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BioAssay: AID 651680

Fluorescence polarization-based biochemical high throughput dose response assay for inhibitors of ArfGAP with SH3 domain, ankyrin repeat and PH domain 1 (ASAP1)

Name: Fluorescence polarization-based biochemical high throughput dose response assay for inhibitors of ArfGAP with SH3 domain, ankyrin repeat and PH domain 1 (ASAP1). ..more
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 Tested Compounds
 Tested Compounds
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Active(8)
 
 
Inactive(81)
 
 
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 Tested Substances
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Active(8)
 
 
Inactive(81)
 
 
AID: 651680
Data Source: The Scripps Research Institute Molecular Screening Center (ASAP1_INH_FP_1536_3XIC50 DRUN)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
Deposit Date: 2012-10-22

Data Table ( Complete ):           View Active Data    View All Data
Target
BioActive Compounds: 8
Related Experiments
AIDNameTypeComment
624377Fluorescence polarization-based biochemical primary high throughput screening assay to identify inhibitors of ArfGAP with SH3 domain, ankyrin repeat and PH domain 1 (ASAP1)Screeningdepositor-specified cross reference: Primary Screen (ASAP1 inhibitors in singlicate)
624386Summary of the probe development effort to identify inhibitors of ArfGAP with SH3 domain, ankyrin repeat and PH domain 1 (ASAP1)Summarydepositor-specified cross reference: Summary (ASAP1 inhibitors)
624431Fluorescence polarization-based biochemical high throughput confirmation assay for inhibitors of ArfGAP with SH3 domain, ankyrin repeat and PH domain 1 (ASAP1)Screeningdepositor-specified cross reference: Confirmation Screen (ASAP1 inhibitors in triplicate)
Description:
Source (MLPCN Center Name): The Scripps Research Institute Molecular Screening Center (SRIMSC)
Affiliation: University of North Carolina at Chapel Hill
Assay Provider: Qisheng Zhang, University of North Carolina at Chapel Hill
Network: Molecular Library Probe Production Centers Network (MLPCN)
Grant Proposal Number: 1R21NS073041 (Fast Track)
Grant Proposal PI: Qisheng Zhang, University of North Carolina at Chapel Hill
External Assay ID: ASAP1_INH_FP_1536_3XIC50 DRUN

Name: Fluorescence polarization-based biochemical high throughput dose response assay for inhibitors of ArfGAP with SH3 domain, ankyrin repeat and PH domain 1 (ASAP1).

Description:

The low molecular weight ADP-ribosylation factors (Arfs) regulate actin remodeling, vesicle trafficking, membrane lipid composition, and phospholipid metabolism (1). Arfs are members of the Ras family of GTP-binding proteins, switching between the GTP- and GDP-bound forms (2). Arf GTP binding and GTP hydrolysis is regulated by ARFGAPs (ARF GTPase-activating proteins) which associate with the Golgi apparatus and possess a conserved zinc-finger GAP catalytic domain. ARFGAPs such as ARFGAP1 and ASAP1 are found in cell structures involved in vesicle production and trafficking, adhesion, migration, and development (3, 4). ARFGAP1 promotes hydrolysis of ARF1-bound GTP and is required for dissociation of coat proteins from Golgi-derived membranes and vesicles. ARFGAP1 is stimulated by phosphoinosides and inhibited by phosphatidylcholine (4). Dysfunctional regulation of ARFGAPs has been implicated in various diseases, including cancer, alzheimer disease, and autism (3). However, the catalytic mechanism and specific disease-associated roles of ARFGAPs are unclear (2), but recent studies suggest a role for Ca2+ in stimulating ARFGAP-mediated GTP hydrolysis (2). As a result the identification of modulators of ARFGAPs would provide useful tools to elucidate ARFGAP biology (4).

References:

1. Donaldson, J.G. and C.L. Jackson, ARF family G proteins and their regulators: roles in membrane transport, development and disease. Nat Rev Mol Cell Biol, 2011. 12(6): p. 362-75.
2. Ismail, S.A., I.R. Vetter, B. Sot, and A. Wittinghofer, The structure of an Arf-ArfGAP complex reveals a Ca2+ regulatory mechanism. Cell, 2010. 141(5): p. 812-21.
3. Sabe, H., Y. Onodera, Y. Mazaki, and S. Hashimoto, ArfGAP family proteins in cell adhesion, migration and tumor invasion. Curr Opin Cell Biol, 2006. 18(5): p. 558-64.
4. Hashimoto, S., A. Hashimoto, A. Yamada, Y. Onodera, and H. Sabe, Assays and properties of the ArfGAPs, AMAP1 and AMAP2, in Arf6 function. Methods Enzymol, 2005. 404: p. 216-31.
5. Sun, W., J.L. Vanhooke, J. Sondek, and Q. Zhang, High-Throughput Fluorescence Polarization Assay for the Enzymatic Activity of GTPase-Activating Protein of ADP-Ribosylation Factor (ARFGAP). J Biomol Screen, 2011.

