Generative Modelling Competition: SPR results
SPR experiments have been performed to evaluate the binding of the compounds designed during the first modelling competition round.
The experiments were carried out in a Biacore T200 instrument. The His-tagged protein was immobilised into an NTA sensor, and I additionally applied amine coupling to avoid the protein from stripping off. Washing the surface to remove the nickel, and inactivation of the amine coupling reaction were carried out before the compounds were tested.
The running buffer contained 20 mM HEPES pH 7.5, 200 mM NaCl, 10 mM MgCl2, and 5% DMSO. Different compound concentrations were tested to be able to determine KD values. AMPPCP was used as a control to confirm the protein was still active at the beginning and end of the experiments. Finally, the experiments were run at 15 C to maintain protein stability during the long SPR runs.
The results showed some compounds binding at 100 uM and one at around 10 uM (compound Z62960752). Some compounds showed none specific binding, therefore other experiments should be performed (structural biology and activity assays) to validate them further.
Next experiments, currently on going, include soaking experiments into EcMurD crystals and enzymatic assays.
