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BioAssay: AID 602397

Late stage Counterscreen for the probe development effort to identify inhibitors of the interaction of the Ras and Rab interactor 1 protein (Rin1) and the c-abl oncogene 1, non-receptor tyrosine kinase (Abl): Fluorescence-based biochemical dose response assay to identify GFP inhibitors and fluorescence quenchers

Name: Late stage Counterscreen for the probe development effort to identify inhibitors of the interaction of the Ras and Rab interactor 1 protein (Rin1) and the c-abl oncogene 1, non-receptor tyrosine kinase (Abl): Fluorescence-based biochemical dose response assay to identify GFP inhibitors and fluorescence quenchers. ..more
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Inactive(23)
 
 
AID: 602397
Data Source: The Scripps Research Institute Molecular Screening Center (GFP_INH_QFRET_1536_3XIC50 MDCSRUN)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
Deposit Date: 2012-03-14
Hold-until Date: 2013-03-13
Modify Date: 2013-03-13

Data Table ( Complete ):           View All Data
Target
Tested Compounds:
Related Experiments
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AIDNameTypeComment
588664TRFRET-based biochemical primary high throughput screening assay to identify inhibitors of the interaction of the Ras and Rab interactor 1 protein (Rin1) and the c-abl oncogene 1, non-receptor tyrosine kinase (Abl)Screeningdepositor-specified cross reference: Primary screen (RIN1-ABL inhibitors in singlicate)
588669Summary of the probe development efforts to identify inhibitors of the interaction of the Ras and Rab interactor 1 protein (Rin1) and the c-abl oncogene 1, non-receptor tyrosine kinase (Abl)Summarydepositor-specified cross reference: Summary (RIN1-ABL inhibitors)
602124TRFRET-based biochemical high throughput confirmation assay for inhibitors of the interaction of the Ras and Rab interactor 1 protein (Rin1) and the c-abl oncogene 1, non-receptor tyrosine kinase (Abl)Screeningdepositor-specified cross reference: Confirmation assay (RIN1-ABL interaction inhibitors in triplicate)
602125Counterscreen for inhibitors of the interaction of the Ras and Rab interactor 1 protein (Rin1) and the c-abl oncogene 1, non-receptor tyrosine kinase (Abl): Fluorescence-based biochemical high throughput assay to identify GFP inhibitors and fluorescence quenchersScreeningdepositor-specified cross reference: Counterscreen (GFP inhibitors and fluorescence quenchers in triplicate)
602181TRFRET-based biochemical high throughput dose response assay for inhibitors of the interaction of the Ras and Rab interactor 1 protein (Rin1) and the c-abl oncogene 1, non-receptor tyrosine kinase (Abl)Confirmatorydepositor-specified cross reference: Dose response assay (RIN1-ABL interaction inhibitors in triplicate)
602182Counterscreen for inhibitors of the interaction of the Ras and Rab interactor 1 protein (Rin1) and the c-abl oncogene 1, non-receptor tyrosine kinase (Abl): Fluorescence-based biochemical high throughput dose response assay to identify GFP inhibitors and fluorescence quenchersConfirmatorydepositor-specified cross reference: Dose response counterscreen(GFP inhibitors and fluorescence quenchers in triplicate)
624123Late stage Counterscreen for the probe development effort to identify inhibitors of the interaction of the Ras and Rab interactor 1 protein (Rin1) and the c-abl oncogene 1, non-receptor tyrosine kinase (Abl): Fluorescence-based biochemical dose response assay to identify GFP inhibitors and fluorescence quenchers (ROUND 1)Confirmatorydepositor-specified cross reference
624124Late stage assay for the probe development effort to identify inhibitors of the interaction of the Ras and Rab interactor 1 protein (Rin1) and the c-abl oncogene 1, non-receptor tyrosine kinase (Abl): TRFRET-based biochemical dose response assay for inhibitors of Rin1-Abl interactions (ROUND 1)Confirmatorydepositor-specified cross reference
624303Late stage assay provider assay for the probe development effort to identify inhibitors of the interaction of the Ras and Rab interactor 1 protein (Rin1) and the c-abl oncogene 1, non-receptor tyrosine kinase (Abl): Chemiluminescence-based biochemical kinase assay to identify inhibitors of Abl-mediated phosphorylation of purified CRK (powders ROUND 1)Otherdepositor-specified cross reference
686965Late stage Counterscreen for the probe development effort to identify inhibitors of the interaction of the Ras and Rab interactor 1 protein (Rin1) and the c-abl oncogene 1, non-receptor tyrosine kinase (Abl): Fluorescence-based biochemical dose response assay to identify GFP inhibitors and fluorescence quenchers (ROUND 2)Confirmatorydepositor-specified cross reference
686966Late stage assay for the probe development effort to identify inhibitors of the interaction of the Ras and Rab interactor 1 protein (Rin1) and the c-abl oncogene 1, non-receptor tyrosine kinase (Abl): TRFRET-based biochemical dose response assay for inhibitors of Rin1-Abl interactions (ROUND 2)Confirmatorydepositor-specified cross reference
602398Late stage assay for the probe development effort to identify inhibitors of the interaction of the Ras and Rab interactor 1 protein (Rin1) and the c-abl oncogene 1, non-receptor tyrosine kinase (Abl): TRFRET-based biochemical dose response assay for inhibitors of Rin1-Abl interactionsConfirmatorysame project related to Summary assay
Description:
Source (MLPCN Center Name): The Scripps Research Institute Molecular Screening Center (SRIMSC)
Affiliation: The Scripps Research Institute, TSRI
Assay Provider: John Colicelli, UCLA
Network: Molecular Library Probe Production Centers Network (MLPCN)
Grant Proposal Number: 1 R01 CA136699-01A1
Grant Proposal PI: John Colicelli, UCLA
External Assay ID: GFP_INH_QFRET_1536_3XIC50 MDCSRUN