Keywords:

DRUN, triplicate, dose, dose response, titration, dilution, biochemical, protein, end-point, endpoint, ASAP1, ArfGAP with SH3 domain, ankyrin repeat and PH domain 1, GTPase, GAP, AMAP1, CENTB4, DDEF1, KIAA1249, PAG2, PAP, ZG14P, rfGAP with SH3 domain, ankyrin repeat and PH domain 1, FP, fluorescence, fluorescence polarization, inhibitor, inhibit, HTS, high throughput screen, AD, cancer, metastatic, neurodegenerative, 1536, Scripps Florida, The Scripps Research Institute Molecular Screening Center, SRIMSC, Molecular Libraries Probe Production Centers Network, MLPCN.
Protocol
Assay Overview:

The purpose of this biochemical assay is to determine ASAP1 inhibitory dose response curves for compounds that confirmed activity in a set of previous experiments entitled, "Fluorescence polarization-based biochemical high throughput confirmation assay for inhibitors of ArfGAP with SH3 domain, ankyrin repeat and PH domain 1 (ASAP1)" (AID 624431). ASAP1 has the ability to increase guanosine triphosphate (GTP) hydrolysis catalyzed by ARFs (ADP-ribosylation factors). The assay measures GDP levels as a function of displacement of a fluorescent GDP analog initially bound to an antibody. Specifically, this assay employs fluorescence polarization to monitor the ability of ASAP1 to enhance the capacity of human ARF1 to hydrolyze GTP (intrinsic GTPase activity) (5). Polarization is a measure of the change in molecular movement of a labeled species and is defined as the ratio of the difference between the vertical and horizontal components of emitted light over their sum. Because polarization is a dimensionless value, it is independent of the emitted light or concentration of fluorophore.

In this assay, purified ASAP1 protein (residues 325-724) is incubated with ARF (lacking its first 17 residues, previously loaded with GTP). After GTP hydrolysis the mixture is then incubated with of a fluorescent version GDP (GDP Alexa 633 Tracer), initially antibody-bound and having high fluorescence polarization (mP). Free GDP derived from ARF-mediated GTP hydrolysis displaces the fluorescent tracer from the antibody, leading to decreased mP. As designed, compounds that act as ASAP1 inhibitors will reduce GTP hydrolysis, thereby preventing displacement of the tracer, resulting in no decrease in mP. Compounds are tested in triplicate using a 10-point 1:3 dilution series starting at a maximum nomimal test concentration of 164.8 uM.

Protocol Summary:

Prior to the start of the assay, 2 uL of a solution containing 2 uM ASAP1 in assay buffer (25 mM HEPES, 150 mM NaCl, 1mM MgCl2, 1 mM DTT, pH 7.5) were dispensed into wells 5-48 and 2 uL assay buffer alone were added to wells 1-4 of a 1536 well-plate. Next, 67.41 nL of test compound in DMSO or DMSO alone (1.26% final concentration) were added to the appropriate wells and incubated for 20 minutes at 25 C.The assay was started by the addition of 2 uL of 4 uM ARF1-GTP to all wells. Plates were centrifuged and after 120 minutes of incubation at 25 C, 4 uL of detection buffer (1X Stop and Detection Buffer, 4 nM GDP Alexa 633 Tracer, and 3.8 ug/mg GDP antibody in assay buffer, were added to all wells. Plates were centrifiged and after 60 minutes incubation at 25 C, fluorescence polarization was read on an EnVision microplate reader (PerkinElmer, Turku, Finland) using a Cy5 FP filter set and a Cy5 dichroic mirror (excitation = 620 nm, emission = 688 nm). Fluorescence polarization was read for 50 seconds for each polarization plane (parallel and perpendicular).

Prior to further calculations, the following formula was used to calculate fluorescence polarization (FP):

FP = ( Raw2 - Raw1 ) / ( Raw1 + Raw2 )

Where:

Raw1 is defined as the P channel.
Raw2 is defined as the S channel.

The percent inhibition for each compound was calculated as follows:

%_Inhibition = 100 * ( ( Test_Compound - Median_Low_Control ) / ( Median_High_Control - Median_Low_Control ) )

Where:

Low_Control is defined as wells containing ASAP1, ARF1-GTP and DMSO.
Test_Compound is defined as wells containing ASAP1 and ARF1-GTP in the presence of test compound.
High_Control is defined as wells containing DMSO, ARF1-GTP but, no ASAP1 protein.

