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BioAssay: AID 588487

Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): fluorescence-based biochemical gel-based competitive Activity-Based Protein Profiling (ABPP) inhibition by HTS hits of PADs 1-4

Name: Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): fluorescence-based biochemical gel-based competitive Activity-Based Protein Profiling (ABPP) inhibition by HTS hits of PADs 1-4. ..more
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 Tested Compounds
 Tested Compounds
All(79)
 
 
Active(35)
 
 
Inactive(44)
 
 
 Tested Substances
 Tested Substances
All(79)
 
 
Active(35)
 
 
Inactive(44)
 
 
AID: 588487
Data Source: The Scripps Research Institute Molecular Screening Center (PAD1-4_INH_FLUO_GELBASEDABPP_1X%INH)
BioAssay Type: Panel
Depositor Category: NIH Molecular Libraries Probe Production Network, Assay Provider
BioAssay Version:
Deposit Date: 2011-10-11
Hold-until Date: 2011-10-13
Modify Date: 2011-10-13

Data Table ( Complete ):           View Active Data    View All Data
BioActive Compounds: 35
Related Experiments
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AIDNameTypeComment
463073Fluorescence polarization-based primary biochemical high throughput screening assay to identify inhibitors of Protein Arginine Deiminase 4 (PAD4)Screeningdepositor-specified cross reference: Primary screen (PAD4 inhibitors in singlicate, NIH 2K Validation)
463083Summary of the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4)Summarydepositor-specified cross reference: Summary (PAD4 inhibitors)
485272Fluorescence polarization-based primary biochemical high throughput screening assay to identify inhibitors of Protein Arginine Deiminase 4 (PAD4) (1536 HTS)Screeningdepositor-specified cross reference: Primary screen (PAD4 inhibitors in singlicate)
488796Fluorescence polarization-based biochemical high throughput confirmation assay for inhibitors of Protein Arginine Deiminase 4 (PAD4)Screeningdepositor-specified cross reference: Confirmation screen (PAD4 inhibitors in triplicate)
492970Fluorescence-based biochemical dose response assay to identify inhibitors of Protein Arginine Deiminase 4 (PAD4)Confirmatorydepositor-specified cross reference: Dose response (PAD5 inhibitors in duplicate)
651627Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate dialysis assay to assess binding mode of test compounds to PAD4Otherdepositor-specified cross reference
651628Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): fluorescence-based biochemical gel-based competitive Activity-Based Protein Profiling (ABPP) assessment of compound selectivityOtherdepositor-specified cross reference
651861Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate dialysis assay to assess binding mode of test compounds to PADs 1-3Otherdepositor-specified cross reference
651865Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to determine rate constants of test compounds for PAD 2 inactivationOtherdepositor-specified cross reference
651866Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to determine rate constants of test compounds for PAD 3 inactivationOtherdepositor-specified cross reference
651867Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to determine rate constants of test compounds for PAD 4 inactivationOtherdepositor-specified cross reference
651868Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to determine rate constants of test compounds for PAD 1 inactivationOtherdepositor-specified cross reference
651887Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): cell-based absorbance-based assay to assess cytotoxicity of test compoundsConfirmatorydepositor-specified cross reference
588416Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to assess potency of compound 16 against PAD4Confirmatorysame project related to Summary assay
588417Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to assess potency of compound 15 against PAD4Confirmatorysame project related to Summary assay
588418Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to assess potency of compound 13 against PAD4Confirmatorysame project related to Summary assay
588419Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to assess potency of compound 12 against PAD4Confirmatorysame project related to Summary assay
588420Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to assess potency of compound 11 against PAD4Confirmatorysame project related to Summary assay
588421Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical assay to assess potency of compound 6 against PAD4Confirmatorysame project related to Summary assay
588422Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical assay to assess potency of compound 2 against PAD4Confirmatorysame project related to Summary assay
588423Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to assess potency of compound 18 against PAD4Confirmatorysame project related to Summary assay
588438Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to assess potency of compound 1 against PAD1-4Confirmatorysame project related to Summary assay
588462Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to assess potency of streptonigrin against PAD1-3Confirmatorysame project related to Summary assay
588471Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to assess potency of compound 3 against PAD1-4Confirmatorysame project related to Summary assay
588472Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to assess potency of compound 14 against PAD1-4Confirmatorysame project related to Summary assay
588484Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to assess potency of compound 10 against PAD1-4Confirmatorysame project related to Summary assay
588486Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to assess potency of compound 21 against PAD1-4Confirmatorysame project related to Summary assay
588488Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to assess potency of HTS hits against PAD1-4Othersame project related to Summary assay
588490Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to assess potency of compound 17 against PAD1-4Confirmatorysame project related to Summary assay
588559Late stage assay provider results from the probe development effort to identify inhibitors of Arginine Deiminase 4 (PAD4): colorimetric biochemical substrate assay to identify inhibitors of PAD4Othersame project related to Summary assay
588560Late stage assay provider results from the probe development effort to identify inhibitors of PAD4: colorimetric biochemical substrate assay to identify inhibitors of PADs 1-4Othersame project related to Summary assay
Description:
Source (MLPCN Center Name): The Scripps Research Institute Molecular Screening Center (SRIMSC)
Center Affiliation: The Scripps Research Institute (TSRI)
Assay Provider: Paul Thompson, TSRI (Florida)
Network: Molecular Libraries Probe Production Centers Network (MLPCN)
Grant Proposal Number: R01 GM079357-01
Grant Proposal PI: Paul Thompson
External Assay ID: PAD1-4_INH_ABS_96_2XIC50_CMPD14

