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?
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