Crystallography as a primary screen seems to be gaining traction. As the old cliché goes, a picture is worth a thousand words. And as Andrey Grishin recently commented on an earlier post, the increasing speed and capacity at synchrotrons lowers the barrier for data collection. A new paper in ChemMedChem by Yafeng Xue and colleagues at AstraZeneca provides yet more support for starting with crystallography.
The researchers were interested in the retinoic-acid related orphan receptor γt (RORγt), a potential target for autoimmune diseases. The protein is a nuclear hormone receptor, and like many members of this family, ligands tend to be lipophilic with poor physical properties. Also, work by other companies around this target had created a thicket of intellectual property claims. To find new and attractive chemical matter, the researchers turned to fragments.
The ligand binding domain of RORγt was crystallized and soaked against a library of 384 fragments chosen on the basis of maximum diversity and previous success in crystallography. Fragments were screened at 75 mM concentration in pools of four, with members chosen to have different shapes. This process did require “extensive optimization”, and even then about 15% of the datasets were not usable. But the effort paid off, resulting in 21 hits from 18 pools. Hits were then tested by SPR, revealing that the best had an affinity of just 0.2 mM (though with an impressive LE of 0.42 kcal mol-1 per heavy atom), while some were > 5 mM.
As expected, many of the fragments bound in the large and lipophilic ligand binding pocket, accessing various binding modes previously seen with other ligands. This is a nice confirmation that fragments are able to sample chemical space very efficiently, as shown five years ago for HSP90. Indeed, for one particularly productive pool, three of the fragments bound simultaneously at different subsites within the ligand binding pocket!
Of course, proteins are often highly dynamic in solution, and one concern with crystallographic screening is that the protein crystals may not allow much movement. In this case the researchers did observe several cases of induced fit, with one side chain residue shifting more than 3 Å to accommodate a fragment. This revealed a type of interaction that was not predicted using a computational approach: a victory – for now – for the power of empiricism.
As discussed earlier this year, secondary ligand binding sites appear to be common, and indeed five fragments bound outside the ligand binding pocket. Three of these bind at what seems to be a protein-protein interface for other receptors, which could lead to highly selective molecules.