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BioAssay: AID 651987

Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA1 and LYPLA2: Fluorescence-based biochemical gel-based ABPP gel filtration assay to assess binding mode

Name: Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA1 and LYPLA2: Fluorescence-based biochemical gel-based ABPP gel filtration assay to assess binding mode. ..more
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 Tested Compounds
 Tested Compounds
All(3)
 
 
Active(2)
 
 
Inactive(1)
 
 
 Tested Substances
 Tested Substances
All(3)
 
 
Active(2)
 
 
Inactive(1)
 
 
AID: 651987
Data Source: The Scripps Research Institute Molecular Screening Center (LYPLA1&2_INH_FLUO_ABPP_BINDINGMODE)
BioAssay Type: Panel
Depositor Category: NIH Molecular Libraries Probe Production Network, Assay Provider
BioAssay Version:
Deposit Date: 2013-01-15
Hold-until Date: 2013-10-18
Modify Date: 2013-10-18

Data Table ( Complete ):           Active    All
BioActive Compounds: 2
Depositor Specified Assays
Show more
AIDNameTypeProbeComment
2202Summary of probe development efforts to identify inhibitors of lysophospholipase 1 (LYPLA1).summary2 Summary (LYPLA1 inhibitors)
2203Summary of probe development efforts to identify inhibitors of lysophospholipase 2 (LYPLA2).summary1 Summary (LYPLA2 inhibitors)
2174Counterscreen for PME1 inhibitors: fluorescence polarization-based primary biochemical high throughput screening assay to identify inhibitors of lysophospholipase 1 (LYPLA1).screening Primary screen (LYPLA1 inhibitors in singlicate)
2233Counterscreen for PME1 inhibitors: fluorescence polarization-based biochemical high throughput confirmation assay for inhibitors of lysophospholipase 1 (LYPLA1).screening Confirmation screen (LYPLA1 inhibitors in triplicate)
2177Counterscreen for PME1 inhibitors: fluorescence polarization-based primary biochemical high throughput screening assay to identify inhibitors of lysophospholipase 2 (LYPLA2).screening Primary screen (LYPLA2 inhibitors in singlicate)
2232Counterscreen for PME1 inhibitors: fluorescence polarization-based biochemical high throughput confirmation assay to identify inhibitors of lysophospholipase 2 (LYPLA2).screening Confirmation screen (LYPLA2 inhibitors in triplicate)
493105Assay provider results from the probe development effort to identify dual inhibitors of LYPLA1 and LYPLA2: Fluorescence-based biochemical gel-based ABPP inhibition of recombinant and endogenous enzymeother Confirmation screen (LYPLA1 and LYPLA2 inhibitors in singlicate)
493108Late stage assay provider results from the probe development effort to identify dual inhibitors of LYPLA1 and LYPLA2: fluorescence-based cell-based inhibitionother Late stage screen (LYPLA1 and LYPLA2 inhibitors in singlicate)
493109Late stage assay provider results from the probe development effort to identify dual inhibitors of LYPLA1 and LYPLA2: LC-MS/MS assay to assess binding of compounds to active siteother Late stage LCMS assay (LYPLA1)
493110Late stage assay provider results from the probe development effort to identify dual inhibitors of LYPLA1 and LYPLA2: Gel-based Activity-Based Protein Profiling (ABPP) IC50 for LYPLA1 and LYPLA2confirmatory Late stage dose response (LYPLA1 and LYPLA2 inhibitors in triplicate)
493111Late stage assay provider results from the probe development effort to identify dual inhibitors of LYPLA1 and LYPLA2: Fluorescence-based biochemical gel-based ABPP inhibition and selectivityother Late stage screen (LYPLA1 and LYPLA2 inhibitors in singlicate)
493154Late stage assay provider results from the probe development effort to identify inhibitors of LYPLA1 and LYPLA2: Gel-based Activity-Based Protein Profiling (ABPP) IC50 for off-target ABHD11confirmatory Late stage dose response counterscreen (ABHD11 inhibitors in triplicate)
493161Late stage assay provider results from the probe development effort to identify dual inhibitors of LYPLA1 and LYPLA2: absorbance-based cell-based dose response assay to determine cytotoxicity of inhibitor compoundsconfirmatory Late stage dose response counterscreen (T-cell cytotoxicity in quadruplicate)
