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 …

Developing an assay of viability in DIPG cell lines

Over the past few weeks I’ve been perfecting a method for screening a small set of therapeutic compounds on DIPG cell lines. Before starting I made sure to discuss the techniques used in other groups to make sure that I design an assay that is comparable to theirs, although I may make my own changes Read More …

Update on fragment screening of ACVR1 co-crystallised with LDN-193189

I’ve put the Molprobity stats for the model I have refined to run my fragment screening datasets against in Zenodo. It looks pretty good, and I was happy when the parameters finally all went into the green. I have about 90 datasets with resolution lower than 2.6 Å, so hopefully I’ll get at least one Read More …

N-terminal vs C-terminal FLAG-tagged HTT

The experimental set-up and results covered in this post can be found here: 10.5281/zenodo.1202292 In my previous post, I used baculovirus to overexpress HTT in mammalian cells. Although I managed to overexpress HTT, this HTT is actually FLAG-tagged, and very strangely, I could not detect FLAG! Let me first explain what a FLAG-tag is. FLAG is Read More …

Over-expression of the NSD3-Short Isoform in H1299 Lung Cancer Cells Alters Cellular Morphology

Recently, a study of cancer-focused protein-protein interactions identified a direct interaction between NSD3 and the oncoprotein Myc in the non-small cell lung cancer cell line H1299 (Li, Z et al. 2017).  Importantly, the study found that increased NSD3 expression levels can activate Myc in H1299 cells as measured by an E-box luciferase reporter. However, the functional significance of Read More …

Co-crystallisation and fine screening of ACVR1 with K62821a, K62980a, and K62981a

As mentioned in my Zenodo post here, I fine screened ACVR1 with the three compounds in the title. I got loads of hits for co-crystallisation with K62821a. I mounted almost two pucks’ worth of crystals (31 crystals) and sent them to Diamond for Monday’s run. Unfortunately, none of them diffracted better than 3.5 Å, so Read More …

Transfectability of different patient-derived DIPG and Glioblastoma cell lines

Whether or not a cell line can be transfected efficiently is an important factor to consider when designing experiments. Often times scientists would like to deliver into the cells DNA or RNA with the instructions to produce specific proteins or to delete away specific proteins. Transfection via liposome (eg: Lipofectamine 2000) is a relatively simple Read More …