For each test compound, percent inhibition was plotted against compound concentration. A four parameter equation describing a sigmoidal dose-response curve was then fitted with adjustable baseline using Assay Explorer software (Accelrys Inc). The reported IC50 values were generated from fitted curves by solving for the X-intercept value at the 50% activation level of the Y-intercept value. In cases where the highest concentration tested (i.e. 164.8 uM) did not result in greater than 50% activation, the IC50 was determined manually as greater than 164.8 uM.

PubChem Activity Outcome and Score:

Compounds with an IC50 greater than 10 uM were considered inactive. Compounds with an IC50 equal to or less than 10 uM were considered active.

Any compound with a percent activity value < 50% at all test concentrations was assigned an activity score of zero. Any compound with a percent activity value >= 50% at any test concentration was assigned an activity score greater than zero.

Activity score was then ranked by the potency of the compounds with fitted curves, with the most potent compounds assigned the highest activity scores.

The PubChem Activity Score range for active compounds is 100-93, and for inactive compounds 92-0.

List of Reagents:

ASAP1 protein (GAP domain) (supplied by Assay Provider)
ARF1-GTP (supplied by Assay Provider)
Assay buffer containing 25 mM HEPES, 150 mM NaCl, 1mM MgCl2, 1 mM DTT at pH 7.5
Detection buffer containing 1X Stop and Detection Buffer (20 mM HEPES, 40 mM EDTA, 0.02% Brij-35), 4 nM GDP Alexa 633 Tracer (BellBrook Labs, Madison, WI), and 3.8 ug/mg GDP antibody (BellBrook Labs, Madison, WI) in assay buffer.
Ethylenediaminetetraacetic acid (Fisher BP2482-1)
Sodium chloride (Fisher, part S640-500)
Dithiothreitol (Acros, part1 6568-0250)
HEPES (Lonza, part 17-737E)
Magnesium chloride (Fisher, part M35-500)
Brij-35 (Astoria-Pacifica, part 90-0710-04)
1536-well plates (Corning, part 7561)
Comment
Due to the increasing size of the MLPCN compound library, this assay may have been run as two or more separate campaigns, each campaign testing a unique set of compounds. All data reported were normalized on a per-plate basis. Possible artifacts of this assay can include, but are not limited to: dust or lint located in or on wells of the microtiter plate, and compounds that modulate well fluorescence. All test compound concentrations reported above and below are nominal; the specific test concentration(s) for a particular compound may vary based upon the actual sample provided by the MLSMR. The MLSMR was not able to provide all compounds selected for testing in this assay.
Categorized Comment - additional comments and annotations
From BioAssay Depositor:
Assay: CurveFit [1]: Equation: =( ( [Maximal Response] * [Concentration]^[Hill Slope] ) / ( [Inflection Point Concentration]^[Hill Slope] + [Concentration]^[Hill Slope] ) ) + [Baseline Response]
Assay: CurveFit [1]: Mask: Excluded Points
Assay: Dictionary: Version: 0.1
From PubChem:
Assay Format: Biochemical
From ChEMBL:
Assay Type: Functional
Result Definitions
Show more
TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1QualifierActivity Qualifier identifies if the resultant data IC50 came from a fitted curve or was determined manually to be less than or greater than its listed IC50 concentration.String
2IC50*The concentration at which 50 percent of the activity in the inhibitor assay is observed; (IC50) shown in micromolar.FloatμM
3LogIC50Log10 of the qualified IC50 (IC50) from the inhibitor assay in M concentrationFloat
4Maximal ResponseThe maximal or asymptotic response above the baseline as concentration increases without bound.Float
5Baseline ResponseAdjustable baseline of the curve fit, minimal response value.Float
6Inflection Point ConcentrationThe concentration value for the inflection point of the curve.FloatμM
7Chi SquareA measure for the 'goodness' of a fit. The chi-square test (Snedecor and Cochran, 1989) is used to test if a sample of data came from a population with a specific distribution.Float
8Hill SlopeThe variable HillSlope describes the steepness of the curve. This variable is called the Hill slope, the slope factor, or the Hill coefficient. If it is positive, the curve increases as X increases. If it is negative, the curve decreases as X increases. A standard sigmoid dose-response curve (previous equation) has a Hill Slope of 1.0. When HillSlope is less than 1.0, the curve is more shallow. When HillSlope is greater than 1.0, the curve is steeper. The Hill slope has no units.Float
