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BioAssay: AID 652141

Counterscreen for inhibitors of the fructose-bisphosphate aldolase (FBA) of M. tuberculosis: Fluroescence-based biochemical high throughput Glycerophosphate Dehydrogenase-Triosephosphate Isomerase (GDH-TPI) assay to identify assay artifacts

Name: Counterscreen for inhibitors of the fructose-bisphosphate aldolase (FBA) of M. tuberculosis: Fluroescence-based biochemical high throughput Glycerophosphate Dehydrogenase-Triosephosphate Isomerase (GDH-TPI) assay to identify assay artifacts. ..more
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 Tested Compounds
 Tested Compounds
All(5569)
 
 
Active(4491)
 
 
Inactive(1078)
 
 
 Tested Substances
 Tested Substances
All(5570)
 
 
Active(4492)
 
 
Inactive(1078)
 
 
 Related BioAssays
 Related BioAssays
AID: 652141
Data Source: The Scripps Research Institute Molecular Screening Center (GDH-TPI_INH_FLINT_1536_3X%INH CSRUN for FBA INH)
BioAssay Type: Primary, Primary Screening, Single Concentration Activity Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
Deposit Date: 2013-03-20

Data Table ( Complete ):           Active    All
BioActive Compounds: 4491
Depositor Specified Assays
AIDNameTypeComment
588337Summary of the probe development efforts to identify inhibitors of the fructose-bisphosphate aldolase (FBA) of M. tuberculosissummarySummary (FBA inhibitors)
588335Counterscreen for inhibitors of the fructose-bisphosphate aldolase (FBA) of M. tuberculosis: Absorbance-based biochemical high throughput Glycerophosphate Dehydrogenase-Triosephosphate Isomerase (GDH-TPI) full deck assay to identify assay artifactsscreeningCounterscreen (GDH inhibitors in singlicate)
588726Fluorescence-based biochemical primary high throughput screening assay to identify inhibitors of the fructose-bisphosphate aldolase (FBA) of M. tuberculosisscreeningPrimary screen (FBA inhibitors in singlicate)
651616Fluorescence-based biochemical high throughput confirmation assay for inhibitors of the fructose-bisphosphate aldolase (FBA) of M. tuberculosisscreeningConfirmation screen (FBA inhibitors in triplicate)
Description:
Source (MLPCN Center Name): The Scripps Research Institute Molecular Screening Center (SRIMSC)
Affiliation: The Scripps Research Institute, TSRI
Assay Provider: Mary Jackson, Colorado State
Network: Molecular Library Probe Production Centers Network (MLPCN)
Grant Proposal Number: 1 R21 NS066438-01
Grant Proposal PI: Mary Jackson, Colorado State
External Assay ID: GDH-TPI_INH_FLINT_1536_3X%INH CSRUN for FBA INH

Name: Counterscreen for inhibitors of the fructose-bisphosphate aldolase (FBA) of M. tuberculosis: Fluroescence-based biochemical high throughput Glycerophosphate Dehydrogenase-Triosephosphate Isomerase (GDH-TPI) assay to identify assay artifacts.

Description:

The rise in antibiotic-resistant Mycobacterium tuberculosis and the lack of drugs capable of efficiently eradicating persistent bacilli responsible for life-long infections in humans emphasize the need for novel anti-TB agents with mechanisms of action different from those of existing drugs(1, 2). In fact, the latent form of Mycobacterium tuberculosis infects approximately a third of the global population (3). Class II fructose-1, 6-bisphosphate aldolase (FBA) is a key enzyme of glycolysis/gluconeogenesis induced in M. tuberculosis grown under oxygen-limiting conditions thought to mimic the physical microenvironment encountered by persistent bacilli in pulmonary lesions. Fructose bisphosphate aldolase (FBA) catalyzes the conversion of fructose bisphosphate into glyceraldehyde phosphate and dihydroxyacetone phosphate in a reversible fashion. As a result, this enzyme is a likely target for molecular tools to kill multi-drug-resistant as well as persistent M. tuberculosis (2).

Selective inhibition of FBA is expected to prevent M. tuberculosis from growing on host-derived fatty acids during persistent infection. Although ubiquitous in living organisms, FBAs can be divided into two classes which differ in their structure and reaction mechanism. While class I FBAs are the only type found in mammals, prokaryotes produce class II FBAs. The absence of class II FBAs from mammalian cells and the specificity of their structure and catalytic mechanism should make it possible to design specific inhibitors of class II enzymes that target pathogenic bacteria without affecting the host's gluconeogenetic and glycolytic pathways.

References:

1. Siegel, R.E., Emerging gram-negative antibiotic resistance: daunting challenges, declining sensitivities, and dire consequences. Respir Care, 2008. 53(4): p. 471-9.
2. Fonvielle, M., M. Coincon, R. Daher, N. Desbenoit, K. Kosieradzka, N. Barilone, B. Gicquel, J. Sygusch, M. Jackson, and M. Therisod, Synthesis and biochemical evaluation of selective inhibitors of class II fructose bisphosphate aldolases: towards new synthetic antibiotics. Chemistry, 2008. 14(28): p. 8521-9.
3. Pegan, S.D., K. Rukseree, S.G. Franzblau, and A.D. Mesecar, Structural basis for catalysis of a tetrameric class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis. J Mol Biol, 2009. 386(4): p. 1038-53.

