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BioAssay: AID 602422

Late stage assay provider assay for AddAB inhibitors: Radioactivity-based biochemical assay to identify inhibitors of the nuclease activity of purified AddAB (100 micromolar dose)

Late stage assay provider assay for AddAB inhibitors: Radioactivity-based biochemical nuclease assay to identify inhibitors of the activity of purified AddAB (100 micromolar dose). ..more
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 Tested Compounds
 Tested Compounds
All(53)
 
 
Active(15)
 
 
Inactive(38)
 
 
 Tested Substances
 Tested Substances
All(54)
 
 
Active(16)
 
 
Inactive(38)
 
 
AID: 602422
Data Source: The Scripps Research Institute Molecular Screening Center (ADDAB-NUCLEASE_INH_RADIOACTIVITY_FILM_3X%INH (+PHAGE))
Depositor Category: NIH Molecular Libraries Probe Production Network, Assay Provider
Deposit Date: 2012-03-20
Hold-until Date: 2013-03-16
Modify Date: 2013-03-16

Data Table ( Complete ):           View Active Data    View All Data
Targets
BioActive Compounds: 15
Related Experiments
Show more
AIDNameTypeComment
435030Absorbance-based primary bacterial cell-based high throughput screening assay to identify inhibitors of AddAB recombination protein complexScreeningdepositor-specified cross reference: Primary screen (AddAB inhibitors in singlicate)
449728Counterscreen for inhibitors of AddAB: absorbance-based bacterial cell-based high throughput screening assay to identify inhibitors of bacterial viabilityScreeningdepositor-specified cross reference: Counterscreen (bacterial viability inhibitors in singlicate)
449731Summary of the probe development effort to identify inhibitors of AddAB recombination protein complexSummarydepositor-specified cross reference: Summary (AddAB inhibitors)
488942Absorbance-based bacterial cell-based high throughput confirmation assay for inhibitors of AddAB recombination protein complexScreeningdepositor-specified cross reference: Confirmation (AddAB inhibitors in triplicate)
488955Counterscreen for AddAB inhibitors: absorbance-based high throughput cell-based assay to identify inhibitors of RecBCDScreeningdepositor-specified cross reference: Counterscreen (RecBCD inhibitors in triplicate)
488956Counterscreen for AddAB inhibitors: absorbance-based bacterial cell-based high throughput confirmation assay for inhibitors of bacterial viabilityScreeningdepositor-specified cross reference: Counterscreen (bacterial viability inhibitors in triplicate)
492957Counterscreen for AddAB inhibitors: absorbance-based bacterial cell-based high throughput dose response assay to identify inhibitors of RecBCDConfirmatorydepositor-specified cross reference: Dose response counterscreen (RecBCD inhibitors in triplicate)
492958Counterscreen for AddAB inhibitors: absorbance-based bacterial cell-based high throughput dose response assay for inhibitors of bacterial viabilityConfirmatorydepositor-specified cross reference: Dose response counterscreen (bacterial viablity in triplicate)
492959Absorbance-based bacterial cell-based high throughput dose response assay for inhibitors of AddAB recombination protein complexConfirmatorydepositor-specified cross reference: Dose response (AddAB inhibitors in triplicate)
623916Late stage assay provider Counterscreen for AddAB inhibitors: Cell-based colony-formation assay to identify inhibitors of the viability of V66 E. coli in Hfr recombination assaysOtherdepositor-specified cross reference
623917Late stage assay provider Counterscreen for AddAB inhibitors: Cell-based colony-formation dose response assay to identify inhibitors of the viability of V66 E. coli in Hfr recombination assaysOtherdepositor-specified cross reference
623918Late stage assay provider Counterscreen for AddAB inhibitors: Cell-based colony formation assay to identify inhibitors of the recombination-promoting activity of RecBCD in V66 E. coli (dose response)Confirmatorydepositor-specified cross reference
623919Late stage assay provider Counterscreen for AddAB inhibitors: Cell-based colony formation assay to identify inhibitors of the recombination-promoting activity of RecBCD in V66 E. coli (100uM)Otherdepositor-specified cross reference
623920Late stage assay provider counterscreen for AddAB inhibitors: Radioactivity-based biochemical dose response assay to identify inhibitors of the nuclease activity of purified RecBCD enzymeConfirmatorydepositor-specified cross reference
623921Late stage assay provider counterscreen for AddAB inhibitors: Radioactivity-based biochemical assay to identify inhibitors of the nuclease activity of purified RecBCD enzyme (at 100 micromolar)Otherdepositor-specified cross reference
623922Late stage assay provider counterscreen for AddAB inhibitors: Radioactivity-based biochemical assay to identify inhibitors of the nuclease activity of purified RecBCD enzyme (at 50 micromolar)Otherdepositor-specified cross reference
623937Late stage assay provider counterscreen for AddAB inhibitors: Radioactivity-based biochemical assay to identify inhibitors of the helicase/Chi cutting activity of purified RecBCDOtherdepositor-specified cross reference
623942Late stage assay provider counterscreen for AddAB inhibitors: Radioactivity-based biochemical dose response assay to identify inhibitors of the helicase/Chi cutting activity of purified RecBCDConfirmatorydepositor-specified cross reference
651942Late stage results for the probe development effort to identify inhibitors of AddAB recombination protein complex: Absorbance-based bacterial cell-based dose response assay for inhibitors of AddAB recombination protein complex (ROUND 2)Confirmatorydepositor-specified cross reference
651943Late stage counterscreen results for the probe development effort to identify inhibitors of AddAB recombination protein complexes: absorbance-based bacterial cell-based dose response assay for inhibitors of bacterial viability (ROUND 2)Confirmatorydepositor-specified cross reference
651944Late stage counterscreen results for the probe development effort to identify inhibitors of AddAB recombination protein complex: absorbance-based bacterial cell-based dose response assay to identify inhibitors of RecBCD (ROUND 2)Confirmatorydepositor-specified cross reference
504677Late stage results for the probe development effort to identify inhibitors of AddAB recombination protein complex: Absorbance-based bacterial cell-based dose response assay for inhibitors of AddAB recombination protein complexConfirmatorysame project related to Summary assay
504678Late stage counterscreen results for the probe development effort to identify inhibitors of AddAB recombination protein complexes: absorbance-based bacterial cell-based dose response assay for inhibitors of bacterial viabilityConfirmatorysame project related to Summary assay
504679Late stage counterscreen results for the probe development effort to identify inhibitors of AddAB recombination protein complex: absorbance-based bacterial cell-based dose response assay to identify inhibitors of RecBCDConfirmatorysame project related to Summary assay
602421Late stage assay provider assay for AddAB inhibitors: Radioactivity-based biochemical dose response assay to identify inhibitors of the nuclease activity of purified AddABConfirmatorysame project related to Summary assay
623954Late stage assay provider Counterscreen for AddAB inhibitors: Cell-based colony-formation assay to identify inhibitors of recombination of E. coli transformed with p(addAB) and p(recA) (100 micromolar compound dose)Othersame project related to Summary assay
623956Late stage assay provider Counterscreen for AddAB inhibitors: Cell-based colony-formation assay to identify inhibitors of recombination of E. coli transformed with p(addAB) and p(recA) (20 micromolar compound dose)Othersame 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: Gerald R. Smith, Fred Hutchinson Cancer Research Center
Network: Molecular Library Probe Production Centers Network (MLPCN)
Grant Proposal Number: GM031693
Grant Proposal PI: Gerald R. Smith
External Assay ID: ADDAB-NUCLEASE_INH_RADIOACTIVITY_FILM_3X%INH (+PHAGE)