9RsquareThis statistic measures how successful the fit explains the variation of the data; R-square is the square of the correlation between the response values and the predicted response values.Float
10Response RangeThe range of Y.Float
11Excluded PointsFlags to indicate which of the dose-response points were excluded from analysis. (1) means the point was excluded and (0) means the point was not excluded.String
12Number of DataPointsOverall number of data points of normalized percent activation that was used for calculations (includes all concentration points); in some cases a data point can be excluded as outlier.Integer
13Inhibition at 0.008 uM [1] (0.008μM**)Value of % inhibition at 0.008 uM inhibitor concentration; replicate [1]Float%
14Inhibition at 0.008 uM [2] (0.008μM**)Value of % inhibition at 0.008 uM inhibitor concentration; replicate [2]Float%
15Inhibition at 0.008 uM [3] (0.008μM**)Value of % inhibition at 0.008 uM inhibitor concentration; replicate [3]Float%
16Inhibition at 0.025 uM [1] (0.025μM**)Value of % inhibition at 0.025 uM inhibitor concentration; replicate [1]Float%
17Inhibition at 0.025 uM [2] (0.025μM**)Value of % inhibition at 0.025 uM inhibitor concentration; replicate [2]Float%
18Inhibition at 0.025 uM [3] (0.025μM**)Value of % inhibition at 0.025 uM inhibitor concentration; replicate [3]Float%
19Inhibition at 0.075 uM [1] (0.075μM**)Value of % inhibition at 0.075 uM inhibitor concentration; replicate [1]Float%
20Inhibition at 0.075 uM [2] (0.075μM**)Value of % inhibition at 0.075 uM inhibitor concentration; replicate [2]Float%
21Inhibition at 0.075 uM [3] (0.075μM**)Value of % inhibition at 0.075 uM inhibitor concentration; replicate [3]Float%
22Inhibition at 0.226 uM [1] (0.226μM**)Value of % inhibition at 0.226 uM inhibitor concentration; replicate [1]Float%
23Inhibition at 0.226 uM [2] (0.226μM**)Value of % inhibition at 0.226 uM inhibitor concentration; replicate [2]Float%
24Inhibition at 0.226 uM [3] (0.226μM**)Value of % inhibition at 0.226 uM inhibitor concentration; replicate [3]Float%
25Inhibition at 0.678 uM [1] (0.678μM**)Value of % inhibition at 0.678 uM inhibitor concentration; replicate [1]Float%
26Inhibition at 0.678 uM [2] (0.678μM**)Value of % inhibition at 0.678 uM inhibitor concentration; replicate [2]Float%
27Inhibition at 0.678 uM [3] (0.678μM**)Value of % inhibition at 0.678 uM inhibitor concentration; replicate [3]Float%
28Inhibition at 2.0 uM [1] (2μM**)Value of % inhibition at 2.0 uM inhibitor concentration; replicate [1]Float%
29Inhibition at 2.0 uM [2] (2μM**)Value of % inhibition at 2.0 uM inhibitor concentration; replicate [2]Float%
30Inhibition at 2.0 uM [3] (2μM**)Value of % inhibition at 2.0 uM inhibitor concentration; replicate [3]Float%
31Inhibition at 6.1 uM [1] (6.1μM**)Value of % inhibition at 6.1 uM inhibitor concentration; replicate [1]Float%
32Inhibition at 6.1 uM [2] (6.1μM**)Value of % inhibition at 6.1 uM inhibitor concentration; replicate [2]Float%
33Inhibition at 6.1 uM [3] (6.1μM**)Value of % inhibition at 6.1 uM inhibitor concentration; replicate [3]Float%
34Inhibition at 18.3 uM [1] (18.3μM**)Value of % inhibition at 18.3 uM inhibitor concentration; replicate [1]Float%
35Inhibition at 18.3 uM [2] (18.3μM**)Value of % inhibition at 18.3 uM inhibitor concentration; replicate [2]Float%
36Inhibition at 18.3 uM [3] (18.3μM**)Value of % inhibition at 18.3 uM inhibitor concentration; replicate [3]Float%
37Inhibition at 54.9 uM [1] (54.9μM**)Value of % inhibition at 54.9 uM inhibitor concentration; replicate [1]Float%
38Inhibition at 54.9 uM [2] (54.9μM**)Value of % inhibition at 54.9 uM inhibitor concentration; replicate [2]Float%
39Inhibition at 54.9 uM [3] (54.9μM**)Value of % inhibition at 54.9 uM inhibitor concentration; replicate [3]Float%
40Inhibition at 164.7 uM [1] (164.7μM**)Value of % inhibition at 164.7 uM inhibitor concentration; replicate [1]Float%
41Inhibition at 164.7 uM [2] (164.7μM**)Value of % inhibition at 164.7 uM inhibitor concentration; replicate [2]Float%
42Inhibition at 164.7 uM [3] (164.7μM**)Value of % inhibition at 164.7 uM inhibitor concentration; replicate [3]Float%

* Activity Concentration. ** Test Concentration.
Additional Information
Grant Number: 1R21NS073041 (Fast Track)

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