Name: Late stage Counterscreen for the probe development effort to identify inhibitors of the interaction of the Ras and Rab interactor 1 protein (Rin1) and the c-abl oncogene 1, non-receptor tyrosine kinase (Abl): Fluorescence-based biochemical dose response assay to identify GFP inhibitors and fluorescence quenchers.

Description:

Chromosome translocations that join the BCR and ABL1 (a.k.a. c-Abl) genes give rise to BCR-ABL1 fusion proteins causative in chronic myeloid leukemia (CML), some cases of acute lymphocytic leukemia (ALL) and occasionally other myeloproliferative disorders (1). In addition, ETV6 forms fusion oncogenes with ABL1 (2) and the closely related ABL2 (a.k.a. ARG) (3) in some leukemias. ABL proteins are non-receptor tyrosine kinases normally under tight regulation, but BCR-ABL1 fusions are constitutively active. The ABL kinase inhibitor imatinib mesylate (a.k.a. STI571 or Gleevec) is an effective treatment for CML (4), demonstrating that direct oncoprotein targeting can be used to manage cancer and perhaps eventually be part of a curative therapy. Some leukemias with activated ABL oncoproteins do not respond to imatinib, however, and for CML patients who do respond there is a significant risk of developing resistance due to strong selective pressure for BCR-ABL1 kinase domain mutations that block inhibitor action (5). Resistance and relapse are even more common in BCR-ABL1 positive ALL. Some attempts have been made to circumvent resistance by reducing BCR-ABL1 expression (6, 7) or stability (8, 9) or by targeting collaborative signaling pathways (10-12). A more direct approach for improving treatment would be to maintain focus on reducing tyrosine kinase activity by targeting oncogenic ABL outside the catalytic site.

RIN1 is a RAS effector protein that binds to and activates ABL tyrosine kinases (13, 14). Signaling is initiated by low affinity binding of a proline rich sequence on RIN1 to the SH3 domain of ABL. This interaction leads to phosphorylation of RIN1 on tyrosine 36, which subsequently associates with the ABL SH2 domain. The resulting stable divalent interaction (RIN1 proline-rich motif and phospho-Tyr36 bound to ABL SH3 and SH2 domains, respectively) relieves the ABL autoinhibitory fold and leads to activation of the ABL kinase through enhanced catalytic efficiency (13). Both ABL1 and ABL2 are activated by RIN1, and this requires only the ABL SH3, SH2 and kinase domains. Activation by RIN1 is independent of ABL trans-phosphorylation and is unaffected by an imatinib-resistance mutation (13). Silencing of RIN1 results in less tyrosine phosphorylation of the ABL substrate CRKL, and deletion of the mouse Rin1 gene causes reduction in basal levels of phospho-CRKL (14). These data demonstrate that RIN1 directly stimulates the tyrosine kinase activity of ABL proteins and is required for maintaining normal ABL kinase activity.

