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bromoKdMAX- Bromodomain Assay Panel

Quantitate compound binding affinity against all 40 BROMOscan bromodomain assays. Inhibitor binding constants (Kd values) are calculated from duplicate 11-point dose-response curves.  Measurements are made under optimized conditions that generate true thermodynamic Kd values and facilitate direct comparison of inhibitor affinity across bromdomains. bromoKdMAX is a powerful screening tool and ideally suited for later stage compounds in preclinical & clinical development. 

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Panel Features & Benefits

  • Quantitative binding affinity data across all 40 bromodomain assays
  • 11-point dose response curves in duplicate
  • Sensitivity & dynamic range: <100 pm to >10uM
  • Reveal unanticipated opportunities & potential liabilities
  • Fast time to results - 3 weeks to data delivery
How it Works

Assay Performance

All BROMOscan assays were validated with small molecule ligands and/or acetylated histone tail peptides. Measured Kd’s were compared to published isothermal calorimetry (ITC) values. Contact us for a complete data validation package.

Family IV Assay Validation – BRD1

A. Ligand Affinity Measurement


 

B. Selective Binding to Acetylated Histone Tail Peptide

Bromodomain Histone Tail Peptide BROMOscan Kd (nM)
BRD1 H4(Ac)1 15,000
BRD1 H42 >100,000
1internally discovered acetylated peptide ligand. 2corresponding non-acetylated peptide.
BRD1 was tested in Kd mode using a known bromodomain ligand (Panel A) and acetylated/non-acetylated histone tail peptide (Panel B).

bromoKdMAX Assay Panel

Listed below are the assays currently available for screening and profiling.
 
 
BGS ▲Bromodomain Protein NameEntrez Gene Symbol
ATAD2AATPase family AAA domain-containing protein 2ATAD2
ATAD2BATPase family, AAA domain containing 2BATAD2B
BAZ2Abromodomain adjacent to zinc finger domain, 2ABAZ2A
BAZ2Bbromodomain adjacent to zinc finger domain, 2BBAZ2B
BRD1bromodomain-containing protein 1BRD1
BRD2(1)bromodomain-containing protein 2 isoform 1, bromodomain 1BRD2
BRD2(1,2)bromodomain-containing protein 2 isoform 1, bromodomains 1 and 2BRD2
BRD2(2)bromodomain-containing protein 2 isoform 1, bromodomain 2BRD2
BRD3(1)bromodomain-containing protein 3, bromodomain 1BRD3
BRD3(1,2)bromodomain-containing protein 3, bromodomains 1 and 2BRD3
BRD3(2)bromodomain-containing protein 3, bromodomain 2BRD3
BRD4(1)bromodomain-containing protein 4 isoform long, bromodomain 1BRD4
BRD4(1,2)bromodomain-containing protein 4 isoform long, bromodomains 1 and 2BRD4
BRD4(2)bromodomain-containing protein 4 isoform long, bromodomain 2BRD4
BRD4(full-length,short-iso.)bromodomain-containing protein 4 isoform shortBRD4
BRD7bromodomain containing 7BRD7
BRD8(1)bromodomain containing 8, bromodomain 1BRD8
BRD8(2)bromodomain containing 8, bromodomain 2BRD8
BRD9bromodomain-containing protein 9 isoform 1BRD9
BRDT(1)bromodomain testis-specific protein isoform b, bromodomain 1BRDT
BRDT(1,2)bromodomain testis-specific protein isoform b, bromodomains 1 and 2BRDT
BRDT(2)bromodomain testis-specific protein isoform b, bromodomain 2BRDT
BRPF1bromodomain and PHD finger containing, 1BRPF1
BRPF3bromodomain and PHD finger containing, 3BRPF3
CECR2cat eye syndrome chromosome region, candidate 2CECR2
CREBBPCREB binding proteinCREBBP
EP300E1A binding protein p300EP300
FALZnucleosome-remodeling factor subunit BPTF isoform 1BPTF
GCN5L2K(lysine) acetyltransferase 2AKAT2A
PBRM1(2)polybromo 1, bromodomain 2PBRM1
PBRM1(5)polybromo 1, bromodomain 5PBRM1
PCAFK(lysine) acetyltransferase 2BKAT2B
SMARCA2SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2SMARCA2
SMARCA4SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4SMARCA4
TAF1(2)TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa, bromodomain 2TAF1
TAF1L(2)TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like, bromodomain 2TAF1L
TRIM24(Bromo.)tripartite motif containing 24TRIM24
TRIM24(PHD,Bromo.)tripartite motif containing 24TRIM24
TRIM33(PHD,Bromo.)tripartite motif containing 33TRIM33
WDR9(2)bromodomain and WD repeat domain containing 1, bromodomain 2BRWD1
 

