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BioAssay: AID 624023

qHTS for Inhibitors of mutant isocitrate dehydrogenase 1 (IDH1): confirmation assay for probe SAR

Malignant glioblastomas (WHO grade IV), including primary and secondary glioblastomas, are among the most lethal with a median survival of one year, and unfortunately they are also the most prevalent type of brain tumors [1]. By and large the standard of care of gliomas remains the use of the oral alkylating agent temozolomide and radiotherapy following surgical tumor resection [2]. There is an urgent unmet medical need for novel therapeutics for gliomas. ..more
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 Tested Compounds
 Tested Compounds
All(25)
 
 
Active(20)
 
 
Inactive(1)
 
 
Inconclusive(4)
 
 
 Tested Substances
 Tested Substances
All(25)
 
 
Active(20)
 
 
Inactive(1)
 
 
Inconclusive(4)
 
 
AID: 624023
Data Source: NCGC (IDH005)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
Deposit Date: 2012-04-05
Hold-until Date: 2013-04-04
Modify Date: 2013-04-04

Data Table ( Complete ):           Active    All
Target
BioActive Compounds: 20
Depositor Specified Assays
AIDNameTypeComment
602183qHTS for Inhibitors of mutant isocitrate dehydrogenase 1 (IDH1): SummarysummarySummary AID
Description:
Malignant glioblastomas (WHO grade IV), including primary and secondary glioblastomas, are among the most lethal with a median survival of one year, and unfortunately they are also the most prevalent type of brain tumors [1]. By and large the standard of care of gliomas remains the use of the oral alkylating agent temozolomide and radiotherapy following surgical tumor resection [2]. There is an urgent unmet medical need for novel therapeutics for gliomas.

IDH mutations occur in up to 70% of grade II-IV secondary glioblastomas, and IDH1 R132H is the most prevalent mutation [3]. Interestingly, IDH mutations are also present in ~10% of AML (acute myeloid leukemia) patients [4]. Wild-type IDH1 catalyzes the conversion of isocitrate to -ketoglutarate with the concomitant reduction of NADP+ to NADPH. In contrast, IDH1 R132H catalyzes the conversion of -ketoglutarate to 2-hydroxyglutarate (2-HG) with the concomitant oxidation of NADPH to NADP+ [5]. Recently, a second significant advancement for the field was the finding that IDH is an oncogene, and that its metabolic product 2-HG may contribute to the pathogenesis of IDH-mutated cancers. Indeed, unbiased metabolite profiling of a U87MG stable cell line engineered to express IDH1 R132H mutant protein demonstrated that mutated IDH1 confers a gain-of-function to produce the onco-metabolite 2-HG, and in effect classifying IDH1 as an oncogene [5]. These studies demonstrated the power of utilizing 2-HG as a biomarker for IDH-mutated cancers, as well as adding to the wealth of data linking the metabolite 2-HG to cancer. Although this link to cancer is tantalizing, the direct evidence of how 2-HG drives pathogenesis of gliomas and AML remains a subject of further research.

The goal of this confirmatory assay is to find small-molecule inhibitors of IDH1 R132H using a biochemical assay that measures substrate NADPH consumption through the use of a diaphorase/resazurin-coupled system. Inhibition of the IDH1 R132H enzymatic reaction leads to an increase in the amount of NADPH relative to a DMSO control and a concomitant increase in the fluorescence of the diaphorase/resazurin enzyme product resorufin at 590 nm. Compounds were screened as concentration-titration series that ranged from 100 microM to 5 nM.

NIH Molecular Libraries Probe Production Network [MLPCN]
NIH Chemical Genomics Center [NCGC]

MLSCN Grant: R03 DA032129
PI Name: Dr. Lenny Dang
Protocol
First, 1 microL/well of compound or DMSO control was dispensed into black, solid 384-well plates. Second, 25 microL/well of substrate buffer was added (20 mM Tris buffer, pH 7.5, containing final concentrations of 10 mM MgCl2, 20 mM NaCl, 0.05% BSA, 0.004 mM NADPH, and 1 mM -ketoglutarate), and the plate was spun briefly at 271xg. Third, 25 microL/well of enzyme buffer was added (20 mM Tris buffer, pH 7.5, containing final concentrations of 10 mM MgCl2, 20 mM NaCl, 0.05% BSA, 2 mM beta-ME and 2.6 nM IDH1 R132H), and the plate was briefly spun at 271xg. The plate was then shaken for 1 minute and allowed to sit at room temperature for 50 minutes before detection reagent was added (20 mM Tris buffer, pH 7.5, containing final concentrations of 10 mM MgCl2, 20 mM NaCl, 0.05% BSA, 0.32 microM diaphorase and 10 microM resazurin). The plate was spun an 271xg briefly and then shaken for 1 minute at room temperature before reading the fluorescence at 590 nm with a Spectramax M5 plate reader (Ex 544, Em 590, bodipy filter). The %Activity was determined from the corrected fluorescence values. As no specific IDH1 R132H inhibitors have been identified in the literature, 1x (2.6 nM) and 0x IDH1 R132H enzyme controls (untreated) were included to normalize %Activity of identified inhibitors; 0x enzyme values corresponded to 100%Activity (full inhibition), while 1x IDH1 R132H enzyme values were used to normalize 0%Activity (no inhibition ).

