SAR Analysis of small molecule UBC13 Polyubiquitin Inhibitors using a Caspase-3 counterscreen - Set 4
Tumor Necrosis Factor Receptor-Associated Factors (TRAFs) are a family of adapter proteins that bind an unusual ubiquitin-conjugating enzyme, Ubc13, which produces polyubiquitin chains linked at lysine 63 of ubiquitin. These lysine 63-linked ubiquitin polymers trigger changes in protein activity. Ubiquitination by Ubc13 of TRAFs and the various protein kinases to which TRAFs bind is recognized as more ..
Depositor Specified Assays
Data Source: Sanford-Burnham Center for Chemical Genomics (SBCCG)
Source Affiliation: Sanford-Burnham Medical Research Institute (SBMRI, San Diego CA)
Network: NIH Molecular Libraries Probe Production Centers Network (MLPCN)
Grant Number: 1R03 MH085677-01
Assay Provider: Dr. John C. Reed, Sanford-Burnham Medical Research Institute, San Diego CA
Tumor Necrosis Factor Receptor-Associated Factors (TRAFs) are a family of adapter proteins that bind an unusual ubiquitin-conjugating enzyme, Ubc13, which produces polyubiquitin chains linked at lysine 63 of ubiquitin. These lysine 63-linked ubiquitin polymers trigger changes in protein activity. Ubiquitination by Ubc13 of TRAFs and the various protein kinases to which TRAFs bind is recognized as a critical step in signaling by TNFRs, TLRs, NLRs, and T-cell and B-cell antigen receptors (TCR/BCR) during innate and acquired immune responses. Since aberrant signaling by these receptor systems is linked to a wide variety of autoimmune, inflammatory, and infectious diseases; compounds that neutralize Ubc13 may prove useful as a novel type of immunosuppressive or anti-inflammatory agent.
This assay uses a Caspase-3 sulfhydryl screen: Caspase-Glo(R) 3/7 Assay (Promega), a luminescent assay, as a counter screen for TR-FRET. The purpose of this assay is to confirm hits from "uHTS identification of UBC13 Polyubiquitin Inhibitors via a TR-FRET Assay", AID 485273 and to study the structure-activity relationship on analogs of the confirmed hits. Compounds active in both the TR-FRET and Caspase-3 assays are considered to be false positives. Samples are either acquired from commercial sources or synthesized internally.
1. Fukushima, T., Matsuzawa, S., Kress, C. L., Bruey, J. M., Krajewska, M., Lefebvre, S., Zapata, J. M., Ronai, Z., and Reed, J.C. (2007) Proc Natl Acad Sci USA 104(15), 6371-6376 (PMC1851032)
2. Yamamoto, M., Okamoto, T., Takeda, K., Sato, S., Sanjo, H., Uematsu, S., Saitoh, T., Yamamoto, N., Sakurai, H., Ishii, K. J., Yamaoka, S., Kawai, T., Matsuura, Y., Takeuchi, O., and Akira, S. (2006) Nat Immunol 7, 962-970
3. Yamamoto, M., Sato, S., Saitoh, T., Sakurai, H., Uematsu, S., Kawai, T., Ishii, K. J., Takeuchi, O., and Akira, S. (2006) J Immunol 177, 7520-7524
4. Akira, S., Takeda, K., and Kaisho, T. (2001) Nat Immunol 2, 675-680
5. Chen, Z. J. (2005) Nat Cell Biol 7, 758-765
6. Karin, M., and Ben-Neriah, Y. (2000) Ann Rev Immunol 18, 621-663
7. Deng, L., Wang, C., Spencer, E., Yang, L., Braun, A., You, J., Slaughter, C., Pickart, C., and Chen, Z. J. (2000) Cell 103, 351-361
8. Wooff, J., Pastushok, L., Hanna, M., Fu, Y., and Xiao, W. (2004) FEBS Lett 566, 229-233
9. Wu, H., and Arron, J. R. (2003) Bioessays 25, 1096-1105
10. McKenna, S., Hu, J., Moraes, T., Xiao, W., Ellison, M. J., and Spyracopoulos, L. (2003) Biochemistry 42, 7922-7930
11. Hau, D. D., Lewis, M. J., Saltibus, L. F., Pastushok, L., Xiao, W., and Spyracopoulos, L. (2006) Biochemistry 45, 9866-9877
Caspase-Glo(R) 3/7 Assay: Promega (Catalogue #: G8092)
Assay buffer: 150 mM Hepes (pH 7.8), 4.0 mM DTT, 1.0 mM EDTA, 0.01% Tween, 0.1% BSA
Assay plate: Corning 1536 Well White Plate (Catalogue #: 3725)
I. Compound Addition:
1. Using LabCyte Echo, transfer 20 nL from a 10 mM Echo qualified plate containing test compounds into assay plate columns 5 - 48 (final concentration of test compounds is 100 microM, 1.0 % DMSO). Transfer 20 nL of DMSO to positive and negative control wells in columns 1 - 4.