Because human ABL fusion oncoproteins consistently retain the autoinhibitory SH3 and SH2 domains, we reasoned that these constitutively active tyrosine kinases might still be subject to positive regulation by RIN1. Indeed, RIN1 binds to and enhances the catalytic, transforming and leukemogenic properties of BCR-ABL1. Deletion of RIN1 blocked transformation of bone marrow cells by BCR-ABL1 and ETV6-ABL1. Transformation was rescued by ectopic RIN1, indicating a cell autonomous mechanism. BCR-ABL1T315I, a drug resistant mutant found in CML patients, was also dependent on RIN1 for transformation. Silencing of RIN1 in human leukemia cells reduced phospho-tyrosine levels and sensitized cells to imatinib. The dependence of BCR-ABL1 on a directly binding regulator (RIN1) provides a unique point of vulnerability that could be exploited to treat kinase inhibitor-resistant leukemias. In addition, combining drugs that inhibit BCR-ABL1 activation by RIN1 with standard ABL kinase inhibitors could provide therapy that is more efficacious and less prone to resistance and disease relapse. Finally, the concept of interference with positive regulators may be applicable to the targeted therapy of other oncogenic kinases.

References:

1. Wong, S. and O.N. Witte, The BCR-ABL story: bench to bedside and back. Annu Rev Immunol, 2004. 22: p. 247-306.
2. Papadopoulos, P., et al., The novel activation of ABL by fusion to an ets-related gene, TEL. Cancer Res, 1995. 55(1): p. 34-38.
3. Iijima, Y., et al., A new ETV6/TEL partner gene, ARG (ABL-related gene or ABL2), identified in an AML-M3 cell line with a t(1;12)(q25;p13) translocation. Blood, 2000. 95(6): p. 2126-2131.
4. Deininger, M., E. Buchdunger, and B.J. Druker, The development of imatinib as a therapeutic agent for chronic myeloid leukemia. Blood, 2005. 105(7): p. 2640-2653.
5. Gorre, M.E., et al., Clinical resistance to STI-571 cancer therapy caused by BCR-ABL gene mutation or amplification. Science, 2001. 293(5531): p. 876-880.
6. Bueno, M.J., et al., Genetic and epigenetic silencing of microRNA-203 enhances ABL1 and BCR-ABL1 oncogene expression. Cancer Cell, 2008. 13(6): p. 496-506.
7. Chen, R., V. Gandhi, and W. Plunkett, A sequential blockade strategy for the design of combination therapies to overcome oncogene addiction in chronic myelogenous leukemia. Cancer Res, 2006. 66(22): p. 10959-10966.
8. Kawano, T., et al., MUC1 oncoprotein regulates Bcr-Abl stability and pathogenesis in chronic myelogenous leukemia cells. Cancer Res, 2007. 67(24): p. 11576-11584.
9. Wu, L.X., et al., Disruption of the Bcr-Abl/Hsp90 protein complex: a possible mechanism to inhibit Bcr-Abl-positive human leukemic blasts by novobiocin. Leukemia, 2008. 22(7): p. 1402-1409.
10. Dierks, C., et al., Expansion of Bcr-Abl-positive leukemic stem cells is dependent on Hedgehog pathway activation. Cancer Cell, 2008. 14(3): p. 238-249.
11. Hess, P., et al., Survival signaling mediated by c-Jun NH(2)-terminal kinase in transformed B lymphoblasts. Nat Genet, 2002. 32(1): p. 201-205.
12. Zhao, C., et al., Hedgehog signalling is essential for maintenance of cancer stem cells in myeloid leukaemia. Nature, 2009. 458(7239): p. 776-779.
13. Cao, X., et al., Enhancement of ABL kinase catalytic efficiency by a direct binding regulator is independent of other regulatory mechanisms. J Biol Chem, 2008. 283(46): p. 31401-31407.
14. Hu, H., et al., RIN1 is an ABL tyrosine kinase activator and a regulator of epithelial-cell adhesion and migration. Curr Biol, 2005. 15(9): p. 815-823.

Keywords:

late stage, powders, purchased, synthesized, MDCSRUN, counterscreen, dose response, artifact, artifacts, non-selective, secondary, GFP, eGFP, enhanced GFP, green, green fluorescence protein, RIN1, Ras and Rab interactor 1, RIN1-ABL, JC99, ras interaction/interference protein 1, protein kinase, kinase, enzyme, Abl1, c-abl oncogene 1, non-receptor tyrosine kinase, bcr/c-abl; proto-oncogene c-Abl; proto-oncogene tyrosine-protein kinase ABL1, tyrosine-protein kinase ABL1, v-abl Abelson murine leukemia viral oncogene homolog 1, biochemical, HTRF, TR-FRET, FRET, terbium, Tb, fluor, fluorescence, inhibit, inhibitor, screen, triplicate, 1536, Scripps Florida, Scripps, The Scripps Research Institute Molecular Screening Center, SRIMSC, Molecular Libraries Probe Production Centers Network, MLPCN.
Protocol
Assay Overview:

The purpose of this assay is to determine whether powder samples of compounds identified as RIN1-ABL inhibitor probe candidates are nonselective due to quenching of eGFP and/or well FRET.

