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 Implementatiion: 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. 2006].

This report summarizes the series of assays used 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 purpose of this screen is to identify small molecules which differ structurally from rapamycin but that mimic Rapamycin functionally or otherwise impact TOR pathway proteins. The primary screen described in this CPDP will detect structurally distinct, but functionally rapamycin-like compounds (rapalogs) by probing four major TOR pathways using the following targets in a multiplex screen:

-RPL19A: YAK kinase branch
-LAP4: MSN4 branch
-MEP2 and AGP1: GLN3 branch
-CIT2: RTG branch

The current report assembles the list of compounds that demonstrated activity across all TOR pathway assays.

This project resulted in one probe compound for the RTG branch (with CIT2 as target protein)
( SID / CID / ML# )
99300522 / 3392161 / ML231

The cell-based multiplex assay is constructed using 5 strains from the Yeast-GFP Collection, representing 4 distinct branches of the TOR pathway. Differential stain barcoding is used to discriminate the different strains in the multiplex using Alexafluor 405 (violet laser excitation) and Alexafluor 633 (red laser excitation). Bar-coded yeast cell populations are discriminated then interrogated for changes in GFP expression (blue laser excitation).

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 for multiplexing with the violet and red alexafluors. Following staining, the yeast are combined and diluted into fresh media at 0.2 OD600. Aliquots of the multiplex are transferred into 384-well plate format and library compounds are added at 10 microM final concentration. The cells are incubated at room temperature for 3 hours at 30 degrees C with end-over-end rotation. Control wells contain the multiplex treated for 3 hours with 200 nanogram/milliliters rapamycin as a positive control and the multiplex treated with an equal volume of DMSO as a negative or solvent-only control. The cells in the multiplex are interrogated for GFP expression levels using established high-throughput flow cytometric methodologies at the UNMCMD. Sample analysis is conducted with the HyperCyt(R) 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). Analysis is performed using time-resolved acquisition into a single data file and analysis using IDLeQuery software to merge the flow cytometry data files with compound worklist files generated by HyperSip software. The raw data are parsed in IDLeQuery to produce annotated fluorescence summary data for each well. The parsed data are then processed through an Excel template file constructed specifically for the assay to segregate data for each target.


Summary and Sequence of Assays

MLSMR analysis

HTS : AID 1862 Multiplex HTS of TOR pathway GFP-fusion proteins in S. cerevisiae, specifically RPL19 (MLSMR validation set)
Method: flow cytometry, multiplex cell-based phenotypic assay
Test concentration: 10 microM
Activity criterion: Response < average response minus 3 standard deviations of the entire screen average response value (for RPL19A, this was 99 -3*4.6)
Number evaluated: 1,993
Number active: 8

HTS : AID 1867 Multiplex HTS of TOR pathway GFP-fusion proteins in S. cerevisiae, specifically MEP2 (MLSMR validation set)
Method: flow cytometry, multiplex cell-based phenotypic assay
Test concentration: 10 microM
Activity criterion: Response < average response plus 3 standard deviations of the entire screen average response value (for MEP2, this was 106 +3*10.9)
Number evaluated: 1,993
Number active: 40

HTS : AID 1870 Multiplex HTS of TOR pathway GFP-fusion proteins in S. cerevisiae, specifically CIT2 (MLSMR validation set)
Method: flow cytometry, multiplex cell-based phenotypic assay
Test concentration: 10 microM
Activity criterion: Response > average response plus 3 standard deviations of the entire screen average response value (for CIT2, this was 101 +3*7.5)
Number evaluated: 1,993
Number active: 8

HTS : AID 1873 Multiplex HTS of TOR pathway GFP-fusion proteins in S. cerevisiae, specifically LAP4 (MLSMR validation set)
Method: flow cytometry, multiplex cell (yeast)-based phenotypic assay using five GFP-tagged protein targets
Test concentration: 10 microM
Activity criterion: Response > average response plus 3 standard deviations of the entire screen average response value (for LAP4, this was 99 +3*16.7)
Number evaluated: 1,993
Number active: 12