Late stage assay provider assay for AddAB inhibitors: Radioactivity-based biochemical nuclease assay to identify inhibitors of the activity of purified AddAB (100 micromolar dose).

Description:

Helicobacter pylori infect approximately half of the world's population and are responsible for inducing chronic gastric inflammation that can progress to gastric cancer (1). At the cellular level, Helicobacter pylori infection of the human stomach is associated with inflammation that elicits DNA damage in both bacterial and host cells (2). This DNA damage must be repaired in order for the bacteria to persist. The H. pylori AddAB helicase-exonuclease is required for DNA repair and efficient stomach colonization (3), and inhibitors of this enzyme may be useful antibacterial drugs for treating these infections. The AddAB class of enzymes is closely related to the RecBCD class of helicase-nucleases; both classes are widely distributed in bacteria but appear to be absent in eukaryotes (4). The protein complex functions in DNA repair by directing free DNA ends into the homologous recombination pathway (5). As a result, the identification of inhibitors of AddAB may be useful tools for elucidating the role of AddAB and RecBCD in bacterial recombination and as potential novel antibiotics with few off-target effects.

References:

1. Fox JG, Wang TC. Inflammation, atrophy, and gastric cancer. J Clin Invest. 2007 Jan;117(1):60-9.
2. Ernst P. Aliment Pharmacol Ther. 1999 Mar;13 Suppl 1:13-8. Review article: the role of inflammation in the pathogenesis of gastric cancer.
3. Dillingham MS, Kowalczykowski SC. RecBCD enzyme and the repair of double-stranded DNA breaks. Microbiol Mol Biol Rev. 2008 Dec;72(4):642-71.
4. Amundsen SK, Fero J, Hansen LM, Cromie GA, Solnick JV, Smith GR, Salama NR, Helicobacter pylori AddAB helicase-nuclease and RecA promote recombination-related DNA repair and survival during stomach colonization. Mol Microbiol, 2008. 69(4): p. 994-1007.
5. Chedin F. and Kowalczykowski S.C. A novel family of regulated helicases/nucleases from Gram-positive bacteria: insights into the initiation of DNA recombination, Mol. Microbiol. 43 (2002), pp. 823-834.