504482Late stage assay provider results from the probe development effort to identify inhibitors of LYPLA1: fluorescence-based cell-based gel-based Activity-Based Protein Profiling (ABPP) IC50 for anti-target ABHD11confirmatory Late stage dose repsonse (ABHD11 inhibitors in triplicate)
504498Late stage assay provider results from the probe development effort to identify inhibitors of LYPLA1: LC-MS/MS assay to assess binding of compounds to active site of anti-target ABHD11other Late stage MOA assay (ABDH11 LCMS)
504505Late stage assay provider results from the probe development effort to identify inhibitors of LYPLA1: fluorescence-based cell-based gel-based Activity-Based Protein Profiling (ABPP) percent inhibition for anti-target ABHD11other Late stage screen (ABHD11 inhibitors in singlicate, in situ)
504507Late stage assay provider results from the probe development effort to identify inhibitors of LYPLA1: fluorescence-based biochemical gel-based Activity-Based Protein Profiling (ABPP) IC50 for anti-target ABHD11 Set 2confirmatory Late stage dose response (ABHD11 inhibitors in triplicate)
504510Late stage assay provider results from the probe development effort to identify inhibitors of LYPLA1: absorbance-based cell-based dose response assay to determine cytotoxicity of inhibitor compounds set 2confirmatory Late stage dose repsonse counterscreen (T-cell cytotoxicity in quadruplicate)
504520Late stage assay provider results from the probe development effort to identify inhibitors of LYPLA1: fluorescence-based biochemical gel-based Activity-Based Protein Profiling (ABPP) inhibition and selectivityother Late stage screen (LYPLA1 and LYPLA2 inhibitors in singlicate)
504522Late stage assay provider results from the probe development effort to identify inhibitors of LYPLA1: LC-MS-based cell-based SILAC Activity-Based Protein Profiling (ABPP) for anti-target ABHD11other Late stage panel screen (ABHD11 SILAC ratio)
504892Late stage assay provider results from the probe development effort to identify inhibitors of ABHD11: Fluorescence-based biochemical gel-based Activity-Based Protein Profiling (ABPP) inhibition of the human isoform of ABHD11other Late stage counterscreen (ABHD11 inhibitors in singlicate)
651998Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA1: Substrate-based fluorescence-based biochemical determination of kinetic parametersconfirmatory
652001Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA2: Substrate-based fluorescence-based biochemical determination of kinetic parametersconfirmatory
652003Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA1: fluorescence-based biochemical dose-response assayconfirmatory
652004Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA2: fluorescence-based biochemical dose-response assayconfirmatory
652018Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA1: LCMS-based Activity-Based Protein Profiling (ABPP) SILAC selectivity analysis in vitro, Set 2other
652029Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA2: Fluorescence-based biochemical gel-based ABPP inhibitionother
652030Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA2: Fluorescence-based biochemical gel-based ABPP inhibition and selectivityother
743117 On Hold
743118 On Hold
743119 On Hold
743127 On Hold
743132 On Hold
743133 On Hold
743134 On Hold
743137 On Hold
Description:
Source (MLPCN Center Name): The Scripps Research Institute Molecular Screening Center (SRIMSC)
Center Affiliation: The Scripps Research Institute (TSRI)
Assay Provider: Benjamin Cravatt, TSRI
Network: Molecular Libraries Probe Production Centers Network (MLPCN)
Grant Proposal Number: 1 R01 CA132630
Grant Proposal PI: Benjamin Cravatt, TSRI
External Assay ID: LYPLA1&2_INH_FLUO_ABPP_BINDINGMODE

Name: Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA1 and LYPLA2: Fluorescence-based biochemical gel-based ABPP gel filtration assay to assess binding mode.

