1. The XChem platform at Diamond
XChem training – April 2019

2. References on XChem Crystal preparation:
Collins, P. M., Douangamath, A., Talon, R., Dias, A., Brandao-Neto, J., Krojer, T., & Von Delft, F. (2018). Achieving a Good Crystal System for Crystallographic X-ray Fragment Screening. Preprints( ). doi: /preprints v1
Crystal soaking:
Collins, P. M., Ng, J. T., Talon, R., Nekrosiute, K., Krojer, T., Douangamath, A., von Delft, F. (2017). Gentle, fast and effective crystal soaking by acoustic dispensing. Acta Crystallogr D Struct Biol, 73(Pt 3), doi: /S X
Fragment library design:
Cox, O. B., Krojer, T., Collins, P., Monteiro, O., Talon, R., Bradley, A., Brennan, P. E. (2016). A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain. Chem Sci, 7(3), doi: /c5sc03115j
Data processing:
Krojer, T., Talon, R., Pearce, N., Collins, P., Douangamath, A., Brandao-Neto, J., von Delft, F. (2017). The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination. Acta Crystallogr D Struct Biol, 73(Pt 3), doi: /S
Fragment hit detection:
Pearce, N. M., Krojer, T., Bradley, A. R., Collins, P., Nowak, R. P., Talon, R., von Delft, F. (2017). A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat Commun, 8, doi: /ncomms15123

3. XChem at Diamond Complete screening experiment: crystal-to-model
Prepare crystals
Measure crystals
Analyse datasets

4. Readout PNP2 enzyme from pyrimidine synthesis
JMJD2D, a histone lysine demethylase
As expected

5. XChem at Diamond Complete screening experiment: crystal-to-model
Prepare crystals
Measure crystals
Analyse datasets

6. XChem Fragment libraries
Fragment library
XChem Fragment libraries
DSi-Poised Library (Diamond-SGC-iNext, ex DSPL, provided by Enamine) fragments, in 500mM d6-dmso
For all other libraries, please contact your local contact well ahead!
Kidd3D Library (University of Cambridge/Pharmenable) -137 fragments, in mM in d6-dmso-125. Contact Pharmenable ahead
Leeds3D 125 fragments, in mM – Contact Adam Nelson ahead
Covalent library – 993 fragments, in 20mM - Contact Nir London ahead
Own libraries in labcyte-compatible plates

7. Poised fragments: cheap single-step expansion
Poised reactions are:
robust and reliable;
make drug-like products;
be possible using commercially available starting points;
compatible with a range of substrates.
Oakley Cox
(Paul Brennan)
Full paper: Cox et al, Chemical Science, 2016

8. Inverted crystallisation plate Fragment library plate
Echo crystal soaking
Inverted crystallisation plate
Fragment library plate
Acoustic droplet ejection
Small volumes and fast
Fine control over drop placement
Random access dispensing (“cherry-picking”)
Labcyte Echo
Fragment library
labcyte

9. Crystal soaking with the Echo
Patrick Collins
P. M. Collins et al. -  Acta Cryst. (2017). D73, 
Compound/solvent diffusion across drop
Crystallisation plate 2.5 nL Echo drops
Requested
Delivered
Compound dispensing patterns

10. Rapid crystal soaking 900 crystal soaks in 30 min Click to target Jia
Crystal targets
Click to target
X -307, y 365
Jia
900 crystal soaks in 30 min