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BioAssay: AID 2621

Multiplex HTS Screen of TOR pathway GFP-fusion proteins in Saccharomyes cerevisiae specifically LAP4 Second Cherry Pick Compounds

The target of rapamycin, TOR, is a ser/thr protein kinase evolutionarily conserved from yeast to man [Wullschleger, et al. 2006]. TOR functions in two distinct protein complexes, TOR complex 1 (TORC1) and TORC2 [Cafferkey, et al. 1993; Stan, et al. 1994]. Curiously, only TOR in TORC1 is bound and inhibited by the lipophilic macrolide rapamycin [Kunz, et al. 1993; Helliwell, et al. 1998; Zhang, et more ..
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 Tested Compounds
 Tested Compounds
All(590)
 
 
Active(118)
 
 
Inactive(472)
 
 
 Tested Substances
 Tested Substances
All(591)
 
 
Active(119)
 
 
Inactive(472)
 
 
AID: 2621
Data Source: NMMLSC (UNM_TOR_Pathway_HTS_in_Saccharomyces_cerevisiae_specifically..)
BioAssay Type: Primary, Primary Screening, Single Concentration Activity Observed
Depositor Category: NIH Molecular Libraries Probe Production Network
BioAssay Version:
Deposit Date: 2010-03-20
Modify Date: 2011-04-05

Data Table ( Complete ):           Active    All
Target
BioActive Compounds: 118
Depositor Specified Assays
AIDNameTypeComment
1908Multiplex HTS Screen of TOR pathway GFP-fusion proteins in Saccharomyes cerevisiaesummarySummary report for TOR screen project
504469Confirmatory Primary Screen Hits KU SAR Set2 Dose Response Multiplex in TOR pathway GFP-fusion proteins for Saccharomyes cerevisiae, specifically LAP4confirmatory
488823Confirmatory Cherry Pick 3 SAR Dose Response Multiplex in TOR pathway GFP-fusion proteins for Saccharomyes cerevisiae, specifically LAP4confirmatory
488795Confirmatory Primary Screen Hits KU SAR Dose Response Multiplex in TOR pathway GFP-fusion proteins for Saccharomyes cerevisiae, specifically LAP4confirmatory
Description:
University of New Mexico Assay Overview:
Assay Support: 1R03 MH086450-01
Project Title: Chemical Screen of TOR pathway GFP fusion proteins in S. cerevisiae
PI: Maggie Werner-Washburne

Center PI: Larry Sklar

Assay Implementation: Jun Chen, Chris Allen, Susan Young, Anna Waller, Mark Carter

Assay Background and Significance:

The target of rapamycin, TOR, is a ser/thr protein kinase evolutionarily conserved from yeast to man [Wullschleger, et al. 2006]. TOR functions in two distinct protein complexes, TOR complex 1 (TORC1) and TORC2 [Cafferkey, et al. 1993; Stan, et al. 1994]. Curiously, only TOR in TORC1 is bound and inhibited by the lipophilic macrolide rapamycin [Kunz, et al. 1993; Helliwell, et al. 1998; Zhang, et al. 2006]. Although the signaling events up- and downstream of TORC2 (which regulates spatial aspects of growth) have yet to be elucidated in detail, it is well established that TORC1 is a central hub of a signaling network that couples cues from hormones and growth factors (in mammalian cells), energy and stresses, and the abundance of nutrients, to cell growth and proliferation. Very recent work has elucidated many details of the signaling events upstream of TORC1 as well as downstream targets of TORC1. Importantly, in this context, most negative regulators of mammalian TORC1 (mTORC1)have been previously identified as tumor suppressor gene products, while many positive regulators of mTORC1 have been identified as proto-oncoproteins and/or are found at elevated levels in tumor-derived cell lines [De Virgilio, et al. 2006a; De Virgilio, et al. 2006b].

The purpose of this HTS screen is to identify small molecule modulators of protein targets in the pathway containing the target of rapamycin (TOR), a multi-protein complex (TORC1 and TORC2) that is highly conserved from yeast to man. The screen will detect structurally distinct, but functionally rapamycin-like compounds (rapalogs) by probing four major TOR pathways using the following targets in a multiplex format:

*RPL 19A: YAK kinase branch
*LAP4: MSN4 branch
*MEP2 and AGP1: GLN3 branch
*CIT2: RTG branch

Each of these target proteins (RPL 19A, LAP4, MEP2, AGP1, CIT2) are GFP (Green Fluorescent Protein) tagged, thus the expression of the proteins can be tracked by monitoring the GFP fluorescence.