Description:

Protein palmitoylation is an essential post-translational modification necessary for trafficking and localization of regulatory proteins that play key roles in cell growth and signaling. Numerous proteins have been identified as targets of palmitoylation, including cytoskeletal proteins, kinases, receptors, and other proteins involved in various aspects of cellular signaling and homeostasis (1). Using a global chemo-proteomic method for the metabolic incorporation and identification of palmitoylated proteins, we were able to identify hundreds of palmitoylated proteins, revealing palmitoylation as a widespread post-translational modification (PTM) (2). Palmitoylation involves an acyl-thioester linkage to specific cysteines (3,4). Given the labile properties of thioesters, palmitoylation is potentially reversible and may be regulated in a manner analogous to other PTMs (e.g., phosphorylation). As such, identification of proteins responsible for the dynamic modulation of palmitoylation is paramount to understanding its patho/physiological roles. For example, multiple oncogenes, including HRAS and SRC, require palmitoylation for malignant transformation (5), suggesting protein palmitoyl thioesterases may have tumor suppressor activity required to repress aberrant growth signaling. More than a decade ago, the cytosolic serine hydrolase acyl-protein thioesterase 1 (APT1) was identified as an in vitro HRAS palmitoyl thioesterase (6). Initially classified as lysophospholipase 1 (LYPLA1) (7), the enzyme has since been demonstrated to have several hundred-fold higher activity as a protein thioesterase. While the in vitro data (6,8) provided an intriguing clue to its possible role in vivo, prior to our studies, little was known about the in vivo thioesterase activity of LYPLA1. Upon retroviral shRNA knockdown of LYPLA1, we found that HRAS was robustly hyper-palmitoylated, providing the first evidence that the endogenous enzyme is a functional protein palmitoyl thioesterase capable of regulating HRAS palmitoylation in mammalian cells. However, shRNA resulted in only an 80% reduction in LYPLA1 expression (unpublished). LYPLA2 (a.k.a. APT2) is 65% identical to LYPLA1, and also exhibits lysophospholipase activity in vitro, but its potential role as a thioesterase is unknown (9). shRNA knockdown studies of LYPLA2 revealed only partial knockdown of the enzyme, making substrate identification inconclusive (unpublished). A principle goal of post-genomic research is the determination of the molecular and cellular role of uncharacterized enzymes like LYPLA1 and LYPLA2. As such, selective inhibitors of LYPLA1 or LYPLA2 would greatly aid investigations into the biological function of these enzymes. Several inhibitors of LYPLA1 have been described (10,11), but none of these agents have proven capable of inhibiting LYPLA1 activity in cells, and no selective inhibitors of LYPLA2 have been reported to date. To comprehensively identify LYPLA1 and LYPLA2 substrates and functionally test the role of these enzymes in dynamic de-palmitoylation and tumorigenesis, development of high affinity inhibitors, capable of achieving temporal and more complete control over activity, is critical.

References:

