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BioAssay: AID 651602

Absorbance-based primary bacterial cell-based high throughput screening assay to identify inhibitors of RecBCD (with phage)

Name: Absorbance-based primary bacterial cell-based high throughput screening assay to identify inhibitors of RecBCD (with phage). ..more
 Tested Compounds
 Tested Compounds
 Tested Substances
 Tested Substances
AID: 651602
Data Source: The Scripps Research Institute Molecular Screening Center (RECBCD_INH_ABS_1536_1X%INH PRUN)
BioAssay Type: Primary, Primary Screening, Single Concentration Activity Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
Deposit Date: 2012-09-27

Data Table ( Complete ):           View Active Data    View All Data
BioActive Compounds: 949
Related Experiments
651606Summary of the probe development efforts to identify inhibitors of RecBCDSummarydepositor-specified cross reference
651982Absorbance-based bacterial cell-based high throughput confirmation assay to identify inhibitors of RecBCDScreeningdepositor-specified cross reference
651983Counterscreen for inhibitors of RecBCD: Absorbance-based cell-based high throughput assay to identify inhibitors of bacterial viabilityScreeningdepositor-specified cross reference
651984Counterscreen for RECBCD inhibitors: absorbance-based high throughput cell-based assay to identify inhibitors of AddAB recombination protein complexScreeningdepositor-specified cross reference
652150Counterscreen for inhibitors of RecBCD: Absorbance-based cell-based high throughput dose response assay to identify inhibitors of bacterial viabilityConfirmatorydepositor-specified cross reference
652151Absorbance-based bacterial cell-based high throughput dose response assay to identify inhibitors of RecBCDConfirmatorydepositor-specified cross reference
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: 1 R03 AI083736
Grant Proposal PI: Gerald R. Smith
External Assay ID: RECBCD_INH_ABS_1536_1X%INH PRUN

Name: Absorbance-based primary bacterial cell-based high throughput screening assay to identify inhibitors of RecBCD (with phage).


The RecBCD enzyme (Exonuclease V) of Escherichia coli is a helicase-nuclease that initiates the repair of double-stranded DNA breaks by homologous recombination. The RecBCD class of enzymes is widely distributed among bacteria (1) but is apparently not present in eukaryotes. The major pathway of double-strand DNA break repair in bacteria involves the coordinated action of nuclease and helicase activities provided by the three-subunit enzyme RecBCD, which is critical for DNA repair(2); recBCD null mutants have reduced cell viability, are hyper-sensitive to DNA damaging agents, and are deficient in homologous recombination involving linear DNA (3-5). Inhibitors of RecBCD would allow us to study the mechanism of this complex helicase-nuclease enzyme. Since this enzyme is crucial for bacterial survival during infection, we anticipate that some of these compounds will, in future work, lead to new, critically needed antibacterial drugs with few off-target effects for human use (6).


1. Cromie, G. A. (2009) Phylogenetic ubiquity and shuffling of the bacterial RecBCD and AddAB recombination complexes, J Bacteriol 191, 5076-5084.
2. Smith, G. (2012) How RecBCD enzyme and Chi promote DNA break repair and recombination - A molecular biologist's view. Microbiol Mol Biol Rev, in press.
3. Howard-Flanders, P., and Theriot, L. (1966) Mutants of Escherichia coli K-12 defective in DNA repair and in genetic recombination, Genetics 53, 1137-1150.
4. Willetts, N. S., and Clark, A. J. (1969) Characteristics of some multiply recombination-deficient strains of Escherichia coli, J Bacteriol 100, 231-239.
5. Willetts, N. S., Clark, A. J., and Low, B. (1969) Genetic location of certain mutations conferring recombination deficiency in Escherichia coli, J Bacteriol 97, 244-249.
6. Amundsen, S. K., Spicer, T., Karabulut, A. C., Londono, L. M., Eberhardt, C., Fernandez Vega, V., Bannister, T. D., Hodder, P., and Smith, G. R. (2012) Small-Molecule Inhibitors of Bacterial AddAB and RecBCD Helicase-Nuclease DNA Repair Enzymes, ACS Chem Biol, 2012 May 18;7(5):879-91. Epub 2012 Mar 23.


