Crystallographic Fragment Screening at the Helmholtz Zentrum Berlin

Event Date: 2018-01-25  

Fragments are small organic molecules, with molecular weights in the 200 Da range. Screening fragments for binding to biological macromolecules has been around for some time now and it has been promoted for the following two reasons: (i) with relatively few fragments, one can to cover a large chemical space and (ii) being rather small, fragments are amenable to optimization by simply enlarging them. Typically, binding fragments are identified by a cascade of biophysical methods and then further analyzed structurally by X-ray crystallography. The major pitfall of this approach is that pre-screening methods tend to disagree with each other in particular for weakly binding entities, which fragments typically are. Consequently, pre-screening seems little effective and leads at best to an enrichment of potential binding hits.

On the other hand, recent advances in synchrotron technologies, X-ray detectors and automated processing of diffraction data have made it possible to collect and process in excess of several hundreds of diffraction data sets per day. This level of throughput has made it possible to use the method X-ray crystallography as a (or the) primary screening technique. In the talk, I will discuss a large fragment-screening study (361 compounds vs. the protease endothiapepsin), as well as some results using a new small, affordable and versatile compound library, which we have recently assembled at the HZB and which is available to the HZB-MX beamline users. Further, I will show the MX-facilities at the HZB, including a new X-ray crystallography beam line dedicated to fragment screening experiments, which is currently being completed at the BESSY II synchrotron. Finally, in order to facilitate high-throughput crystallography I will also show an example for the efficient identification of fragment hits.