1. Dekker, F.J., et al., Small-molecule inhibition of APT1 affects Ras localization and signaling. Nat. Chem. Biol., 2010. 6(6): p. 449-56.
2. Duncan, J.A. and A.G. Gilman, A cytoplasmic acyl-protein thioesterase that removes palmitate from G protein alpha subunits and p21(RAS). J. Biol. Chem., 1998. 273(25): p. 15830-7.
3. Sugimoto, H., H. Hayashi, and S. Yamashita, Purification, cDNA cloning, and regulation of lysophospholipase from rat liver. J. Biol. Chem., 1996. 271(13): p. 7705-11.
4. Toyoda, T., H. Sugimoto, and S. Yamashita, Sequence, expression in Escherichia coli, and characterization of lysophospholipase II. Biochim. Biophys. Acta, 1999. 1437(2): p. 182-93.
5. Biel, M., et al., Synthesis and evaluation of acyl protein thioesterase 1 (APT1) inhibitors. Chemistry, 2006. 12(15): p. 4121-43.
6. Deck, P., et al., Development and biological evaluation of acyl protein thioesterase 1 (APT1) inhibitors. Angew. Chem. Int. Ed. Engl., 2005. 44(31): p. 4975-80.
7. Jessani, N., et al., Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness. Proc. Natl. Acad. Sci. U. S. A., 2002. 99(16): p. 10335-40.
8. Leung, D., et al., Discovering potent and selective reversible inhibitors of enzymes in complex proteomes. Nat. Biotechnol., 2003. 21(6): p. 687-91.
9. Bachovchin, D.A., et al., Identification of selective inhibitors of uncharacterized enzymes by high-throughput screening with fluorescent activity-based probes. Nat. Biotechnol., 2009. 27(4): p. 387-94.
10. Forner, F., et al., Quantitative proteomic comparison of rat mitochondria from muscle, heart, and liver. Mol. Cell. Proteomics, 2006. 5(4): p. 608-19.
11. Schubert, C., The genomic basis of the Williams-Beuren syndrome. Cell. Mol. Life Sci., 2009. 66(7): p. 1178-97.

Keywords:

late stage, late stage AID, assay provider, powders, LYPLA1, lysophospholipase 1, LYPLA2, lysophospholipase 2, APT1, acyl-protein thioesterase 1, APT2, acyl-protein thioesterase 2, serine hydrolase, palmitoylation, counterscreen, inhibitor, activity-based protein profiling, ABPP, gel-based ABPP, fluorophosphonate peg rhodamine, FP-PEG-Rh, HEK293T cells, gel filtration, reversible, irreversible, binding mode, Scripps, Scripps Research Institute Molecular Screening Center, SRIMSC, Molecular Libraries Probe Production Centers Network, MLPCN
Panel Information
Targets
PID§NameSubstancePanel TargetsDescriptionAdditional Information
ActiveInactive
1LYPLA112acyl-protein thioesterase 1 [Homo sapiens] [gi:5453722]
Taxonomy id: 9606
Gene id: 10434
2LYPLA212acyl-protein thioesterase 2 [Homo sapiens] [gi:9966764]
Taxonomy id: 9606
Gene id: 11313

§ Panel component ID.
Protocol
Assay Overview:

The purpose of this assay is to determine whether powder samples of test compounds inhibit LYPLA1 and LYPLA2 in a reversible or irreversible manner. In this assay, a complex proteome is incubated with test compound and a fraction of the assay mixture is passaged over a Sephadex G-25M column before reaction with the serine-hydrolase-specific fluorophosphonate-PEG-rhodamine (FP-PEG-Rh) probe. FP-PEG-Rh is similar to FP-Rh, but shows slower reaction kinetics, facilitating analysis of target inhibition by reversible compounds. The reaction products are separated by SDS-PAGE and visualized in-gel using a flatbed fluorescence scanner. The percentage activity remaining is determined by measuring the integrated optical density (IOD) of the bands relative to a DMSO (no compound) control. As designed, test compounds that act as irreversible inhibitors will prevent enzyme-probe interactions both before and after gel filtration, leading to low fluorescence intensity in the band in the gel. In contrast, compounds that act as reversible inhibitors will show recovery of probe labeling (and higher fluorescence intensity in the band in the gel) following gel filtration to remove small molecules (including probe) from the sample.

Protocol Summary:

Soluble proteome (2 mL of 1 mg/ml in DPBS) of HEK293T cells was treated with 10 uM or 20 uM test compound (50x stock in DMSO) or DMSO (control). Test compounds were incubated for 30 minutes at 37 C. An aliquot (50 uL) was removed from each reaction, and the remaining sample was passaged over a Sephadex G-25M column 1, 2, or 3x, with an aliquot (50 uL) set aside after each passage. Aliquot volumes were adjusted to equalize protein concentrations across all samples and reacted with FP-PEG-Rh (50x stock in DMSO; 5 uM final concentration). The reaction was incubated for 30 minutes at 25 C, quenched with 2x SDS-PAGE loading buffer, separated by SDS-PAGE and visualized by in-gel fluorescent scanning. The percentage activity remaining was determined by measuring the integrated optical density of the LYPLA1 and LYPLA2 bands relative to a DMSO-only (no compound) control.

