Name: Late stage assay provider assay for AddAB inhibitors: Radioactivity-based biochemical dose response assay to identify inhibitors of the nuclease activity of purified AddAB. ..more
Targets
| Sequence: unnamed protein product [Helicobacter pylori 26695] Protein Family: PD-(D/E)XK nuclease superfamily Gene:HP1553 Related Protein 3D Structures |
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BioActive Compounds: 12
Depositor Specified Assays
Show more |
| AID | Name | Type | Comment |
|---|---|---|---|
| 435030 | Absorbance-based primary bacterial cell-based high throughput screening assay to identify inhibitors of AddAB recombination protein complex | screening | Primary screen (AddAB inhibitors in singlicate) |
| 449731 | Summary of the probe development effort to identify inhibitors of AddAB recombination protein complex | summary | Summary (AddAB inhibitors) |
| 449728 | Counterscreen for inhibitors of AddAB: absorbance-based bacterial cell-based high throughput screening assay to identify inhibitors of bacterial viability | screening | Counterscreen (bacterial viability inhibitors in singlicate) |
| 488942 | Absorbance-based bacterial cell-based high throughput confirmation assay for inhibitors of AddAB recombination protein complex | screening | Confirmation (AddAB inhibitors in triplicate) |
| 488955 | Counterscreen for AddAB inhibitors: absorbance-based high throughput cell-based assay to identify inhibitors of RecBCD | screening | Counterscreen (RecBCD inhibitors in triplicate) |
| 488956 | Counterscreen for AddAB inhibitors: absorbance-based bacterial cell-based high throughput confirmation assay for inhibitors of bacterial viability | screening | Counterscreen (bacterial viability inhibitors in triplicate) |
| 492957 | Counterscreen for AddAB inhibitors: absorbance-based bacterial cell-based high throughput dose response assay to identify inhibitors of RecBCD | confirmatory | Dose response counterscreen (RecBCD inhibitors in triplicate) |
| 492958 | Counterscreen for AddAB inhibitors: absorbance-based bacterial cell-based high throughput dose response assay for inhibitors of bacterial viability | confirmatory | Dose response counterscreen (bacterial viablity in triplicate) |
| 492959 | Absorbance-based bacterial cell-based high throughput dose response assay for inhibitors of AddAB recombination protein complex | confirmatory | Dose response (AddAB inhibitors in triplicate) |
| 623922 | Late 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) | other | |
| 623937 | Late stage assay provider counterscreen for AddAB inhibitors: Radioactivity-based biochemical assay to identify inhibitors of the helicase/Chi cutting activity of purified RecBCD | other | |
| 623917 | Late 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 assays | other | |
| 623920 | Late stage assay provider counterscreen for AddAB inhibitors: Radioactivity-based biochemical dose response assay to identify inhibitors of the nuclease activity of purified RecBCD enzyme | confirmatory | |
| 623916 | Late 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 assays | other | |
| 623919 | Late 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) | other | |
| 623942 | Late stage assay provider counterscreen for AddAB inhibitors: Radioactivity-based biochemical dose response assay to identify inhibitors of the helicase/Chi cutting activity of purified RecBCD | confirmatory | |
| 623918 | Late 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) | confirmatory | |
| 623921 | Late 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) | other | |
| 651942 | On Hold | ||
| 651943 | On Hold | ||
| 651944 | On Hold |
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_3XIC50 (+PHAGE)
Name: Late stage assay provider assay for AddAB inhibitors: Radioactivity-based biochemical dose response assay to identify inhibitors of the nuclease activity of purified AddAB.
Description:
Helicobacter pylori infects approximately half of the world's population and is 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:
dose response, 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.
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_3XIC50 (+PHAGE)
Name: Late stage assay provider assay for AddAB inhibitors: Radioactivity-based biochemical dose response assay to identify inhibitors of the nuclease activity of purified AddAB.
Description:
Helicobacter pylori infects approximately half of the world's population and is 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:
dose response, 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. This assay determines IC50 values for selected compounds. 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).
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 inhibition for each compound was calculated as follows:
%_Inhibition = 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.
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 Prism 5 software (GraphPad Software, 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. 100 uM) did not result in greater than 50% inhibition, the IC50 was determined manually as greater than 100 uM.
PubChem Activity Outcome and Score:
Compounds with an IC50 greater than 100 uM were considered inactive. Compounds with an IC50 equal to or less than 100 uM were considered active.
Activity score was then ranked by the potency of the compounds with fitted curves, with the most potent compounds assigned the highest activity scores.
The PubChem Activity Score range for active compounds is 100-1, and for inactive compounds 0-0.
List of Reagents:
Uniformly labeled phage T7 [3H] DNA; purified AddAB enzyme.
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. This assay determines IC50 values for selected compounds. 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).
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 inhibition for each compound was calculated as follows:
%_Inhibition = 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.
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 Prism 5 software (GraphPad Software, 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. 100 uM) did not result in greater than 50% inhibition, the IC50 was determined manually as greater than 100 uM.
PubChem Activity Outcome and Score:
Compounds with an IC50 greater than 100 uM were considered inactive. Compounds with an IC50 equal to or less than 100 uM were considered active.
Activity score was then ranked by the potency of the compounds with fitted curves, with the most potent compounds assigned the highest activity scores.
The PubChem Activity Score range for active compounds is 100-1, and for inactive compounds 0-0.
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
BAO: version: 1.4b1090
BAO: bioassay specification: assay stage: lead optimization
BAO: bioassay specification: assay biosafety level: bsl1
BAO: assay format: cell-based format
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: meta target: molecular target: protein target: enzyme: generic hydrolase
BAO: meta target: biological process target: regulation of molecular function
BAO: meta target detail: binding reporter specification: interaction: protein-small molecule
BAO: assay design: viability reporter: protease activity
BAO: detection technology: radiometry: scintillation counting: scintillation proximity assay
BAO: bioassay specification: bioassay type: functional: enzyme activity
BAO: bioassay specification: assay footprint: vial
BAO: bioassay specification: assay measurement throughput quality: concentration response multiple replicates
BAO: assay format detail: assay phase characteristic: homogeneous 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: bioassay specification: assay stage: lead optimization
BAO: bioassay specification: assay biosafety level: bsl1
BAO: assay format: cell-based format
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: meta target: molecular target: protein target: enzyme: generic hydrolase
BAO: meta target: biological process target: regulation of molecular function
BAO: meta target detail: binding reporter specification: interaction: protein-small molecule
BAO: assay design: viability reporter: protease activity
BAO: detection technology: radiometry: scintillation counting: scintillation proximity assay
BAO: bioassay specification: bioassay type: functional: enzyme activity
BAO: bioassay specification: assay footprint: vial
BAO: bioassay specification: assay measurement throughput quality: concentration response multiple replicates
BAO: assay format detail: assay phase characteristic: homogeneous 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
Result Definitions
| TID | Name | Description | Histogram | Type | Unit | |
|---|---|---|---|---|---|---|
| Outcome | The BioAssay activity outcome | Outcome | ||||
| Score | The BioAssay activity ranking score |  | Integer | |||
| 1 | Qualifier | Activity 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 | |||
| 2 | IC50* | The concentration at which 50 percent of the activity in the inhibitor assay is observed; (IC50) shown in uM. | | Float | μM |
* Activity Concentration.
Additional Information
Grant Number: GM031693
Data Table (Concise)
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