exonuclease V, helicase, nuclease, RecBCD, RECBCD, RECBCDV66, RecBCD complex, recB, recC, recD, beta subunit, gamma chain, alpha chain, Escherichia coli, E. coli, bacteria, phage, T4, infection, DNA, dsDNA, DNA damage, DNA repair, DNA binding, ATP-binding, homologous recombination, recombination, Chi, inhibit, inhibition, inhibitor, optical density, OD, absorbance, HTS, high throughput screen, singlicate, primary, 1536, Scripps Florida, The Scripps Research Institute Molecular Screening Center, SRIMSC, Molecular Libraries Probe Production Centers Network, MLPCN.
Assay Overview:

The purpose of this assay is to identify compounds that act as inhibitors of bacterial RecBCD activity. This bacterial cell-based assay involves infecting E. coli with a T4 bacteriophage that carries three nonsense mutations in gene 2, whose wild-type protein product protects viral DNA from RecBCD-mediated degradation after infection. The mutant T4 phage is able to infect and block the growth of V67 E. coli (recB21, a recBCD null mutation) which lack RecBCD nuclease activity. The mutant phage also infect V66 E. coli (recBCD+), but V66 proliferate because of the RecBCD helicase and nuclease activity against the unprotected mutant phage. In this assay, V66 E. coli are infected with mutant T4 phage in the presence of test compounds, followed by measurement of well optical density as an indicator of bacterial growth. As designed, compounds that inhibit RecBCD will allow the virus to replicate, thereby reducing or blocking V66 bacterial growth, leading to reduced well absorbance. Compounds are tested in singlicate at a nominal test concentration of 11.86 uM.

Protocol Summary:

Prior to the start of the assay, V66 and V67 bacterial cultures were grown at 37 C until it reached an OD600 of 0.05 or 2.5E7 cfu/mL. To start the assay, 3 uL of Assay Buffer (0.1% Glycerol + Cation Mueller Hinton Broth) was dispensed into all wells. Next, 60 nL of test compound in DMSO, Ciprofloxacin (0.95 ug/ml final concentration) or DMSO alone (1.2% final concentration) were added to the appropriate wells. Then, 1 uL of V66 (recBCD+) or V67 (phage control) bacterial cultures were dispensed into the appropriate wells and plates were incubated for 60 minutes at 37 C.

Next, 1 uL of mutant T4 2 149 bacteriophage was dispensed to the appropriate wells at a multiplicity of infection (MOI) of 0.02. Plates were centrifuged and after 18 hours of incubation at 37 C, absorbance (OD600) was read on a Envision microplate reader (PerkinElmer, Turku, Finland) using 10 flashes per well.

The percent inhibition for each compound was calculated as follows:

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


High_Control is defined as wells containing V66 + Ciprofloxacin + phage
Low_Control is defined as wells containing V66 + DMSO + phage.
Test_Compound is defined as wells containing V66 in the presence of test compound + phage.

PubChem Activity Outcome and Score:

A mathematical algorithm was used to determine nominally inhibiting compounds in the primary screen. Two values were calculated: (1) the average percent inhibition of all compounds tested, and (2) three times their standard deviation. The sum of these two values was used as a cutoff parameter, i.e. any compound that exhibited greater % inhibition than the cutoff parameter was declared active.

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

The PubChem Activity Score range for active compounds is 100-10, and for inactive compounds 10-0.

List of Reagents:

V66 (recBCD+) and V67 (recB21) E. coli bacteria (supplied by Assay Provider)
T4 2 149 mutant bacteriophage (supplied by Assay Provider)
Ciprofloxacin (Sigma, part 17850)
Cation-Adjusted Mueller Hinton II Broth (BD, part 297963)
1536-well plates (Aurora, part 19326)
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 modulate well absorbance. 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 by the MLSMR.
Result Definitions
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1Inhibition at 11.86 uM (11.86μM**)Normalized percent inhibition of the primary screen at a compound concentration of 11.86 micromolar.Float%

** Test Concentration.
Additional Information
Grant Number: 1 R03 AI083736

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