Keywords:

counterscreen, DCSRUN, dose response, titration, CRC, triplicate, artifact, non-selective, GDH, glycerol phosphate dehydrogenase, bacteria, tuberculosis, M. Tb. TB, infection, aldolase, fructose-bisphosphate aldolase, FBA, NADH, oxidation, NAD, absorbance, abs, inhibition, enzyme, GDH, inhibitor, inhibit, decrease, HTS, high throughput screen, 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 counterscreen is to determine whether compounds act as fluorescent assay artifacts or inhibitors of the GDH-TPI helper enzymes. This assay serves as a counterscreen for the primary screen entitled "Fluorescence-based biochemical primary high throughput screening assay to identify inhibitors of the fructose-bisphosphate aldolase (FBA) of M. tuberculosis" (AID 588726).

This counterscreen is similar in format to the aforementioned assay with the only two following differences: (i) the fructose-1,6-bisphosphate substrate is replaced with glyceraldehyde 3 phosphate, a product of its conversion by FBA and (ii) no (FBA) is used. The counterscreen hence recapitulates the two steps involved in the monitoring of FBA activity through the conversion of FB into the triose product glyceraldehyde 3 phosphate (G3P), which would be converted to dihydroxyacetone phosphate (DHAP) by the helper enzyme triose phosphate isomerase (TPI). A second helper enzyme, glycerophosphate dehydrogenase (GDH), converts the dihydroxyacetone phosphate to glycerol-3-phosphate with the concomitant oxidation of NADH to NAD, which is monitored by measuring the absorbance at 340 nm. In this new assay format, the A340 is independent of FBA activity, hence compounds that reduce absorbance at 340 nm are either absorbance artifacts or helper enzyme inhibitors that will not be pursued. Compounds are tested in triplicate at a nominal concentration of 1 uM.

Protocol Summary:

Prior to the start of the assay, 5 uL /well of Buffer A (50 mM HEPES, 0.01% Triton X-100, 10% Glycerol, pH8.0) supplemented with 400 nM ZnCl2, 160 uM NADH and the helper enzymes GDH-TPI (4 U/mL) was dispensed into all wells of a 1536-well plate. Positive controls wells received the same buffer, but with no GDH-TPI helper enzymes. Next, 10 nL of test compounds were delivered to each well using a PinTool. Both Positive and Negative Control wells were pinned with DMSO only. The assay was then initiated by dispensing 5 uL of Buffer A supplemented with 240 uM G3P. Plates were incubated at room temperature for 20 minutes before fluorescence was measured (Ex. 340 nm; Em. 450 nm) using the ViewLux plate reader (Perkin Elmer).

The percent inhibition for each compound was calculated as follows:

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

Where:

Test_Compound is defined as wells containing test compound.
Low_Control is defined as wells containing DMSO.
High_Control is defined as wells lacking the GDH-TPI helper enzymes and treated with DMSO

PubChem Activity Outcome and Score:

The average percent inhibition and standard deviation of each compound tested were calculated. Any compound that exhibited an average percent inhibition greater than the cutoff calculated for the Primary screen was declared active.

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

The PubChem Activity Score range for active compounds is 100-1, and for inactive compounds 1-0.

List of Reagents:

ZnCl2 (Fisher Scientific, part Z33-500)
NADH (EMD Biosciences, part 481913)
GDH-TPI (Sigma, part G1881)
HEPES (EMD Biosciences, part EM-5310)
Triton X-100 (Sigma, part T8787)
Glycerol (Fisher, part AC327255000)
Glyceraldehyde-3-phosphate (Sigma, part D7137)
TD3 reference control (Assay Provider)
1536-well plates (Corning, part 7298)
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. In this case the results of each separate campaign were assigned "Active/Inactive" status based upon that campaign's specific compound activity cutoff value. 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 quench or emit absorbance or fluorescence within the well. All test compound concentrations reported are nominal; the specific concentration for a particular test compound may vary based upon the actual sample provided by the MLSMR. The MLSMR was not able to provide all compounds selected for testing.
Result Definitions
TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1Average Inhibition at 1 uM (1μM**)Normalized percent inhibition of the primary screen at a compound concentration of 1 uM.Float%
2Standard DeviationStandard deviation derived from the normalized percent inhibition of the triplicate data for each compoundFloat
3Inhibition at 1 uM [1] (1μM**)Percent inhibition of the primary screen at a compound concentration of 1 uM.Float%
4Inhibition at 1 uM [2] (1μM**)Percent inhibition of the primary screen at a compound concentration of 1 uM.Float%
5Inhibition at 1 uM [3] (1μM**)Percent inhibition of the primary screen at a compound concentration of 1 uM.Float%

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

Data Table (Concise)
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