A growing team of groundbreaking scientists around the world are now sharing their lab notebooks online
Following the successful synthesis of the furopyridine scaffold via an alternative synthetic route, conditions have been worked out to optimize yields on the synthesis of the key intermediate: 5-bromobenzofuran-3(2H)-one. Thus far the following set of analogs, Figure 1, have been generated by building diversity on the pyridine ring. These analogs together with with proposed others Read More …
Hello Open Sciences World! In my very first post for the SGC’s Extreme Open Sciences project, I will start by providing an overview of my project – Gene therapy for Dravet Syndrome. Dravet Syndrome is a catastrophic, rare form of infantile epilepsy. The disease onset occurs in the first year of life where children with Read More …
Hello again! As a follow up to my previous post,I’ve continued the search for an antibody to detect EZH1. I’m happy to report that I finally found one. I was able to detect a band in HEK293 cells using the Cell Signaling Antibody. Using knockdowns targeting EZH1, I was able to determine that the band Read More …
This is what is planned to be the last small set of compounds prepared as STK17B/DRAK2 kinase inhibitors. Here, chemical modifications are made in the “top part” of the parent compound AP-39. The goal is to evaluate the role of other functional groups such as imidazole, tetrazole, and sulfonamides (1-3). Other changes include replacement of Read More …
In my previous post, I introduced our fragment screening results on HAO1. Specifically, I told you that we identified five promising fragment hits, from a little over 400 collected structures, clustering to three biologically relevant sites: the active site (fragments 1 and 2), the gating loop (fragment 5) and the subunit interface (fragments 6 and Read More …
Having previously purified BMPR1A (Alk3) and BMPR1B (Alk6), I spent some time purifying FKBP12 to form complexes with each of the receptors. FKBP12 binds to BMPR1A and BMPR1B via a similar GS domain to that seen in ACVR1, on the N-terminal side of the kinase domain and may help stabilize the structures and thus help Read More …
For those following the USP5 project on my open notebook, you will recognize that assay development has been quite a challenge for screening ligands against USP5 zinc finger ubiquitin binding domain (Zf-UBD). In the past, I was unsuccessful in developing a differential scanning fluorimetry, and fluorescence polarization screening assay. I then tried 19F NMR spectroscopy screening, Read More …
The experimental set-up and results covered in this post can be found here: doi.org/10.5281/zenodo.1420537 I was previously using an HTT overexpression model to look at any changes in proteins related to HTT or its function. Unfortunately, none of the related proteins I looked at showed any significant change in protein levels with HTT overexpression. There Read More …
I used a medium-throughput 19F NMR assay to screen my second batch of compounds against USP5 zinc finger ubiquitin binding domain (Zf-UBD). To recap, the 19F NMR assay detects ligand binding by measuring perturbations in the resonance of a fluorinated tryptophan at the binding pocket. I selected the compounds for my second screen from SGC’s in Read More …
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 …
