Sequence: Chain A, Human Bcl2-A1 In Complex With Bim-Bh3 Peptide Protein Family: Bcl-2_like Related Protein 3D Structures

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AID	Name	Type	Probe	Comment
2526	Summary of Broad Institute MLPCN A1 Apoptosis Project	summary	1
449755	Luminescence Cell-Based Counterscreen to Identify Inhibitors of A1 Apoptosis (HMC 1-8 low)	confirmatory
449761	Luminescence Cell-Based Counterscreen to Identify Inhibitors of A1 Apoptosis (non-primed)	confirmatory
2765	Luminescence Cell-Based Dose Retest to Identify Inhibitors of A1 Apoptosis	confirmatory
449754	Luminescence Cell-Based Counterscreen to Identify Inhibitors of A1 Apoptosis (Bax-Bak knockout)	confirmatory
449757	Luminescence Cell-Based Secondary Screen to Identify Inhibitors of A1(alternate construct)	confirmatory

Keywords: apoptosis, BH3 domain, Bcl2-A1, BIM, caspase, cancer

Primary Collaborator: Todd Golub, Broad Institute, golub@broadinstitute.org

Assay Overview:
The fate of cell survival versus apoptosis is determined by the balance of anti and pro-apoptotic proteins. Expression of activator BH3-only proteins, such as BIM or tBID, leads to downstream caspase activation and apoptosis. A1 can functionally bind to and sequester BIM or tBID. In this assay, the parental control cells do not depend on A1 for survival. However, they can be primed to depend on A1 by co-expressing A1 and BIM. The primed cells still maintain a balance between anti and pro-apoptotic proteins, but rely on A1 to sequester BIM.
An A1 inhibitor causes the release of A1-bound BIM, which activates BAX/BAK, and leads to caspase activation that can be quantitatively measured using a luciferin-linked caspase substrate (peptide sequence DEVD) available commercially as Promega's Caspase Glo 3/7 reagent.

Expected Outcome: Compounds that cause caspase activation will show an increase in luminescence signal as measured by the caspase glo reagent. Additional assays will determine whether this caspase activation is being caused by general toxicity or off target effects (as is the case for the nonspecific positive control, clofoctol) or due to the on-target disruption of the A1-BIM interaction (as is the case for the specific but weaker positive control, ABT-263, which mimics the BH3 homology domain of BIM.)

Assay Protocol:
1. MEF cells expressing A1-2A-BIM are cultured in 150mm TC dishes with 30mls of growth media supplemented with 0.5-1 ug/ml blasticidin in a 37oC incubator (5% CO2). Use 30 ml media for a 150 mm dish. Do let cells go beyond 95% confluency (about 30X106 cells per 150mm dish). Split cells 1 to 6-10 (3-4X106 cells) for subsequent passage every other day.
2. Day1 morning. MEF cells grow on T200 mm cell culture flasks are washed once with 1XPBS (Gibco), and digested with 1ml (or 3ml) 1X trypsin (CellGro Mediatech) for 1-2 minutes.
3. Add 10ml complete growth media (RPMI-1640 (Cellgrow Mediatech), 10% heat inactivated FBS (Thermo), 1X penn/strep/glutamine (Gibco)) to the plate, mix cells and break clumps, then transfer the cells to a 50ml centrifuge tube through a cell strainer (BD Falcon # 352340) to get rid of any clumps. Count the cells, and centrifuge cells at 1000 rpm for 4 minutes.
4. Aspirate off the supernatant, and resuspend the cells in complete media at density of 1X105 cells/ml.
5. Plate cells in white 384 well plates (Corning 3570), 30ul/well (2500 cells/well), with Combi (Thermo) while gently stirring the media.
6. Day2. Pin transfer 50 nL of compound to the cells and incubate 37 degrees 5% CO2 95% humidity for 3 hours.
7. Remove the plate from the incubator and cool down to room temperature for 30 minutes.
8. Add 10ul of 1:1 diluted CaspaseGlo (Promega) (diluted with 50mM HEPES) to each well with Combi multidrop (Thermo.) Shake the plate on the Combi nest for 1 minute. Incubate at room temperature for 1h.
9. Measure luminescence in Envision (Perkin Elmer)

HTS Data Analysis:
32 negative control wells (DMSO) were included on every plate. Positive controls were run on separate plates, and their activity values calibrated and applied to each assay plate. Compound activity was scaled to the negative and positive control, with DMSO activity measuring 0% and positive control measuring 100% activity. Pattern correction was performed by Genedata software using a runwise additive algorithm.

The PubChem_Activity_Score was derived using the follow procedure:
1. A background-subtracted value was calculated for each well by subtracting the median value of the negative control wells on each plate from the value of each well on that plate.

2. An activity score was derived for each well by dividing the background-subtracted value for each well by the median of the background-subtracted value of the clofoctol positive control wells in the same run and multiplying the resulting fraction by 100.

3. Runwise patterns were smoothed using an additive algorithm in Genedata software

4. The final PubChem_Activity_Score represents the mean of all valid replicate activity scores obtained.

The PubChem_Activity_Outcome class was assigned as described below:

Activity_Outcome = 1 (inactive)
PubChem_Activity_Score for more than half the replicate activity scores <10.

Activity_Outcome = 2 (active)
PubChem_Activity_Score for more than half the replicate activity scores >10, or one half of replicates had a replicate activity score >10 and the PubChem_Activity_Score was >10.

Activity_Outcome = 3 (inconclusive)
PubChem_Activity_Score <10 but half the replicates had an activity score >10.

Grant Number: 1 R03 DA028853-01