HTS : AID 1887 Multiplex HTS of TOR pathway GFP-fusion proteins in S. cerevisiae, specifically AGP1 (MLSMR validation set)
Method: flow cytometry, multiplex cell (yeast)-based phenotypic assay using five GFP-tagged protein targets
Test concentration: 10 microM
Activity criterion: Response > average response plus 3 standard deviations of the entire screen average response value (for AGP1, this was 99 + 3*8.5)
Number evaluated: 1,993
Number active: 3

HTS : AID 2025 Multiplex HTS of TOR pathway GFP-fusion proteins in S. cerevisiae, specifically RPL19 for MLPCN
Method: flow cytometry, multiplex cell-based phenotypic assay
Test concentration: 10 microM
Activity criterion: Response < 50%
Number SID evaluated: 325,379
Number active: 982

HTS : AID 2016 Multiplex HTS of TOR pathway GFP-fusion proteins in S. cerevisiae, specifically MEP2 for MLPCN
Method: flow cytometry, multiplex cell-based phenotypic assay
Test concentration: 10 microM
Activity criterion: Response > 175%
Number evaluated: 326,658
Number active: 1,682

HTS : AID 2029 Multiplex HTS of TOR pathway GFP-fusion proteins in S. cerevisiae, specifically CIT2 for MLPCN
Method: flow cytometry, multiplex cell-based phenotypic assay
Test concentration: 10 microM
Activity criterion: Response > 150%
Number evaluated: 321,541
Number active: 210

HTS : AID 2023 Multiplex HTS of TOR pathway GFP-fusion proteins in S. cerevisiae, specifically LAP4 for MLPCN
Method: flow cytometry, multiplex cell (yeast)-based phenotypic assay using five GFP-tagged protein targets
Test concentration: 10 microM
Activity criterion: Response > 150%
Number evaluated: 324,670
Number active: 1,090

HTS : AID 2066 Multiplex HTS of TOR pathway GFP-fusion proteins in S. cerevisiae, specifically AGP1 for MLPCN
Method: flow cytometry, multiplex cell (yeast)-based phenotypic assay using five GFP-tagged protein targets
Test concentration: 10 microM
Activity criterion: Response > 150%
Number evaluated: 322,823
Number active: 51

HTS : AID 2270 Multiplex HTS of TOR pathway GFP-fusion proteins in S. cerevisiae, specifically RPL19 for Cherry Picked Compounds
Method: flow cytometry, multiplex cell-based phenotypic assay
Test concentration: 10 microM
Activity criterion: Response < 50%
Number SID evaluated: 1,756
Number active: 3

HTS : AID 2272 Multiplex HTS of TOR pathway GFP-fusion proteins in S. cerevisiae, specifically MEP2 for Cherry Picked Compounds
Method: flow cytometry, multiplex cell-based phenotypic assay
Test concentration: 10 microM
Activity criterion: Response > 175%
Number evaluated: 1,756
Number active: 40

HTS : AID 2274 Multiplex HTS of TOR pathway GFP-fusion proteins in S. cerevisiae, specifically CIT2 for Cherry Picked Compounds
Method: flow cytometry, multiplex cell-based phenotypic assay
Test concentration: 10 microM
Activity criterion: Response > 150%
Number evaluated: 1,756
Number active: 33

HTS : AID 2271 Multiplex HTS of TOR pathway GFP-fusion proteins in S. cerevisiae, specifically LAP4 for Cherry Picked Compounds
Method: flow cytometry, multiplex cell (yeast)-based phenotypic assay using five GFP-tagged protein targets
Test concentration: 10 microM
Activity criterion: Response > 150%
Number evaluated: 1,756
Number active: 246

HTS : AID 2273 Multiplex HTS of TOR pathway GFP-fusion proteins in S. cerevisiae, specifically AGP1 for Cherry Picked Compounds
Method: flow cytometry, multiplex cell (yeast)-based phenotypic assay using five GFP-tagged protein targets
Test concentration: 10 microM
Activity criterion: Response > 150%
Number evaluated: 1,756
Number active: 4

HTS : AID 2643 Multiplex HTS Screen of TOR pathway GFP-fusion proteins in Saccharomyes cerevisiae specifically AGP1 Second Cherry Pick Compounds
Method: flow cytometry, multiplex cell (yeast)-based phenotypic assay using five GFP-tagged protein targets
Test concentration: 10 microM
Activity criterion: Response > 150%
Number evaluated: 591
Number active: 4