This AID reports the responses elicited from the single concentration confirmation of the primary screening hits. These cherry picked compounds were assessed in a slightly altered protocol compared to the primary screening protocol. The strains were collected in single plex manner, therefore eliminated the need for having dual staining to distinguish the different strain populations. And compared with the previous assessment of cherry picked compounds, for this set of cherry picked compounds there were no color staining to look at potential response difference that might occur between the different generational populations.
Protocol
The yeast cell-based multiplex assay is constructed using 5 strains from the Yeast-GFP Collection (Invitrogen, USA), representing 4 distinct branches of the TOR pathway: YAK Kinase, MSN4, GLN3 and RTG. Data were collected in single plex mode, meaning data from each individual strain were separately. The strains, however, were labeled with Alexafluor 633 (red laser excitation) in order to discriminate between generational populations, i.e., separate mothers and daughters of the same strain. The yeast cell populations are discriminated then interrogated for changes in GFP expression (blue laser excitation).

Similar to the primary screening campaign, the assay is performed in a total volume of 10.1 microliters in 384-well microtiter plates. The strains are grown separately overnight in synthetic complete liquid media in a shaking incubator at 30 degrees C, and then stained with the red alexafluor. Following staining, the each individual yeast strain was diluted into fresh media at 0.2 OD600. Aliquots of the yeast are transferred into 384-well microtiter plates and library compounds are added at 10microM final concentration. The cells are incubated for 3 hours at 30 degrees C with end-over-end rotation. Control wells contain the yeast strain treated for 3 hours with 400nanogram/milliliter Rapamycin as a positive control and the yeast strain with an equal volume of DMSO as a solvent control. The cells are interrogated for GFP expression levels using established high-throughput flow cytometric methodologies at the UNMCMD. Sample analysis is conducted with the HyperCyt(R) (Intellicyt, USA) high throughput flow cytometry platform. The HyperCyt system interfaces a flow cytometer and autosampler for high-throughput microliter-volume sampling from 384-well microtiter plates [Kuckuck, et al. 2001]. Flow cytometric data are collected on a Cyan Flow Cytometer (Dako, USA).

Data analysis of the original flow cytometric data was done using HyperView (R) (Intellicyt, USA) software. The data are gated on forward scatter versus side scatter to distinguish the single yeast population. This gate is equivalent to the 'All' cells gate utilized during the first set of cherry picked compounds. HyperView applies this gate and parses the time-resolved data file to produce annotated fluorescence summary data for each well, which are merges with compound worklist files generated by HyperSip(R) (Intellicyt, USA) software. The parsed data are then processed through an Excel (R) (Microsoft, USA) template file constructed specifically for the assay to calculate the percent response.

Calculations:

Percent Response is calculated in comparison to negative control (wells with DMSO) using the following equation:
%Response = 100*RawMCF_Sample/PlateAve_RawMCF_NCntrl
where RawMCF_Sample is the median channel fluorescence measured from the well with sample compound and PlateAve_RawMCF_NCntrl is the average of the median channel fluorescence measured from all the negative control wells on the plate. Note, in order to eliminate effects of potential spillover from innate fluorescent compounds into the control wells, the plate average of the negative control wells are only of the control wells that are within 1 standard deviation of all 16 control wells on the plate.

Compounds were demeaned Active if the percent response was greater than 150.

PUBCHEM_ACTIVITY_SCORE was calculated from the %Response:
SCORE = %Response - 100
Thus any %Responses less than 100% were given SCORE values of 0. An Active compound has a PUBCHEM_ACTIVITY_SCORE greater than 50.

If there were less than 70 events measured for on yeast strain, then the compound was listed as "Inconclusive".

Zprime was calculated from the average and standard deviations of the rapamycin control and DMSO control. For these sets of plates the average 0.70 +/- 0.08.
Result Definitions
TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1RESPONSE (10μM**)Percent response calculated as ratio to DMSO negative control based on All gateFloat%
2Z_PRIMEZprime calculated from rapamycin control and DMSO control per plateFloat

** Test Concentration.
Additional Information
Grant Number: 1R03 MH086450-01

Data Table (Concise)
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