This assay determines dose response curves for compounds. This biochemical assay employs the ABL1-eGFP fusion construct incubated in the presence of test compounds, but in the absence of its binding partner RIN1-SBP. Since no interaction can occur between RIN1 and ABL in the absence of RIN1, compounds active in this assay act directly on the ABL1-eGFP protein alone or interfere with well fluorescence, and thus are not true inhibitors of the interaction between the RIN1 and ABL proteins. Compounds active in this assay are considered artifacts and will not be pursued. Compounds are tested in triplicate using a 10-point 1:3 dilution series starting at a maximum nominal concentration of 67.5 uM.

Protocol Summary:

The assay was started by dispensing 5 uL of Assay Buffer (1X Phosphate Buffered Saline) into columns 1 thru columns 3 of 1536 microtiter plates. Next, 5 uL of assay buffer containing 100 nM of ABL-eGFP were dispensed into columns 4 thru 48. Then, the plates were centrifuged and pinned with 34 nL of test compound in DMSO or DMSO alone (0.68% final concentration). The plates were incubated for 10 minutes at 25 C. Fluorescence was read on a Viewlux microplate reader (PerkinElmer, Turku, Finland) using a FITC filter set (excitation = 480 nm, emission = 540 nm) and a FITC dichroic mirror for 1 second.

The percent inhibition for each compound was calculated using as follows:

%_Inhibition = 100 * ( Ratio_Test_Compound - Median_Ratio_Low_Control ) / ( Median_Ratio_High_Control - Median_Ratio_Low_Control ) )

Where:

Test_Compound is defined as wells containing ABL-eGFP in the presence of test compound.
High_Control is defined as wells containing the no ABL-eGFP protein.
Low_Control is defined as wells containing the ABL-eGFP + DMSO.

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 (Symyx Technologies Inc). The reported IC50 values were generated from fitted curves by solving for the X-intercept value at the 50% inhibition level of the Y-intercept value. In cases where the highest concentration tested (i.e. 67.5uM) did not result in greater than 50% inhibition, the IC50 was determined manually as greater than 67.5 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, with the most potent compounds assigned the highest activity scores.

The PubChem Activity Score range for inactive compounds is 0-0. There are no active compounds.

List of Reagents:

