In Vitro Kinase Inhibition Assays: All kinase assays were performed in 96-well FlashPlates from Perkin Elmer/NEN (Boston, Mass., USA) in a 50 μl reaction volume. The reaction mixture was pipetted in four steps in the following order:20 μl of assay buffer (standard buffer),5 μl of ATP solution (in H2O),5 μl of test compound (in 10% DMSO),10 μl of substrate/10 μl of enzyme solution (premixed),The assay for all enzymes contained 60 mM HEPES-NaOH, pH 7.5, 3 mM MgCl2, 3 mM MnCl2, 3 μM Na-Orthovanadate, 1.2 mM DTT, 50 μg/ml PEG20000, 1 μM [-33P]-ATP (approx. 5×1005 cpm per well).
LANCE ULight TR-FRET Kinase Assay: CDK9 enzyme activities were measured using LANCE ULight TR-FRET kinase assay reagents (PerkinElmer, Waltham, Mass.). Compounds were directly added in 100% DMSO to white low volume assay plates (Perkin Elmer Proxiplate 6008289) using a Labcyte Echo acoustic dispenser. Assay reagents in serine/threonine kinase assay buffer containing 20 mM HEPES, 10 mM MgCl2, 100 mM Na3VO4, and 0.0075% Triton X-100. were added for final reaction mixture concentrations of 1000 uM ATP, 100 nM U-light MBP peptide (Perkin Elmer TRF0109M) and reaction initiated with 4 nM CDK9/Cyclin T1 (Carna Biosciences 04-110). The kinase reaction was carried out for 30 minutes before addition of stopping buffer to a final of 20 mM EDTA and 0.5 nM of LANCE Ultra Europium anti-phospho-MBP antibody (PerkinElmer TRF0201M) in LANCE detection buffer (PerkinElmer CR97-100). The reaction was equilibrated for 1 hour and the signal read in the Perkin Elmer Envision in TR-FRET mode.
In Vitro Kinase Inhibition Assay: In vitro kinase assay analysis may be performed using standard techniques described in the art. These techniques are also used by commercial services providers in order to offer in vitro kinase activity assay services, e.g. the assays offered by Millipore Inc. (worldwide website www(dot)millipore.com), ProQinase GmbH (worldwide website www(dot)proqinase.de) and others. All kinase assays were performed in 96-well FlashPlates from Perkin Elmer/NEN (Boston, Mass., USA) in a 50ul reaction volume. The reaction mixture was pipetted in four steps in the following order: 20ul of assay buffer (standard buffer),5ul of ATP solution (in H2O, 5 ul of test compound (in 10% DMSO), 10ul of substrate/10ul of enzyme solution (premixed)The assay for all enzymes contained 60 mM HEPES-NaOH (pH 7.5), 3 mM MgCl2, 3 mM MnCl2, 3uM Na-Orthovanadate, 1.2 mM DTT, 50 ug/ml PEG2000, 1 uM [33P]-ATP (approx. 5x1005 cpm per well).
Kinase Assay: To evaluate the in-vitro kinase potency of the compounds, they were screened against CDK 2 and CDK9. Kinase assays were performed in 96-well plates using recombinant CDK/cyclins generated at Cyclacel. Ltd Dundee, UK.