According to our last poll, ligand-detected NMR is the most popular method for finding fragments. And among the several ligand-detected NMR techniques, the most popular appears to be saturation transfer difference (STD) NMR. The basic concept behind this approach is to selectively irradiate a protein, which then transfers its magnetization to any bound ligand, thus “saturating” (reducing the signals) for the ligand. Subtracting this spectrum from a reference spectrum reveals which ligand (if a mixture) or individual protons within a ligand are in close proximity to the protein.
Although STD NMR is fast and easy to run, it does have drawbacks. One is the fact that it requires pure protein: if there are other proteins in solution, it will be impossible to tell whether the small molecule binds to the protein of interest or to something else. This shortcoming has been overcome in a paper published recently in J. Biomol. NMR by Tamas Martinek and collaborators at the University of Szeged, the Hungarian Academy of Sciences, and the University of Debrecen.
In a normal STD experiment, the protein protons that are irradiated are far upfield (often around -0.5 ppm) – a region not relevant to most small molecules. These protons then transfer the magnetization throughout the protein and ultimately to any bound small molecules. In order to choose a specific protein, the researchers add an 15N-labeled antibody selective for the protein. They can then selectively irradiate the 15N-labeled antibody, which transfers its magnetization to the bound protein and from there to any bound ligand. They call this approach monoclonal antibody-relayed 15N-group-selective STD, or mAb-relayed 15N-GS STD.
To demonstrate the approach, the researchers observed the binding of 2 mM lactose to galectin-1 (Gal-1) using an 15N-labeled antibody against Gal-1. Lactose binds to Gal-1 with a dissociation constant of 0.155 mM, which is a relevant affinity for fragment screening. Gal-1 was present at 20 µM and the antibody was present at 10 µM, both of which are reasonably low. Control experiments established that both Gal-1 and the antibody were necessary, and the experiment was successful even in a cell extract.