Data Analysis & Interpretation

Definitions

Percent of Control (%Ctrl)

The results for single concentration (primary screen) binding interactions for tested compound(s) are reported in your study report and spreadsheets as '%Ctrl' and is calculated in the following manner:

    test compound = client supplied compound
    negative control = DMSO (100% control)
    positive control = control compound (0% control)

Binding Constant (Kd)

The results for an 11-point dose response curve compound/kinase interactions are reported in your study report and spreadsheets as Kd, which are values derived using the Hill equation:
Hill equation used for calculating binding constants
The Hill Slope is set to -1. Curves are fitted using a non-linear least square fit with the Levenberg-Marquardt algorithm.

Selectivity Score (S-Scores)

Selectivity Score or S-score is a quantitative measure of compound selectivity. It is calculated by dividing the number of kinases that compounds bind to by the total number of distinct kinases tested, excluding mutant variants.
selectivity score calculation

This value can be calculated using %Ctrl as a potency threshold (below) and provides a quantitative method of describing compound selectivity to facilitate comparison of different compounds.

   S(35) = (number of non-mutant kinases with %Ctrl <35)/(number of non-mutant kinases tested)

   S(10) = (number of non-mutant kinases with %Ctrl <10)/(number of non-mutant kinases tested)

     S(1) = (number of non-mutant kinases with %Ctrl <1)/(number of non-mutant kinases tested)

Using S-Score Data to Quantitate Selectivity

Selectivity Profile for 38 Small Molecule Kinase Inhibitors

32 small molecule compound calibration curve
KINOMEscan's in vitro competition binding assay was used to evaluate 38 kinase inhibitors against a panel of 287 distinct human protein kinases (~55% of the predicted human protein kinome), and three lipid kinases. The compounds tested included 21 tyrosine kinase inhibitors, 15 serine-threonine kinase inhibitors, 1 lipid kinase inhibitor, and staurosporine. S(35), 10uM = (number of non-mutant kinases with %Ctrl <35)/(290 kinases tested; 27 mutant variants were excluded from this analysis). Compounds approved for use in humans (as of August, 2007) are highlighted (gray bars)  [click graph to enlarge].

TREEspot Kinase Dendrograms: A Visual Representation of Compound Selectivity

TREEspot is an innovative compound profile visualization tool for visualizing screening data. Kinases found to bind are marked with red circles, where larger circles indicate higher-affinity binding.

RSK Inhibitor 

RSK Inhibitor small panel versus large panel selectivity

RSK inhibitor was reported in published findings to be a selective RSK kinase inhibitor on the basis of kinase profiling against a panel of 54 kinases.  Selectivity profiling against the scanMAX kinase assay panel (then 402) revealed additional interactions not previously identified [click graph to enlarge].

TREEspot Compound Profile Visualization Tool

TREEspot is an innovative, secure access, web-based, compound profile visualization tool for analysis of KINOMEscan screening data. TREEspot is an ideal companion tool for existing data analysis applications and facilitates compound profile visualization through its simple yet powerful user interface.

Gain new perspectives of kinase profile data in a visual environment and distill essential knowledge to drive your discovery programs.  TREEspot is provided as a complimentary tool to our clients. To learn more about how you can visualize your data using TREEspot or to request access credentials, please contact KINOMEscan.

  • Easy-to-use
  • Facilitates evaluation and analysis of profiling data
  • Generates publication quality of TREEspot images
  • Provides global visualization of profile data
  • Visualize your data in a whole new way
 

scanMAX Kinase Dendrogram