A growing team of groundbreaking scientists around the world are now sharing their lab notebooks online
A large number of ACVR1/ALK2 inhibitors were previously synthesised by Paul Brenner’s team (Target Discovery Center, University of Oxford) for the purpose of treating Fibrodysplasia Ossificans Progressiva (FOP). Although these compounds were not designed with blood-brain-barrier permeability in mind, they can serve as good bench-marks for my cellular assays. Therefore, 30 of these legacy compounds Read More …
The EC50 of Tracer-6908 with ACVR1-c-nanoLuc and ideal conditions for the target engagement assay have been determined in a previous experiment. However, it is still necessary to verify that the IC50 values determined in the assay are closed enough approximation to the actual IC50 values of the compounds. If the IC50 values are strongly influenced Read More …
In my previous post, I presented different CLK2 inhibitors (https://openlabnotebooks.org/clk-chemical-probe/), including structures, and IC50 curves that were generated using a cell target engagement assay called NanoBRET. My colleagues Carrow Wells and Julie Pickett generated these data. The BRET of NanoBRET stands for bioluminescence resonance energy transfer, and it is an in-vitro quantitative technique to identify Read More …
It’s been a busy couple of weeks in and out of the lab for me which is why it’s been some time since my last post. I previously identified small molecule compounds of interest using a 19F NMR spectroscopy assay. To quantify and validate these small molecule compounds, I used a surface plasmon resonance (SPR) Read More …
As a last step, to check if the assay qualifies for the screening purposes, Z’-factor was calculated. The dataset can be viewed on Zenodo.
For the purpose of compound library screenings, the compounds would be made available in DMSO and thus, when they would be incubated with the protein, the protein solution will now contain DMSO as well. It is important to determine the concentration of DMSO that could be tolerated by the protein such that the protein stays Read More …
The presence of detergent can prevent the sticking of the fluorophore to the sides of the wells of the plate and thus improve the signals. Hence, the effect of detergent was observed on the overall signals and the activity of HDAC11. The dataset can be viewed on Zenodo.
The linearity for HDAC11 activity for Boc-Lys-(TFA)-AMC substrate was monitored using the newly optimized buffer conditions. This was followed upon by Km calculation. The dataset can be viewed on zenodo.
An effect of adding reducing agent on the HDAC11 activity was monitored. Dataset can be found on Zenodo.
XIAP and its interaction with type I and type II receptors. Having spent time over the past few weeks purifying all the components needed for a pull down with XIAP, I did the experiment that looked for interactions between XIAP and various type I and type II receptors in both the un-phosphorylated and phosphorylated form. Read More …