ABL1-eGFP fusion protein (supplied by Assay Provider)
PBS (Fisher, part BP399)
1536-well plates (Corning, part 7234)
Comment
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/FRET. 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.
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
BAO: assay design: conformation reporter: protein
BAO: assay format: biochemical format: protein format: protein complex format
BAO: bioassay specification: assay biosafety level: bsl1
BAO: bioassay specification: assay footprint: microplate: 1536 well plate
BAO: bioassay specification: assay measurement throughput quality: concentration response multiple replicates
BAO: bioassay specification: assay measurement type: endpoint assay
BAO: bioassay specification: assay readout content: assay readout method: regular screening
BAO: bioassay specification: assay readout content: content readout type: single readout
BAO: bioassay specification: assay stage: secondary: counter screening
BAO: bioassay specification: bioassay type: binding
BAO: detection technology: fluorescence: fret: tr-fret
BAO: meta target detail: binding reporter specification: interaction: protein-protein
BAO: meta target: biological process target: regulation of molecular function
BAO: meta target: molecular target: protein target: enzyme: transferase: kinase
BAO: version: 1.4b1090
From PubChem:
Assay Format: Biochemical
Result Definitions
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TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
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
4Hill 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
5Baseline ResponseAdjustable baseline of the curve fit, minimal response value.Float
6Maximal ResponseThe maximal or asymptotic response above the baseline as concentration increases without bound.Float
7Inflection Point ConcentrationThe concentration value for the inflection point of the curve.FloatμM
8Response RangeThe range of Y.Float
9Chi 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
10RsquareThis 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
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 inhibition that was used for calculations (includes all concentration points); in some cases a data point can be excluded as outlier.Integer
13Inhibition at 0.003 uM [1] (0.003μM**)Value of percent inhibition at 0.003 uM compound concentration; replicate [1]Float%
14Inhibition at 0.003 uM [2] (0.003μM**)Value of percent inhibition at 0.003 uM compound concentration; replicate [2]Float%
15Inhibition at 0.003 uM [3] (0.003μM**)Value of percent inhibition at 0.003 uM compound concentration; replicate [3]Float%
16Inhibition at 0.010 uM [1] (0.01μM**)Value of percent inhibition at 0.010 uM compound concentration; replicate [1]Float%
17Inhibition at 0.010 uM [2] (0.01μM**)Value of percent inhibition at 0.010 uM compound concentration; replicate [2]Float%
18Inhibition at 0.010 uM [3] (0.01μM**)Value of percent inhibition at 0.010 uM compound concentration; replicate [3]Float%
19Inhibition at 0.031 uM [1] (0.031μM**)Value of percent inhibition at 0.031 uM compound concentration; replicate [1]Float%
20Inhibition at 0.031 uM [2] (0.031μM**)Value of percent inhibition at 0.031 uM compound concentration; replicate [2]Float%
21Inhibition at 0.031 uM [3] (0.031μM**)Value of percent inhibition at 0.031 uM compound concentration; replicate [3]Float%
22Inhibition at 0.093 uM [1] (0.093μM**)Value of percent inhibition at 0.093 uM compound concentration; replicate [1]Float%
23Inhibition at 0.093 uM [2] (0.093μM**)Value of percent inhibition at 0.093 uM compound concentration; replicate [2]Float%
24Inhibition at 0.093 uM [3] (0.093μM**)Value of percent inhibition at 0.093 uM compound concentration; replicate [3]Float%
25Inhibition at 0.278 uM [1] (0.278μM**)Value of percent inhibition at 0.278 uM compound concentration; replicate [1]Float%
26Inhibition at 0.278 uM [2] (0.278μM**)Value of percent inhibition at 0.278 uM compound concentration; replicate [2]Float%
27Inhibition at 0.278 uM [3] (0.278μM**)Value of percent inhibition at 0.278 uM compound concentration; replicate [3]Float%
28Inhibition at 0.834 uM [1] (0.834μM**)Value of percent inhibition at 0.834 uM compound concentration; replicate [1]Float%
29Inhibition at 0.834 uM [2] (0.834μM**)Value of percent inhibition at 0.834 uM compound concentration; replicate [2]Float%
30Inhibition at 0.834 uM [3] (0.834μM**)Value of percent inhibition at 0.834 uM compound concentration; replicate [3]Float%
31Inhibition at 2.5 uM [1] (2.5μM**)Value of percent inhibition at 2.5 uM compound concentration; replicate [1]Float%
32Inhibition at 2.5 uM [2] (2.5μM**)Value of percent inhibition at 2.5 uM compound concentration; replicate [2]Float%
33Inhibition at 2.5 uM [3] (2.5μM**)Value of percent inhibition at 2.5 uM compound concentration; replicate [3]Float%
34Inhibition at 7.5 uM [1] (7.5μM**)Value of percent inhibition at 7.5 uM compound concentration; replicate [1]Float%
35Inhibition at 7.5 uM [2] (7.5μM**)Value of percent inhibition at 7.5 uM compound concentration; replicate [2]Float%
36Inhibition at 7.5 uM [3] (7.5μM**)Value of percent inhibition at 7.5 uM compound concentration; replicate [3]Float%
37Inhibition at 22.5 uM [1] (22.5μM**)Value of percent inhibition at 22.5 uM compound concentration; replicate [1]Float%
38Inhibition at 22.5 uM [2] (22.5μM**)Value of percent inhibition at 22.5 uM compound concentration; replicate [2]Float%
39Inhibition at 22.5 uM [3] (22.5μM**)Value of percent inhibition at 22.5 uM compound concentration; replicate [3]Float%
40Inhibition at 67.5 uM [1] (67.5μM**)Value of percent inhibition at 67.5 uM compound concentration; replicate [1]Float%
41Inhibition at 67.5 uM [2] (67.5μM**)Value of percent inhibition at 67.5 uM compound concentration; replicate [2]Float%
42Inhibition at 67.5 uM [3] (67.5μM**)Value of percent inhibition at 67.5 uM compound concentration; replicate [3]Float%

* Activity Concentration. ** Test Concentration.
Additional Information
Grant Number: 1 R01 CA136699-01A1

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