Bookmark and Share
BioAssay: AID 652004

Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA2: fluorescence-based biochemical dose-response assay

Name: Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA2: fluorescence-based biochemical dose-response assay. ..more
_
   
 Tested Compounds
 Tested Compounds
All(1)
 
 
Inactive(1)
 
 
 Tested Substances
 Tested Substances
All(1)
 
 
Inactive(1)
 
 
AID: 652004
Data Source: The Scripps Research Institute Molecular Screening Center (LYPLA2_INH_FLUO_4XIC50)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: NIH Molecular Libraries Probe Production Network, Assay Provider
BioAssay Version:
Deposit Date: 2013-01-30
Hold-until Date: 2013-10-18
Modify Date: 2013-10-18

Data Table ( Complete ):           All
Target
Tested Compound:
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)
651980Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA2: LCMS-based cell-based Activity-Based Protein Profiling (ABPP) SILAC selectivity analysis in situother Late stage assay (SILAC selectivity analysis in situ)
651979Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA1: LCMS-based cell-based Activity-Based Protein Profiling (ABPP) SILAC selectivity analysis in situother Late stage assay (SILAC selectivity analysis in situ)
651981Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA2: LCMS-based Activity-Based Protein Profiling (ABPP) SILAC selectivity analysis in vitroother Late stage assay (SILAC selectivity analysis in vitro)
651978Late 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 vitroother Late stage assay (SILAC selectivity analysis in vitro)
651985Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA1 and LYPLA2: Fluorescence-based biochemical gel-based ABPP evaluation of activity in vivoother Late stage assay (LYPLA1 and LYPLA2 inhibitors activity in vivo)
651987Late 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 modeother Late stage assay (binding mode)
651986Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA1 and LYPLA2: Fluorescence-based biochemical gel-based ABPP evaluation of activity in situother Late stage assay (LYPLA1 and LYPLA2 inhibitors activity in situ)
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: LYPLA2_INH_FLUO_4XIC50

Name: Late stage assay provider results from the probe development effort to identify selective inhibitors of LYPLA2: fluorescence-based biochemical dose-response assay.

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, LYPLA2, lysophospholipase 2, APT2, acyl-protein thioesterase 2, serine hydrolase, palmitoylation, counterscreen, inhibitor, inhibition, substrate, resorufin acetate, IC50, dose response, Scripps, Scripps Research Institute Molecular Screening Center, SRIMSC, Molecular Libraries Probe Production Centers Network, MLPCN
Protocol
Assay Overview:

The purpose of this assay is to determine IC50 values for powder samples of test compounds that act as reversible inhibitors for LYPLA2 using a fluorogenic substrate (resorufin acetate)-based assay. For this assay, LYPLA2 is incubated with varying concentrations of inhibitor at a fixed substrate concentration, and fluorescence intensity is monitored as a function of time. Initial velocities determined for each inhibitor concentration are used to calculate IC50 values. For all assays, enzyme activity is calculated relative to a catalytically-dead (LYPLA2-S122A) enzyme control.

Protocol Summary:

Substrate resorufin acetate was dissolved in DMSO. Active or catalytically-dead LYPLA2 enzyme solutions (10 nM) were prepared in DPBS adjusted to pH 6.5 with sodium acetate and 0.2% pluronic F127. Enzyme was incubated with varying inhibitor concentrations (8-point 2-fold dilution series from 100 uM to 78 nM, and 0 nM) for 15 minutes (95 uL total volume), and then aliquoted into black-bottom half-area 96-well plate wells containing a fixed concentration of resorufin acetate substrate (50 uM, 5 uL) using a multi-channel pipette. Reactions were quickly mixed by pipetting up and down several times. Fluorescence intensity was measured on a Tecan F500 plate reader at room temperature every 30 seconds using a 525/35 nM excitation filter, a 600/10 nM emission filter, and a 560 LP dichroic filter. Each concentration was performed as 4 separate replicates for both the active and dead enzymes. After subtracting background (average fluorescence intensity of catalytically-dead enzyme at each time point for each assay condition), fluorescence intensity was plotted vs. time and initial velocities were calculated using standard straight-line plots (with non-linear regression) in GraphPad Prism using the first ~6 minutes of the reaction. The initial velocities (+/- SEM, plotted vs. inhibitor concentration) were analyzed to derive IC50 values (standard one phase decay, GraphPad Prism). Software-generated values and SEM are reported. In the event that the highest test concentration did not result in at least 50% inhibition, the IC50 value is reported as being greater than 10 uM.

