The Insidious Underbelly of Protein Aggregation

It is well known, and accepted, that it is essential to have “high quality” protein at the outset of a target based, small molecule drug discovery campaign. But what does “high quality” mean?
Certainly biological activity is a must. A high degree of purity (typically ≥95%) is another crucial requirement. Most often “purity” is defined based on the presence of other proteins in the preparation, but the presence of small molecules, whether or not of biological origin, also needs to be considered. However, the aggregation state is only rarely considered, and yet it significantly impacts…

Can Surface Plasmon Resonance Provide a Biologically Relevant Assay Readout?

Is your biochemical assay not sensitive enough to characterize inhibitors with affinities of hundreds of µM?  Does your assay suffer from false readout from the intrinsic fluorescence of compounds at high concentration?  Did you know that Surface Plasmon Resonance (SPR) can be set up in such a way that the readout represents the biologically relevant interaction of two biological partners, and therefore it can directly detect compounds disrupting such interactions?

Know Your Data

Imagine you’ve just titrated 50 compounds using any modern assay and instrumentation. The software is certainly capable of automatically extracting the response for each concentration and fitting it to extract the affinity/potency. You might then see the curve above (Figure 1) and the fit values in a table. If the affinity or potency is in the range you expect, with a quick look, the binding curve might pass muster with a possible note that the compound has some solubility issues at the highest concentration used. You might then pass on the data to the medicinal chemist, unfortunately that would be a mistake…