Fragments vs membrane proteins with TINS

Fragment-based ligand discovery owes much of its success to the rise of biophysical techniques such as NMR, crystallography, and – more recently – surface plasmon resonance. These have allowed the discovery of fragments against a wide range of proteins, but one notable exception has been membrane proteins, the targets of more than half of marketed drugs. In a recent issue of Chemistry and Biology, Gregg Siegal and colleagues take a crack at this diverse group of proteins.

The researchers, from Leiden University, ZoBio, and elsewhere, use an NMR-based technique called target immobilized NMR screening, or TINS. In this method, a protein is immobilized onto a solid support. A reference protein is also immobilized; this reference is usually a well-characterized protein that does not bind to many small molecules. Each protein is then put into its own compartment of a two-compartment flow-cell, and this is inserted into an NMR spectrometer. Mixtures of fragments are then flowed through both chambers: those that interact with protein show a reduction in the amplitudes of their NMR spectra. By choosing fragments that show such a reduction for the target protein and not the reference protein, fragments that bind to the target can be differentiated from those that bind to proteins in general. After each NMR experiment, the fragments are washed away and replaced with a new set of fragments. TINS has been applied to a number of soluble proteins, as reviewed here. Remarkably, the immobilized protein samples often remain stable through hundreds of screening cycles.

Membrane proteins are notoriously difficult to crystallize or characterize by NMR. Moreover, it is often difficult to obtain enough protein to work with. However, since TINS relies on a decrease in signal from the fragment rather than a signal from the protein itself, Siegal and colleagues tested whether they could use the technology to discover fragments that bind to membrane proteins.

The researchers chose a protein called disulphide bond forming protein B (DsbB), which is found on the inner membrane of E. coli and other Gram-negative bacteria and may be important in virulence factor folding. One of the challenges of membrane proteins is keeping them properly folded, and the researchers used two different approaches to do this, either detergent micelles or “nanodiscs,” lipid bilyaers surrounded by a scaffold protein. Using less than 2 milligrams of DsbB, the researchers used TINS to screen a set of 1071 fragments in groups of about 5 each, with each fragment present at 500 micromolar concentration, a process that took 5 and a half days.

The TINS process led to 93 hits, a respectable hit rate of 8.7%. Each of these was then tested in a functional assay at 250 micromolar concentration, and more than half of the hits inhibited DsbB activity by at least 30%. Eight of these were subsequently characterized using full IC50 curves and kinetic analysis. The potencies were impressive, ranging from 7 micromolar to 193 micromolar, with ligand efficiencies as high as 0.45 kcal/mol/atom. DsbB has the advantage that it has been characterized structurally, and the researchers used chemical shift information from 2-dimensional NMR experiments to show that the fragments could be divided into two groups, with one set competing with a quinone cofactor and the other binding at a different site.

This paper demonstrates that it is possible to find fragments that bind to membrane proteins. Of course, the next question is, what can you do with the fragments? In this case there were structural data about the target, but this will not generally be true for membrane proteins, and in the absence of structure, advancing fragments to leads can be challenging. On the other hand, medicinal chemists have been developing drugs against membrane targets for decades without knowing their precise structures, so perhaps the challenge is as much psychological as scientific.