and DNA-damaging drugs. A key enzyme in this system is the bi-functional DNA polymerase known as DNA polymerase Beta (Pol Beta). ..more
_
   
 Tested Compounds
 Tested Compounds
All(254)
 
 
Active(220)
 
 
Inconclusive(34)
 
 
 Tested Substances
 Tested Substances
All(254)
 
 
Active(220)
 
 
Inconclusive(34)
 
 
AID: 540280
Data Source: NCGC (PolB702)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
Deposit Date: 2011-07-21

Data Table ( Complete ):           Active    All
Target
BioActive Compounds: 220
Depositor Specified Assays
AIDNameTypeComment
485311Probe Development Summary for Inhibitors of DNA Polymerase BetasummarySummary AID of project
Description:
The base excision repair system in human cells is a target for therapeutic modulation of the response to irradiation treatment and DNA-damaging drugs. A key enzyme in this system is the bi-functional DNA polymerase known as DNA polymerase Beta (Pol Beta).

The following is a homogeneous kinetic assay to study the primer extension and strand-displacement reaction catalyzed by pol beta.
Protocol
A stepwise description of the 1536-well assay is shown in next Table. Three microliters of reagents (buffer in column 3 and 4 as negative control and 10 nM Pol beta in columns 1, 2, and 5-48) was dispensed into 1,536-well black solid-bottomed plate. Compounds (23 nL) were transferred via Kalypsys pin tool equipped with 1536-pin array (10 nL slotted pins, V&P Scientific, San Diego, CA). The plates were incubated for 15 min at room temperature, and 1 uL substrate (50 nM final concentration) were added to start the reaction and immediately read at 0 min read on Viewlux reader. The plate were further incubated for 10 min at room temperature, and then read on Viewlux again. Throughout the screen, reagent bottle and all liquid lines were chilled and made light-tight to minimize reagent degradation. All screening operations were performed on a fully integrated robotic system (Kalypsys, San Diego, CA) containing one RX-130 and two RX-90 anthropomorphic robotic arms (Staubli, Duncan, SC). Library plates were screened starting from the lowest and proceeding to the highest concentration, and a double-dipping step of the highest concentration was required to access higher concentrations of compounds. Vehicle-only plates, with DMSO being pin-transferred to the entire column 5-48 compound area, were inserted uniformly at the beginning and the end of each library in order to monitor for and record any shifts in the background, which can be affected by reagent dispensers or loss in enzyme activity overtime. Screening data were corrected, normalized, and concentration-effect relationships were derived by using publicly-available curve fitting algorithms developed in-house (http://ncgc.nih.gov/pub/openhts). A four parameter Hill equation was fitted to the concentration-response data by minimizing the residual error between the modeled and observed responses.
Comment
Compound Ranking:

1. Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. See data field "Curve Description". For this assay, apparent inhibitors are ranked higher than compounds that showed apparent activation.
2. For all inactive compounds, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. Inconclusive compounds have PUBCHEM_ACTIVITY_SCORE between 1 and 39. Fit_LogAC50 was used for determining relative score and was scaled to each curve class' score range.
Result Definitions
Show more
TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1PhenotypeIndicates type of activity observed: inhibitor, activator, fluorescent, cytotoxic, inactive, or inconclusive.String
2Potency*Concentration at which compound exhibits half-maximal efficacy, AC50. Extrapolated AC50s also include the highest efficacy observed and the concentration of compound at which it was observed.FloatμM
3EfficacyMaximal efficacy of compound, reported as a percentage of control. These values are estimated based on fits of the Hill equation to the dose-response curves.Float%
4Analysis CommentAnnotation/notes on a particular compound's data or its analysis.String
5Curve_DescriptionA description of dose-response curve quality. A complete curve has two observed asymptotes; a partial curve may not have attained its second asymptote at the highest concentration tested. High efficacy curves exhibit efficacy greater than 80% of control. Partial efficacies are statistically significant, but below 80% of control.String
6Fit_LogAC50The logarithm of the AC50 from a fit of the data to the Hill equation (calculated based on Molar Units).Float
7Fit_HillSlopeThe Hill slope from a fit of the data to the Hill equation.Float
8Fit_R2R^2 fit value of the curve. Closer to 1.0 equates to better Hill equation fit.Float
9Fit_InfiniteActivityThe asymptotic efficacy from a fit of the data to the Hill equation.Float%
10Fit_ZeroActivityEfficacy at zero concentration of compound from a fit of the data to the Hill equation.Float%
11Fit_CurveClassNumerical encoding of curve description for the fitted Hill equation.Float
12Excluded_PointsWhich dose-response titration points were excluded from analysis based on outlier analysis. Each number represents whether a titration point was (1) or was not (0) excluded, for the titration series going from smallest to highest compound concentrations.String
13Max_ResponseMaximum activity observed for compound (usually at highest concentration tested).Float%
14Activity at 0.0001441714 uM (0.000144171μM**)% Activity at given concentration.Float%
15Activity at 0.0003225718 uM (0.000322572μM**)% Activity at given concentration.Float%
16Activity at 0.0004325714 uM (0.000432571μM**)% Activity at given concentration.Float%
17Activity at 0.0009677155 uM (0.000967716μM**)% Activity at given concentration.Float%
18Activity at 0.00130 uM (0.00129771μM**)% Activity at given concentration.Float%
19Activity at 0.00290 uM (0.00290315μM**)% Activity at given concentration.Float%
20Activity at 0.00465 uM (0.00464851μM**)% Activity at given concentration.Float%
21Activity at 0.00871 uM (0.00870948μM**)% Activity at given concentration.Float%
22Activity at 0.012 uM (0.0116794μM**)% Activity at given concentration.Float%
23Activity at 0.019 uM (0.0186012μM**)% Activity at given concentration.Float%
24Activity at 0.026 uM (0.0261358μM**)% Activity at given concentration.Float%
25Activity at 0.077 uM (0.0771516μM**)% Activity at given concentration.Float%
26Activity at 0.253 uM (0.25291μM**)% Activity at given concentration.Float%
27Activity at 0.705 uM (0.705467μM**)% Activity at given concentration.Float%
28Activity at 1.190 uM (1.18988μM**)% Activity at given concentration.Float%
29Activity at 2.116 uM (2.1164μM**)% Activity at given concentration.Float%
30Activity at 2.838 uM (2.8381μM**)% Activity at given concentration.Float%
31Activity at 5.810 uM (5.81023μM**)% Activity at given concentration.Float%
32Activity at 8.514 uM (8.51429μM**)% Activity at given concentration.Float%
33Activity at 19.05 uM (19.0476μM**)% Activity at given concentration.Float%
34Activity at 25.54 uM (25.5429μM**)% Activity at given concentration.Float%
35Activity at 57.14 uM (57.1429μM**)% Activity at given concentration.Float%
36Compound QCNCGC designation for data stage: 'qHTS', 'qHTS Verification', 'Secondary Profiling'String

* Activity Concentration. ** Test Concentration.
Additional Information
Grant Number: MH090863

Data Table (Concise)
Classification
PageFrom: