Recent Experiments

Overexpression of Expanded HTT

The experimental set-up and results covered in this post can be found here: 10.5281/zenodo.1218375 The etiology of HD is the expansion of Q repeats or CAG repeats in the HTT gene, which produces the huntingtin protein. This causes improper folding of the protein and leads to protein aggregation in neuronal cells, which ultimately causes the Read More …

Crystallization of USP5 Zf-UBD #2

In my last post, I analyzed a structure of USP5 zinc-finger ubiquitin binding domain with a cysteine-glutathione disulphide bond. These crystals were not suitable for ligand soaking due to the formation of a disulphide bond at Cys195 with a glutathione additive that occupies the ubiquitin binding pocket in the adjacent molecule in the crystal lattice. Read More …

Purification of ACVR1 for co-crystallisation with new compounds and for fragment screening crystals

I was away on leave last week, but happily, before I left, I set up 25 crystal plates of ACVR1 with various compounds. The details of the protein purification, the compounds used and some of the crystals obtained are here, on Zenodo. So I was able to at least come back to something after my Read More …

Compound 11 update (SNS-032 analogues)

Following previous post, https://opennotebook.thesgc.org/sns-032-analogues-update/, compound 11 was chosen to further investigate the structure activity relationships (SAR) of the oxazole ring system with the hope to enhance potency and improve selectivity towards each respective target. The criteria to pick the building blocks to further study the SAR is based on electronics, size and shape. I have Read More …

Determining the plasticity of CD34 expression

Previously, we established that OCI-AML-20 requires stroma to maintain CD34 expression (https://zenodo.org/record/1187083#.Wr5-1C7wbIV). In this experiment, we wanted to see whether those cells grown in suspension are able to regain CD34 expression when cells are reintroduced to stroma. We find that OCI-AML-20 regains CD34 expression when put back on to stroma (either MS5 or OP9). Full Read More …

Structural Analysis of USP5 Zf-UBD

In a previous post, I determined a crystallization condition that produced nice 3D crystals of USP5 Zf-UBD that diffracted well. Rachel Harding, a postdoc at the SGC collected data images for these crystals and solved the structure using computational techniques. You can see the solved crystal structure and a more detailed analysis of the structure Read More …

First set of selected compounds against DRAK2 kinase

Several compounds derived from thienopyrimidine scaffolds were recently synthesized to be tested as inhibitors of DRAK2/STK17B kinase. Among these, a set of 12 were selected to determine their potency as IC50 values on a DRAK2 cellular assay. These compounds have different functional groups around the phenyl ring and variation in the position of the sulfur Read More …