ITC Assay: The synthesized compounds of Formula I may be screened by one-dimensional 1H nuclear magnetic resonance spectroscopy (1D-1H NMR) binding assays against Bcl-XL. Active compounds in 1D-1H NMR binding assays are then selected and evaluated in the Isothermal Titration Calorimetry assays (ITC), cell viability assays and competitive fluorescence polarization assays (FPA). A group of compounds of Formula I display high binding affinity for Bcl-XL in these assays. The most potent compounds induce significant chemical shift changes in the active site methyl groups (region between 0.38 and 0.42 ppm) in the one-dimensional 1H-NMR spectra of Bcl-XL and also have an IC50 value in the FP displacement assays, which is more effective than Apogossypol. To confirm results of the NMR binding data and the FP assays, binding affinity of the compounds of Formula I for Bcl-XL using ITC assay were tested.
Fluorescence Polarization Assay: A Bak BH3 peptide (F-BakBH3) (GQVGRQLAIIGDDINR (SEQ ID NO:1)) was labeled at the N-terminus with fluorescein isothiocyanate (FITC) (Molecular Probes) and purified by HPLC. For competitive binding assays, 100 nM GST-BCL-XL DTM protein was preincubated with the tested compound at varying concentrations in 47.5 uL PBS (pH=7.4) in 96-well black plates at room temperature for 10 min, then 2.5 uL of 100 nM FITC-labeled Bak BH3 peptide was added to produce a final volume of 50 uL. The wild-type and mutant Bak BH3 peptides were included in each assay plate as positive and negative controls, respectively. After 30 min incubation at room temperature, the polarization values in millipolarization units were measured at excitation/emission wavelengths of 480/535 nm with a multilabel plate reader (PerkinElmer). IC50 was determined by fitting the experimental data to a sigmoidal dose-response nonlinear regression model.
Fluorescence Polarization Assay: A Bak BH3 peptide (F-BakBH3) (GQVGRQLAIIGDDINR (SEQ ID NO:1)) was labeled at the N-terminus with fluorescein isothiocyanate (FITC) (Molecular Probes) and purified by HPLC. For competitive binding assays, 100 nM GST-BCL-XL DTM protein was preincubated with the tested compound at varying concentrations in 47.5 uL PBS (pH=7.4) in 96-well black plates at room temperature for 10 min, then 2.5 uL of 100 nM FITC-labeled Bak BH3 peptide was added to produce a final volume of 50 uL. The wild-type and mutant Bak BH3 peptides were included in each assay plate as positive and negative controls, respectively. After 30 min incubation at room temperature, the polarization values in millipolarization units were measured at excitation/emission wavelengths of 480/535 nm with a multilabel plate reader (PerkinElmer). IC50 was determined by fitting the experimental data to a sigmoidal dose-response nonlinear regression model.