Fragment screening on a benchtop NMR

Practical Fragments has been on an NMR theme for the last two weeks, and this post continues that trend. One of the main barriers to entry for NMR methods is the instrument itself: not only are the machines large, requiring a good size room, the price starts at several hundred thousand dollars. Then there is the maintenance, which includes regular refills of liquid helium, which is both costly and often scarce. And if the helium runs out, your precious superconducting magnet “quenches”, which looks like this.

 

Large magnets such as those in 600 MHz instruments are unlikely to change until room temperature superconductors become a reality. Less powerful permanent magnets are available though, and you can purchase a benchtop 80 MHz machine for less than $100,000. But the low sensitivity requires very high concentrations of sample, too high for fragment screening. Unless, that is, you could increase the sensitivity. This has now been described in a new (open-access) Angew. Chem. Int. Ed. paper by Felix Torres, Roland Riek, and collaborators at the Swiss Federal Institute of Technology, Bruker, and NexMR.

 

The somewhat complicated method is called photochemically induced dynamic nuclear polarization (photo-CIDNP), which we wrote about in June. As the name suggests, this involves light excitation of a photosensitizer molecule which can then increase sensitivity for detecting other small molecules, particularly when they are not bound to proteins. Weirdly and fortuitously, photo-CIDNP theory predicts that polarization transfer is actually higher at lower magnetic fields, making it ideal for benchtop NMR.

 

The researchers first tested three fragments, each at 500 µM, using 25 µM fluorescein as the photosensitizer. Just 3 minutes of measurements each gave very clear spectra after light irradiation at 450 nm. In the absence of light it would take between 22 hours and 10 years to achieve comparable signal-to-noise enhancement.

 

Next, the researchers screened 32 fragments from their custom-designed "NMhare1.0 library” we previously described, which contains molecules suitable for photo-CIDNP. As before they used the protein PIN1 (at 10 µM) and collected data for 3 minutes per sample. Six compounds had reduced polarization in the presence of protein, four of which had been previously detected as binders and validated using a 600 MHz NMR. Of the two new hits, one confirmed using protein-detected NMR while the other did not.

 

To explore the limits of sensitivity, the researchers conducted a series of experiments lowering the concentrations of protein and small molecules. One of the compounds could be detected at concentrations as low as 250 nM and quantified at 1 µM in just 3 minutes. At 50 µM this compound clearly showed binding to 5 µM protein, despite having an affinity in the low millimolar range.

 

This is a fun paper, and I particularly like the fact that it expands fragment screening to an instrument previously not thought to be suitable. As we wrote previously, one limitation of photo-CIDNP is that only some molecules are able to be photo-sensitized. A solution would be to find one such ligand and then run a displacement assay to see whether a second ligand could compete with it, akin to what has been done for fluorine NMR. I look forward to seeing how this technique develops.