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BioAssay: AID 624431

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

Name: Fluorescence polarization-based biochemical high throughput confirmation assay for inhibitors of ArfGAP with SH3 domain, ankyrin repeat and PH domain 1 (ASAP1) ..more
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 Tested Compounds
 Tested Compounds
All(622)
 
 
Active(230)
 
 
Inactive(392)
 
 
 Tested Substances
 Tested Substances
All(622)
 
 
Active(230)
 
 
Inactive(392)
 
 
AID: 624431
Data Source: The Scripps Research Institute Molecular Screening Center (ASAP1_INH_FP_1536_3X%INH CRUN)
BioAssay Type: Primary, Primary Screening, Single Concentration Activity Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
BioAssay Version:
Deposit Date: 2012-07-31
Modify Date: 2012-08-03

Data Table ( Complete ):           View Active Data    View All Data
Target
BioActive Compounds: 230
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)
651680Fluorescence polarization-based biochemical high throughput dose response assay for inhibitors of ArfGAP with SH3 domain, ankyrin repeat and PH domain 1 (ASAP1)Confirmatorydepositor-specified cross reference
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_3X%INH CRUN

Name: Fluorescence polarization-based biochemical high throughput confirmation 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:

confirm, confirmation, triplicate, CRUN, 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 confirm ASAP1 inhibitory activity of compounds identified as active in a set of previous experiments entitled, "Fluorescence polarization-based biochemical primary high throughput screening assay to identify inhibitors of ArfGAP with SH3 domain, ankyrin repeat and PH domain 1 (ASAP1)" (AID 624377). 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 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 at a final nominal concentration of 16.5 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.

PubChem Activity Outcome and Score:

The average percent inhibition and standard deviation of each compound tested were calculated. Any compound that exhibited a percent inhibition greater than the hit cutoff calculated for the primary screen (AID 624377) was declared active.

The reported PubChem Activity Score has been normalized to 100% observed primary inhibition. Negative % inhibition values are reported as activity score zero.

The PubChem Activity Score range for active compounds is 100-6, and for inactive compounds 6-0.

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 PubChem:
Assay Format: Biochemical
Result Definitions
TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1Average Inhibition at 16.5 uM (16.5μM**)Normalized percent inhibition of the confirmation screen at a compound concentration of 16.5 uM.Float%
2Standard DeviationStandard deviation derived from the normalized percent activation of the triplicate data for each compoundFloat
3Inhibition at 16.5 uM [1] (16.5μM**)Normalized percent inhibition of the confirmation screen at a compound concentration of 16.5 uM; replicate [1].Float%
4Inhibition at 16.5 uM [2] (16.5μM**)Normalized percent inhibition of the confirmation screen at a compound concentration of 16.5 uM; replicate [2].Float%
5Inhibition at 16.5 uM [3] (16.5μM**)Normalized percent inhibition of the confirmation screen at a compound concentration of 16.5 uM; replicate [3].Float%

** 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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