Keywords:

phage, radioactivity, radiation, film, late stage, late stage AID, chemistry, purchased, synthesis, synthesized, powders, helicase, nuclease, exonuclease, ATP-dependent nuclease, AddAB, ADDAB, AddAB complex, RecBCD enzyme, beta subunit, gamma chain, alpha chain, Escherichia coli, E. coli, bacteria, Helicobacter pylori, phage, T4, DNA, dsDNA, DNA damage, DNA repair, DNA binding, inhibition, inhibitor, triplicate, Scripps Florida, 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 probe candidates can inhibit AddAB enzymatic activities, using AddAB purified from E. coli. Nuclease activity is assayed as the formation of trichloroacetic acid-soluble radioactive material, detected with a scintillation counter, from uniformly labeled [3H] double-stranded (ds) DNA. As designed, compounds that inhibit AddAB will reduce the nuclease activity (less acid-soluble material after standard incubation). In this assay compounds were tested at a nominal concentration of 100 uM.
Protocol Summary:
Nuclease assays measured the formation of TCA-soluble radioactive material from phage T7 [3H] DNA (2 ug/mL; 6 uM nucleotides) substrate in a 20 min incubation at 37 C. AddAB assays were in 50 mM Tris-HCl (pH 8.5), 10 mM MgCl2, polyvinylpyrrolidone (1 mg/mL), 1 mM DTT, and 50 uM ATP. 2 nM AddAB enzyme was used in this assay.
Compounds were diluted in DMSO and added to enzyme in assay buffer on ice; final DMSO concentration was 5.0% (v/v) in each assay. DNA substrate was added, and after < 5 min the reactions were started by transferring the samples to 37 C. Reactions were stopped by addition of calf thymus DNA to 0.2 mg/mL and TCA to 5% (w/v). After 10 min on ice, the mixtures were centrifuged for 5 min at 16,100 x g, and the soluble radioactive material was determined in a scintillation counter.
The percent activity of AddAB activity for each compound was calculated as follows:
%_Activity = 100 * ( 1- ( ( Test_Compound - Background ) / ( Mean_DMSO_Control - Background ) ) )
Where:
Mean_DMSO_Control is defined as TCA-soluble radioactive product formed by AddAB ds exonuclease in 20 min with the presence of 5.0 %(v/v) DMSO.
Background is defined as TCA-soluble radioactive product formed without the presence of AddAB enzyme in the assay conditions.
Test_Compound is defined as TCA-soluble radioactive product formed in the presence of compound diluted in 5.0% (v/v) DMSO.
PubChem Activity Outcome and Score:
Any compound with a percent activity value > 52% relative to DMSO control at all test concentrations was considered inactive. Any compound with a percent activity value <= 52% at any test concentration was assigned as active.
The reported PubChem Activity Score has been normalized to 0% observed activity.
The PubChem Activity Score range for active compounds is 100-63, and for inactive compounds 60-1.
List of Reagents:
Uniformly labeled phage T7 [3H] DNA; purified AddAB enzyme.
Comment
This assay was run in the assay provider's lab. This assay may have been run as two or more separate campaigns, each campaign testing a unique set of compounds. 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.
Categorized Comment - additional comments and annotations
From BioAssay Depositor:
BAO: assay design: viability reporter: protease activity
BAO: assay format: cell-based format
BAO: assay format detail: assay phase characteristic: homogeneous assay
BAO: bioassay specification: assay biosafety level: bsl1
BAO: bioassay specification: assay footprint: vial
BAO: bioassay specification: assay measurement throughput quality: single concentration single measurement
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: lead optimization
BAO: bioassay specification: bioassay type: functional: enzyme activity
BAO: detection technology: radiometry: scintillation counting: scintillation proximity assay
BAO: detection technology detail: detection instrumentation: flipr tetra
BAO: detection technology detail: detection instrumentation manufacturer: molecular devices
BAO: endpoint detail: perturbagen concentration: concentration unit: micromolar
BAO: meta target detail: binding reporter specification: interaction: protein-small molecule
BAO: meta target: biological process target: regulation of molecular function
BAO: meta target: molecular target: protein target: enzyme: generic hydrolase
BAO: version: 1.4b1090
From PubChem:
Assay Format: Biochemical
Result Definitions
TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1Activity at 100 uM (100μM**)Value of AddAB Nuclease Activity after Treatement with 100 uM inhibitor concentration.Float%

** Test Concentration.
Additional Information
Grant Number: GM031693

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