Concentration-response curves were fitted to the signals arising from the resulting fluorescence. The concentration-response curves were then classified based on curve quality (r2), response magnitude and degree of measured activity, and compounds were subsequently categorized based on their curve class. Active inhibitors showed concentration-dependent decreases in fluorescence, concordant with a decrease in IDH1 R132H activity and less substrate NADPH utilization. Inactive compounds showed no effect on fluorescence signal relative to the DMSO control.

Keywords: Isocitrate dehydrogenase, IDH1, IDH1 R132H, 2-HG, 2-hydroxyglutarate, AML, glioma, MLSMR, MLPCN, NIH Roadmap, qHTS, NCGC
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.


References:

1. Ohgaki H: Epidemiology of brain tumors. Methods Mol Biol 2009, 472:323-342.
2. Dubbink HJ, Taal W, van Marion R, Kros JM, van Heuvel I, Bromberg JE, Zonnenberg BA, Zonnenberg CB, Postma TJ, Gijtenbeek JM et al: IDH1 mutations in low-grade astrocytomas predict survival but not response to temozolomide. Neurology 2009, 73(21):1792-1795.
3. Yan H, Parsons DW, Jin G, McLendon R, Rasheed BA, Yuan W, Kos I, Batinic-Haberle I, Jones S, Riggins GJ et al: IDH1 and IDH2 mutations in gliomas. N Engl J Med 2009, 360(8):765-773.
4. Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath SD et al: Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 2009, 361(11):1058-1066.
5. Dang L, White DW, Gross S, Bennett BD, Bittinger MA, Driggers EM, Fantin VR, Jang HG, Jin S, Keenan MC et al: Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 2009, 462(7274):739-744.
Result Definitions
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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
5Activity_ScoreActivity score.Integer
6Curve_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
7Fit_LogAC50The logarithm of the AC50 from a fit of the data to the Hill equation (calculated based on Molar Units).Float
8Fit_HillSlopeThe Hill slope from a fit of the data to the Hill equation.Float
9Fit_R2R^2 fit value of the curve. Closer to 1.0 equates to better Hill equation fit.Float
10Fit_InfiniteActivityThe asymptotic efficacy from a fit of the data to the Hill equation.Float%
11Fit_ZeroActivityEfficacy at zero concentration of compound from a fit of the data to the Hill equation.Float%
12Fit_CurveClassNumerical encoding of curve description for the fitted Hill equation.Float
13Excluded_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
14Max_ResponseMaximum activity observed for compound (usually at highest concentration tested).Float%
15Activity at 0.00508 uM (0.00508053μM**)% Activity at given concentration.Float%
16Activity at 0.010 uM (0.0101611μM**)% Activity at given concentration.Float%
17Activity at 0.015 uM (0.0152416μM**)% Activity at given concentration.Float%
18Activity at 0.030 uM (0.0304832μM**)% Activity at given concentration.Float%
19Activity at 0.046 uM (0.0457247μM**)% Activity at given concentration.Float%
20Activity at 0.091 uM (0.0914495μM**)% Activity at given concentration.Float%
21Activity at 0.137 uM (0.137174μM**)% Activity at given concentration.Float%
22Activity at 0.274 uM (0.274348μM**)% Activity at given concentration.Float%
23Activity at 0.412 uM (0.411523μM**)% Activity at given concentration.Float%
24Activity at 1.224 uM (1.22396μM**)% Activity at given concentration.Float%
25Activity at 2.469 uM (2.46914μM**)% Activity at given concentration.Float%
26Activity at 3.704 uM (3.7037μM**)% Activity at given concentration.Float%
27Activity at 7.407 uM (7.40741μM**)% Activity at given concentration.Float%
28Activity at 11.11 uM (11.1111μM**)% Activity at given concentration.Float%
29Activity at 22.22 uM (22.2222μM**)% Activity at given concentration.Float%
30Activity at 33.33 uM (33.3333μM**)% Activity at given concentration.Float%
31Activity at 66.67 uM (66.6667μM**)% Activity at given concentration.Float%
32Activity at 100.00 uM (100μM**)% Activity at given concentration.Float%
33Activity at 200.0 uM (200μM**)% Activity at given concentration.Float%
34Compound QCNCGC designation for data stage: 'qHTS', 'qHTS Verification', 'Secondary Profiling'String

* Activity Concentration. ** Test Concentration.
Additional Information
Grant Number: DA032129

Data Table (Concise)
Classification
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