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It’s important to have more than one assay in place to validate experimental results. In addition to the fluorescence polarization assay, I am also trying to develop a differential scanning fluorimetry (DSF) assay. DSF measures the interaction of small molecules to the protein as the protein progressively unfolds. The melting temperature of USP5 Zf-UBD is Read More …
Preparation of GW807982X analogues can be find in Tavares’s patent from 2004 (WO2004/35588, 2004, A1). This involves a 4‑step synthesis starting from commercially available 3,6-dichloropyridazine (see previous blog, https://openlabnotebooks.org/project-overview-work-towards-a-clk-probe). From my experience in the lab, formation of the highly nitrogenated pyrazolopyridazine 3 is not a trivial step. This is probably because the formation of the charged Read More …
Preliminary tests to check if the Fluor-de-Lys-green HDAC activity kit could be used for developing a high-throughput HDAC11 assay have been performed here using controls and recombinantly purified HDAC11. Details on Zenodo.
I haven’t done that much lab work lately as I have been working on crystal data processing among other things. However, a couple of weeks ago I purified some ACVR1/ALK2 for crystallisation for fragment screening (which happened on Friday) and for co-crystallisation with some of our compounds. The experimental details are here, on Zenodo. As Read More …
ALK2 and ALK5 are Type I receptors on the cell surface that can be activated by specific ligands (illustrated in the diagram below). Once activated by ligand, ALK2 or ALK5 interact with Type II receptor to be phosphorylated (phospho-group chemically attached to the protein). Subsequently, ALK2 phorphorylates SMAD1/5/8 while ALK5 phorphorylates SMAD2. Phosphorylated SMADs then Read More …
Towards the SGC goal of creating a kinase chemogenomic set (KCGS) we have been receiving and profiling kinase inhibitors donated by pharmaceutical companies. One such compound is PFE-PKIS 43 (Scheme 1a). We received this compound from Pfizer and it was screened against 403 kinases at DiscoverX. This compound, originally synthesized and published as part of Read More …
The early stages of a project often involve spending considerable time building tools to effectively tackle the problem. In cell biology, this often includes testing antibodies and expression constructs in your cell lines of interest. Putting in the work to properly validate these reagents early on in a study is critical. Poorly validated antibodies are, at least Read More …
The experimental set-up and results covered in this post can be found here: 10.5281/zenodo.1172644 One of the main aims of my project is to understand the role of normal and mutant HTT in mammalian cells. To do so, I will be overexpressing HTT in mammalian cells using baculovirus. The use of baculovirus for protein expression Read More …
There have been some exciting developments in the lab since my last post…I’ve got apo crystals of USP5 Zf-UBD! Experimental details can be found on Zenodo. The apo structure, which has no ligands bound in the receptor pocket has already been solved. The purified protein sample I have been working with for USP5 Zf-UBD is Read More …
At the SGC-UNC we are interested in building a set of inhibitors that “covers” the whole kinome. Here’s a reference that talks about our plans for the Kinase Chemogenomic Set (KCGS): http://journals.plos.org/plosone/article/related?id=10.1371/journal.pone.0181585. We are building the set with what we call “narrow spectrum” inhibitors – inhibitors that inhibit only a small set of kinases. To help Read More …