Name: Late stage assay provider results from the probe development effort to identify inhibitors of Protein Arginine Deiminase 4 (PAD4): fluorescence-based biochemical gel-based competitive Activity-Based Protein Profiling (ABPP) inhibition by HTS hits of PADs 1-4.

Description:

Rheumatoid Arthritis (RA) is a chronic and progressive autoimmune disorder that affects about one percent of the US population (1). Existing therapies treat the symptoms of the disease but not the underlying cause, and are associated with numerous side effects (2). The activity of Protein Arginine Deiminase 4 (PAD4), one of four known active PAD isozymes, is increased in RA; where it is thought to generate a subset of antigens that the immune system recognizes as foreign (3). Genetic, serological, and biochemical evidence suggests that dysregulated PAD4, and potentially PAD2, activities play a role in both the onset and progression of RA (1). Cl-amidine, a compound that specifically inactivates PAD4, reduces disease severity and incidence in the collagen-induced model of arthritis (CIA) (unpublished observations). However, because Cl-amidine inhibits all of the PAD isozymes with equipotency, it is unclear whether the observed reduction in disease severity is due to the inhibition of single or multiple PADs. This is particularly relevant because both PAD 2 and 4 are overexpressed in the joints of patients with RA (4). Thus, the identification of PAD selective inhibitors would facilitate the characterization of their individual contributions to the onset and progression of RA and represent a promising novel therapeutic approach for RA.

References:

1. Vossenaar, E.R., et al., PAD, a growing family of citrullinating enzymes: genes, features and involvement in disease. Bioessays, 2003. 25(11): p. 1106-18.
2. Smolen, J.S. and G. Steiner, Therapeutic strategies for rheumatoid arthritis. Nat Rev Drug Discov, 2003. 2(6): p. 473-88.
3. Vossenaar, E.R., et al., Expression and activity of citrullinating peptidylarginine deiminase enzymes in monocytes and macrophages. Ann Rheum Dis, 2004. 63(4): p. 373-81.
4. Lundberg, K., et al., Citrullinated proteins have increased immunogenicity and arthritogenicity and their presence in arthritic joints correlates with disease severity. Arthritis Res Ther, 2005. 7(3): p. R458-67.

Keywords:

late stage, late stage AID, assay provider, cherry picks, protein arginine deiminase type-1, protein arginine deiminase type-2, protein arginine deiminase type-3, protein arginine deiminase type-4, PAD1, PAD2, PAD3, PAD4, rheumatoid arthritis, RA, collagen-induced model of arthritis, activity-based protein profiling, ABPP, gel-based ABPP, rhodamine-conjugated F-amidine, RFA, Scripps, The Scripps Research Institute Molecular Screening Center, SRIMSC, Molecular Libraries Probe Production Centers Network, MLPCN
Panel Information
Targets
    Data Table(Active)    Data Table(All)Show more
PID§NameSubstancePanel TargetsDescriptionAdditional Information
ActiveInactive
1PAD1574protein-arginine deiminase type-1 [Homo sapiens] [gi:122056685]
Taxonomy id: 9606
Gene id: 29943
2PAD21564protein-arginine deiminase type-2 [Homo sapiens] [gi:122939159]
Taxonomy id: 9606
Gene id: 11240
3PAD3376protein-arginine deiminase type-3 [Homo sapiens] [gi:122939161]
Taxonomy id: 9606
Gene id: 51702
4PAD41861protein-arginine deiminase type-4 [Homo sapiens] [gi:216548487]
Taxonomy id: 9606
Gene id: 23569