2. Centrifuge plates at 1000 rpm for 1 min.
3. Seal the plates and leave them at RT.
Note: Compounds are added to the plates before reagent addition
II. Set up of Caspase-3 assay:
4. Prepare assay buffer
5.Caspase 3: Dilute Caspase 3 in assay buffer to make 2X intermediate solution at 0.046 nM
6. Caspase Glo substrate: Dilute 1X substrate solution in assay buffer to make 2X intermediate solution at 0.75X
III. Reagent Addition:
7. Add 1 ul assay buffer to columns 1 & 2
8. Add 1 ul 2X intermediate Caspase 3 to columns 3 - 48
9. Add 1 ul 2X intermediate Caspase Glo substrate to all columns
10. Incubate at RT for 60 mins
IV. Reading plates:
11. Read plates using PerkinElmer ViewLux using SENP Luminescence 60 sec protocol.
Compounds that demonstrated activity of <100 uM are defined as actives in this assay.
To simplify the distinction between the inactives of the primary screen and of the confirmatory screening stage, the Tiered Activity Scoring System was developed and implemented. Its utilization for the assay is described below.
Activity scoring rules were devised to take into consideration compound efficacy, its potential interference with the assay and the screening stage that the data was obtained. Details of the Scoring System will be published elsewhere. Briefly, the outline of the scoring system utilized for the assay is as follows:
1) First tier (0-40 range) is reserved for primary screening data and is not applicable in this assay.
2) Second tier (41-80 range) is reserved for dose-response confirmation data and is not applicable in this assay
3) Third tier (81-100 range) is reserved for resynthesized true positives and their analogues
a. Inactive compounds of the confirmatory stage are assigned a score value equal 81.
b. The score is linearly correlated with a compound potency and, in addition, provides a measure of the likelihood that the compound is not an artifact based on the available information.
c. The Hill coefficient is taken as a measure of compound behavior in the assay via an additional scaling factor QC:
QC = 2.6*[exp(-0.5*nH^2) - exp(-1.5*nH^2)]
This empirical factor prorates the likelihood of target-specific compound effect vs. its non-specific behavior in the assay. This factor is based on expectation that a compound with a single mode of action that achieved equilibrium in this assay demonstrates the Hill coefficient value of 1. Compounds deviating from that behavior are penalized proportionally to the degree of their deviation.
d. Summary equation that takes into account the items discussed above is
Score = 82 + 3*(pIC50 - 3)*QC,
where pIC50 is a negative log(10) of the IC50 value expressed in mole/L concentration units. This equation results in the Score values above 85 for compounds that demonstrate high potency and predictable behavior. Compounds that are inactive in the assay or whose concentration-dependent behavior are likely to be an artifact of that assay will generally have lower Score values.
* Activity Concentration. ** Test Concentration.
Data Table (Concise)