HTS : AID 2622 Multiplex HTS Screen of TOR pathway GFP-fusion proteins in Saccharomyes cerevisiae specifically MEP2 Second Cherry Pick Compounds
Method: flow cytometry, multiplex cell (yeast)-based phenotypic assay using five GFP-tagged protein targets
Test concentration: 10 microM
Activity criterion: Response > 150%
Number evaluated: 591
Number active: 83

HTS : AID 2621 Multiplex HTS Screen of TOR pathway GFP-fusion proteins in Saccharomyes cerevisiae specifically LAP4 Second Cherry Pick Compounds
Method: flow cytometry, multiplex cell (yeast)-based phenotypic assay using five GFP-tagged protein targets
Test concentration: 10 microM
Activity criterion: Response > 150%
Number evaluated: 591
Number active: 119

HTS : AID 2623 Multiplex HTS Screen of TOR pathway GFP-fusion proteins in Saccharomyes cerevisiae specifically RPL19A Second Cherry Pick Compounds
Method: flow cytometry, multiplex cell (yeast)-based phenotypic assay using five GFP-tagged protein targets
Test concentration: 10 microM
Activity criterion: Response < 65%
Number evaluated: 591
Number active: 19

HTS : AID 2624 Multiplex HTS Screen of TOR pathway GFP-fusion proteins in Saccharomyes cerevisiae specifically CIT2 Second Cherry Pick Compounds
Method: flow cytometry, multiplex cell (yeast)-based phenotypic assay using five GFP-tagged protein targets
Test concentration: 10 microM
Activity criterion: Response > 150%
Number evaluated: 591
Number active: 47

AID: 2745 Dose Response of TOR pathway GFP-fusion proteins in Saccharomyes cerevisiae specifically LAP4 based on MLPCN hits
Method: flow cytometry, dose response, cell (yeast)-based phenotypic assay using GFP-tagged protein target
Test concentration: 0.01 to 33 microM
Activity criterion: EC50 < 33 microM
Number evaluated: 613
Number active: 205

AID: 2743 Dose Response of TOR pathway GFP-fusion proteins in Saccharomyes cerevisiae specifically AGP1 based on MLPCN hits
Method: flow cytometry, dose response, cell (yeast)-based phenotypic assay using GFP-tagged protein target
Test concentration: 0.01 to 33 microM
Activity criterion: EC50 < 33 microM
Number evaluated: 613
Number active: 19

AID: 2744 Dose Response of TOR pathway GFP-fusion proteins in Saccharomyes cerevisiae specifically CIT2 based on MLPCN hits
Method: flow cytometry, dose response, cell (yeast)-based phenotypic assay using GFP-tagged protein target
Test concentration: 0.01 to 33 microM
Activity criterion: EC50 < 33 microM
Number evaluated: 613
Number active: 19

AID: 2742 Dose Response of TOR pathway GFP-fusion proteins in Saccharomyes cerevisiae specifically MEP2 based on MLPCN hits
Method: flow cytometry, dose response, cell (yeast)-based phenotypic assay using GFP-tagged protein target
Test concentration: 0.01 to 33 microM
Activity criterion: EC50 < 33 microM
Number evaluated: 613
Number active: 12

AID: 2740 Dose Response of TOR pathway GFP-fusion proteins in Saccharomyes cerevisiae specifically RPL19A based on MLPCN hits
Method: flow cytometry, dose response, cell (yeast)-based phenotypic assay using GFP-tagged protein target
Test concentration: 0.01 to 33 microM
Activity criterion: EC50 < 33 microM
Number evaluated: 613
Number active: 101

AID: 2757 Test compound autofluorescence in Saccharomyes cerevisiae specifically s288c.
Method: flow cytometry, compound fluorescence, cell (yeast)-based
Test concentration: 0.01 to 33 microM
Activity criterion: Fold increase kMESF > 25 at 33 microM
Number evaluated: 613
Number active: 9

This summary is for a multiplex project in which five protein targets are assayed simultaneously.

Grant Number: 1R03 MH086450-01