%_Inhibition = ( 1 - ( IOD_Test_Compound - IOD_Low_Control ) / ( IOD_High_Control - IOD_Low_Control ) ) * 100

Where:

Test_Compound is defined as target or anti-target treated with test compound.
High_Control is defined as target or anti-target treated with DMSO only (no compound).
Low_Control is defined as background in a blank region of the gel.

Binding Mode:

Compounds were designated as reversible inhibitors if they exhibited less than 50% inhibition (i.e., greater than or equal to 50% recovery) of probe labeling following two or more gel filtrations. Compounds were designated as irreversible inhibitors if they exhibited greater than or equal to 50% inhibition (i.e., less than 50% recovery) of probe labeling following two or more gel filtrations. If compounds did not show inhibition of a protein target prior to gel filtration, their binding mode is listed as "not applicable" (NA) for that particular protein target.

PubChem Activity Outcome and Score:

The following applies to each panel in this assay:

Compounds designated as "reversible" inhibitors were considered active. Compounds designated as "irreversible" inhibitors were considered inactive.

Overall Outcome and Score:

Compounds were considered active if they were active in at least one assay. Compounds were considered inactive if they were inactive in all assays.

The PubChem Activity Score is assigned a value of 100 for active compounds, and 0 for inactive compounds.

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

List of Reagents:

Soluble proteome of HEK293T cells (provided by the Assay Provider)
FP-PEG-Rh (provided by the Assay Provider)
DPBS (Cellgro 20-031-CV)
Sephadex G-25M column (GE Healthcare)
Comment
This assay was performed by the assay provider with powder samples of synthetic compounds.
Result Definitions
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TIDNameDescriptionPID§Panel TargetsHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1Outcome [LYPLA1]One of Active, Inactive, or Not Tested1acyl-protein thioesterase 1 [Homo sapiens]Outcome
2Binding mode [LYPLA1]One of Reversible, Irreversible, or Not Tested (NT)1String
3Inhibition [prior to gel filtration, LYPLA1]The value for percent inhibition of endogenous human LYPLA1 prior to gel filtration as assessed by ABPP.1Integer%
4Inhibition [1 gel filtration, LYPLA1]The value for percent inhibition of endogenous human LYPLA1 following one gel filtration as assessed by ABPP.1Integer%
5Inhibition [2 gel filtrations, LYPLA1]The value for percent inhibition of endogenous human LYPLA1 following two gel filtrations as assessed by ABPP.1Integer%
6Inhibition [3 gel filtrations, LYPLA1]The value for percent inhibition of endogenous human LYPLA1 following three gel filtrations as assessed by ABPP.1Integer%
7Outcome [LYPLA2]One of Active, Inactive, or Not Tested2acyl-protein thioesterase 2 [Homo sapiens]Outcome
8Binding mode [LYPLA2]One of Reversible, Irreversible, or Not Tested (NT)2String
9Inhibition [prior to gel filtration, LYPLA2]The value for percent inhibition of endogenous human LYPLA2 prior to gel filtration as assessed by ABPP.2Integer%
10Inhibition [1 gel filtration, LYPLA2]The value for percent inhibition of endogenous human LYPLA2 following one gel filtration as assessed by ABPP.2Integer%
11Inhibition [2 gel filtrations, LYPLA2]The value for percent inhibition of endogenous human LYPLA2 following two gel filtrations as assessed by ABPP.2Integer%
12Inhibition [3 gel filtrations, LYPLA2]The value for percent inhibition of endogenous human LYPLA2 following three gel filtrations as assessed by ABPP.2Integer%
Additional Information
Grant Number: 1 R01 CA132630

Classification
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