Fragment Screening - XChem at Diamond
Fragment-based screening has become increasingly popular over the last 10 years and has proven to be a viable alternative to high-throughput screening. The appeal has been driven by several features
- “Fragment Space” is smaller than “Chemical Space” and can be more effectively probed with a relatively small library
- A million compounds cover only a small fraction of the suggested 1060 Chemical Space, whilst 2000 compounds can probe much of the 106 Fragment Space
- Protein requirements should be smaller
- Binding Efficiency for small molecules is likely to be higher
- Hit rates for Fragment-based screening appear to be higher, typically 3-10%.
Whilst there are a number of biophysical methods used for Fragment-based screening structural information is often a critical step in moving the programme forward. X-ray crystallography is a very powerful technology for use in converting a "hit" into a lead for drug discovery. However, the experimental overheads have historically been too high for it to be widely used for primary screening. The X-Chem project at Diamond aims to make the technology more widely accessible.
At Diamond beamline I04-1, the full X-ray screening experiment has now been implemented as a highly streamlined process, allowing up to 1000 compounds to be screened individually in less than a week (including 36 hours' unattended beamtime). The process covers soaking, harvesting, automatic data collection, and data analysis; fragment libraries are available, though users can bring their own.
An overview of the process is available here in practice, users must generate the crystals in their home lab, and are required to come and perform soaking and harvesting themselves. Users do not need to be present for the X-ray data collection when data is collected automatically. Data analysis builds on the existing automatic data processing, and they have developed tools to streamline density interpretation and refinement (PanDDA and XChemExplorer). Use of these tools at Diamond is optional but highly recommended.
Whilst users are free to bring their own libraries a number of libraries are also available these include the Maybridge 1000, Edelris fragments, and Diamond-SGC Poised Library (DSPL), a fragment library designed to allow rapid, cheap follow-up synthesis to provide quick SAR data. The calculated physicochemical properties of the DSPL fragment collection are shown below.
For more details on the design of the library O. B. Cox, K. Krojer, P. Collins, O. Monteiro, R. Talon, A. Bradley, O. Fedorov, J. Amin, B. D. Marsden, J. Spencer, F. von Delft, P. E. Brennan, A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain. Chem. Sci.,2016. 7: p. 2322-2330 DOI.
There is more information in this podcast https://www.ndm.ox.ac.uk/frank-von-delft-x-rays-for-drug-discovery