Capillary electrophoresis revisited

Among the various fragment-finding methods, capillary electrophoresis (CE) seems to be among the least-used, at least according to our polls. Indeed, we last wrote about CE in 2012, and since then the company that was popularizing the technique seems to have quietly dropped it from its website. A new paper by Marianne Fillet and collaborators at the University of Liege and the University of Namur in Analytica Chimica Acta presents a how-to guide for CE.

As we previously discussed, the most general CE assay involves filling a capillary with a protein solution as well as a “probe ligand” with affinity for the target protein. Interactions between the probe ligand and the protein will increase the migration time of the probe ligand compared to its progress through a capillary without protein (i.e., the probe ligand will move more slowly through the capillary in the presence of protein).

If a “test ligand” is introduced into the capillary and displaces the probe ligand, the migration time of the probe ligand will again decrease. By changing the concentration of test ligand and measuring the shift in migration time of the probe ligand, the affinity of the test ligand can be determined.

The researchers applied CE to thrombin, a drug target that is often used for validating fragment-finding methods. The low nanomolar inhibitor NAPAP was chosen as the probe ligand due to its strong chromophore (simplifying detection) and positive charge (allowing it to move in the electric field of the capillary). They tested three literature compounds with inhibition constants ranging from high nanomolar to high micromolar and found good agreement with published results.

Next, the researchers applied CE to a small library of fragments, generating several hits. They also describe a method for detecting irreversible binding: this involves screening the protein with an even higher concentration of probe ligand to see whether the test ligand itself can be displaced.

This is a nice study, but it perhaps also illustrates why the technique hasn’t caught on. First and most importantly is throughput; the runs shown are on the order of 14 minutes. Second, it does require a probe ligand. (Screening test ligands directly only works if they are positively charged.) On the other hand, CE can work with native protein, unlike immobilization-based techniques such as SPR and WAC.

Have you tried CE yourself – and if so how did it perform?

Capillary Electrophoresis

One of the fun aspects of fragment-based lead discovery is the number of ingenious biophysical methods for finding low-affinity fragments. In a recent issue of J. Biomol. Screen., Carol Austin and colleagues at Selcia describe their approach, capillary electrophoresis, which they term CEfrag.

Capillary electrophoresis itself has been around for quite a while. It involves applying a high voltage across a thin capillary filled with liquid; a solution to be analyzed is injected, and the voltage causes migration of analytes (for example, proteins or small molecules). Analyte movement through the capillary depends on charge and “hydrodynamic radius,” which is a function of molecular size and shape. In the case of CEfrag, the idea is to start with a reporter molecule that can be readily detected, for example via UV absorbance. Under a standard set of conditions, this “probe ligand” will have a characteristic mobility. If an excess of protein that binds to the probe ligand is present in the running buffer, the migration time will shift. If an inhibitor is also present in the running buffer, this will prevent the probe ligand from binding to the protein, also causing the migration time to change. By running different concentrations of inhibitor and measuring the changes in mobility, the inhibition constant can be determined.

The researchers demonstrated their approach using that old work-horse of FBLD, the cancer target Hsp90. The known Hsp90 inhibitor radicicol was used as the probe ligand. A total of 609 fragments were screened individually at an initial concentration of 0.5 mM, yielding 42 fragments that reproducibly inhibited radicicol mobility by 20% or more. This ~7% hit rate is similar to that found by others for this target.

Only 12 of the 42 hits identified by CEfrag were also detected in a confirmatory fluorescence polarization (FP) assay, of which only 5 gave measurable IC₅₀ values. However, FP is not ideal for evaluating fragments. In fact, one of the CE hits that didn’t reproduce by FP was ethamivan, the starting fragment for the program that ultimately led to Astex’s AT13387, now in a phase 2 clinical trial for GIST.

To get a better sense of the quality of the CE hits, the researchers put 6 fragments into crystallography trials: 3 hits from both CE and FP, two from CE alone, and one that hit neither. The negative control didn’t produce a structure, whereas two of the FP-confirmed hits produced co-crystal structures (the one that did not had solubility issues). One of the two CE-only hits (ethamivan) also did.

With a throughput of 100 compounds per day per instrument, this is not a high-throughput method, but it is comparable to many other biophysical approaches. Also, the low protein consumption and ability to use unmodified protein are selling points. Have you tried CEfrag? If so, what do you think?