PubChem Activity Outcome and Score:

Compounds with an IC50 value of less than or equal to 10 uM were considered active. Compounds with an IC50 value of greater than 10 uM were considered inactive.

Activity score was then ranked by the potency of the compounds, with the most potent compounds assigned the highest activity scores.

The PubChem Activity Score range for inactive compounds is 0-0. There are no active compounds.

List of Reagents:

Resorufin acetate (SigmaAldrich, 83636)
Recombinant human LYPLA2 (provided by the Assay Provider)
Catalytically-dead (S122A) recombinant human LYPLA2 (provided by the Assay Provider)
DPBS (Cellgro 20-031-CV)
Sodium acetate (FisherScientific, BP333)
Pluronic F127 (Invitrogen, P6866)
Comment
This assay was performed by the assay provider with powder samples of synthetic compounds.
Categorized Comment
Assay: Dictionary: Version: 0.1

Assay: CurveFit [1]: Equation: = ( [Y0] - [Plateau] ) * exp( -[Rate Constant] * [Concentration] ) + [Plateau]

Result Definitions
Show more
TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
1QualifierQualifier identifies if the resultant IC50 was determined manually to be less than or greater than its listed IC50.String
2IC50*The average concentration at which 50 percent inhibiton is observed; (IC50), calculated from the initial reaction velocity as described in the text; shown in micromolar.FloatμM
3Y0Y0 is the initial velocity when concentration is zero.Float
4PlateauPlateau is the initial velocity value at infinite concentration.Float
5Rate ConstantIs the rate constant of the equation. Expressed in inverse uM.Float
6SpanSpan is the difference between Y0 and Plateau.Float
7Average Initial Velocity at 0.78 uM (0.78μM**)Normalized average initial velocity at 0.78 uM compound concentration.Floatratio
8Standard Error of Initial Velocity at 0.78 uMStandard error of average initial velocity at 0.78 uM compound concentration.Floatratio
9Average Initial Velocity at 1.56 uM (1.56μM**)Normalized average initial velocity at 1.56 uM compound concentration.Floatratio
10Standard Error of Initial Velocity at 1.56 uMStandard error of average initial velocity at 1.56 uM compound concentration.Floatratio
11Average Initial Velocity at 3.13 uM (3.13μM**)Normalized average initial velocity at 3.13 uM compound concentration.Floatratio
12Standard Error of Initial Velocity at 3.13 uMStandard error of average initial velocity at 3.13 uM compound concentration.Floatratio
13Average Initial Velocity at 6.25 uM (6.25μM**)Normalized average initial velocity at 6.25 uM compound concentration.Floatratio
14Standard Error of Initial Velocity at 6.25 uMStandard error of average initial velocity at 6.25 uM compound concentration.Floatratio
15Average Initial Velocity at 12.5 uM (12.5μM**)Normalized average initial velocity at 12.5 uM compound concentration.Floatratio
16Standard Error of Average Velocity at 12.5 uMStandard error of average initial velocity at 12.5 uM compound concentration.Floatratio
17Average Initial Velocity at 25 uM (25μM**)Normalized average initial velocity at 25 uM compound concentration.Floatratio
18Standard Error of Initial Velocity at 25 uMStandard error of average initial velocity at 25 uM compound concentration.Floatratio
19Average Initial Velocity at 50 uM (50μM**)Normalized average initial velocity at 50 uM compound concentration.Floatratio
20Standard Error of Initial Velocity at 50 uMStandard error of average initial velocity at 50 uM compound concentration.Floatratio
21Average Initial Velocity at 100 uM (100μM**)Normalized average initial velocity at 100 uM compound concentration.Floatratio
22Standard Error of Initial Velocity at 100 uMStandard error of average initial velocity at 100 uM compound concentration.Floatratio

* Activity Concentration. ** Test Concentration.
Additional Information
Grant Number: 1 R01 CA132630

Data Table (Concise)
PageFrom: