Surface Plasmon Resonance Assay (SPR). SPR is commonly used to determine the kinetics of target-analyte binding. The assay detects changes in the molecular mass of a target after binding of the analyte. The target is immobilized to a sensor chip, and the analyte flows to the target. Target binding is monitored in real-time for both, association and dissociation.
Isothermal Titration Calorimetry (ITC). ITC is used to determine the binding affinity, stoichiometry, and enthalpy as well as entropy of the binding event of an agent to a target. The assay measures temperature changes when the agent binds to a target determining the mechanism of action on the molecular level.
Example of a cofactor analysis by SPR. EPZ015666 is a substrate-competitive inhibitor that binds to its target enzyme, PRMT5/ MEP50, only in the presence of SAM or SAM analogs such as MTA and SAH.
No dose-dependent responses were observed for analyte binding to apoprotein (left figure). The binding to the MTA-bound target is relatively weak (KD~16μM) with fast kinetics (on/off). The binding affinity increased by ~10-fold for the SAH-bound target (KD~1μM). While the on-rates are similar for the MTA- and SAH-bound conditions, the off-rates are approximately 100X slower. The highest affinity (KD~3nM) and slowest off-rate (100x less than SAH-bound) was observed for analyte binding to the SAM-bound target. Single-cycle kinetics, that do not require a return to the baseline in between doses, was used due to the slow off-rate observed for this condition. A slower off-rate indicates longer occupancy of the analyte on the target.
The analyte was tested with 7 concentrations depicted in different colors.
EPZ015666 = a substrate-competitive inhibitor that binds only in the presence of SAM or SAM analog.
LLY-283 = an inhibitor that binds the SAM-binding pocket but appears to be non-competitive for both SAM and substrate.
JNJ-64619178 = a pseudo-irreversible inhibitor that binds the SAM-binding pocket and reaches into the substrate pocket.
PRMT5:MEP50 complex was immobilized to a sensor chip and the binding of tool molecules was measured. In the absence of co-factor (SAM or SAM analogs SAH or MTA), EPZ015666 exhibited a relatively weak affinity for PRMT5:MEP50 with minimal signal changes observed. LLY-283 and JNJ-64619178, however, exhibited tight binding. While the on-rates are similar for the two compounds, the off-rates differ by ~10-fold with JNJ-64619178 exhibiting longer target engagement resulting in tighter binding. A kinetic titration was used to inject the molecules from low to a high concentration in a single cycle due to the slow off-rates.