§ Panel component ID.
Protocol
Assay Overview:
The purpose of this assay is to determine whether cherry picked HTS hit compounds can inhibit PADs 1-4 in a gel-based activity-based proteomic profiling (ABPP) assay. In this assay, the target enzyme (PAD1, 2, 3 or 4) is incubated with test compound followed by reaction with a rhodamine-conjugated F-amidine (RFA) activity-based probe. 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. As designed, test compounds that act as PAD inhibitors will prevent enzyme-probe interactions, thereby decreasing the proportion of bound fluorescent probe, giving lower fluorescence intensity in the band in the gel. Percent inhibition is calculated relative to a DMSO (no compound) control.
Protocol Summary:
Recombinant PAD1 (Assay 1), PAD2 (Assay 2), PAD3 (Assay 3), or PAD4 (Assay4) (10 uM) in assay buffer (50 mM NaCl, 10 mM CaCl2, 2 mM DTT, 100 mM HEPES, pH 8.0) was treated with test compound (10 uM) or DMSO for 15 minutes at 37 C. RFA was added to a final concentration of 1 uM. The reaction was incubated for 30 minutes in the dark at 37 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 target enzyme (PAD1, 2, 3, or 4) band 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 enzyme treated with test compound.
High_Control is defined as target enzyme treated with DMSO only (no compound).
Low_Control is defined as background in a blank region of the gel.
PubChem Activity Outcome and Score:
The following applies to each panel in this assay:
Compounds with greater than or equal to 50% inhibition were considered active. Compounds with less than 50% inhibition were considered inactive.
The reported PubChem Activity Score has been normalized to 100% observed inhibition. Negative % inhibition values are reported as activity score zero.
PAD1 Score: The PubChem Activity Score range for active compounds is 100-71 and for inactive compounds 63-0.
PAD2 Score: The PubChem Activity Score range for active compounds is 100-54 and for inactive compounds 51-0.
PAD3 Score: The PubChem Activity Score range for active compounds is 100-86 and for inactive compounds 74-0.
PAD4 Score: The PubChem Activity Score range for active compounds is 100-54 and for inactive compounds 50-0.
Overall Outcome and Score:
The overall outcome was active if the compound was active in at least one panel, inactive otherwise.
The overall score is 0 if the compound was inactive, otherwise the score is taken as the fraction of panels where the compound is active, multiplied by 100.
The PubChem Activity Score range for active compounds is 50-25 and for inactive compounds 0-0.
List of Reagents:
Recombinant PADs 1-4 (supplied by Assay Provider)
RFA (supplied by Assay Provider)
NaCl (Sigma, part S6546)
CaCl2 (Sigma, part C3881)
DTT (RPI, part D110000)
HEPES (Sigma, part 54457)
Comment
This assay was performed by the assay provider with liquid cherry-picked compounds.
Categorized Comment - additional comments and annotations
From BioAssay Depositor:
BAO: bioassay specification: assay biosafety level: bsl1
BAO: bioassay specification: assay measurement type: endpoint assay
BAO: bioassay specification: assay readout content: assay readout method: regular screening
BAO: bioassay specification: assay readout content: content readout type: single readout
BAO: bioassay specification: assay stage: compound profiling
BAO: detection technology: fluorescence: fluorescence intensity
BAO: meta target detail: binding reporter specification: interaction: protein-small molecule
BAO: meta target: molecular target: protein target: enzyme: generic hydrolase
BAO: version: 1.4b1080
From PubChem:
Assay Format: Biochemical
Result Definitions
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TIDNameDescriptionPID§Panel TargetsHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
ScoreThe BioAssay activity ranking scoreInteger
1Outcome [PAD1]One of Active, Inactive, or Not Tested1protein-arginine deiminase type-1 [Homo sapiens]Outcome
2Score [PAD1]The BioAssay activity ranking score1Integer
3Inhibition at 10 uM [PAD1] (10μM**)Inhibition of recombinant PAD1 upon 10 uM compound treatment as assessed by gel-based competitive ABPP.1Float%
4Outcome [PAD2]One of Active, Inactive, or Not Tested2protein-arginine deiminase type-2 [Homo sapiens]Outcome
5Score [PAD2]The BioAssay activity ranking score2Integer
6Inhibition at 10 uM [PAD2] (10μM**)Inhibition of recombinant PAD2 upon 10 uM compound treatment as assessed by gel-based competitive ABPP.2Float%
7Outcome [PAD3]One of Active, Inactive, or Not Tested3protein-arginine deiminase type-3 [Homo sapiens]Outcome
8Score [PAD3]The BioAssay activity ranking score3Integer
9Inhibition at 10 uM [PAD3] (10μM**)Inhibition of recombinant PAD3 upon 10 uM compound treatment as assessed by gel-based competitive ABPP.3Float%
10Outcome [PAD4]One of Active, Inactive, or Not Tested4protein-arginine deiminase type-4 [Homo sapiens]Outcome
11Score [PAD4]The BioAssay activity ranking score4Integer
12Inhibition at 10 uM [PAD4] (10μM**)Inhibition of recombinant PAD4 upon 10 uM compound treatment as assessed by gel-based competitive ABPP.4Float%

** Test Concentration. § Panel component ID.
Additional Information
Grant Number: R01 GM079357-01

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