Update on the huntingtin PAR binding story

One of the major findings of the HDSA-funded project to find huntingtin interactors relevant DNA repair was that many proteins that interact with huntingtin are modified by poly ADP ribose (PAR). Previous posts have described our hypothesis that huntingtin binds poly ADP ribose, our preliminary evidence that it does so, frustrating attempts to understand why it Read More …

Deposition of structure of ALK2 with M4K2117

One of the big aims of the M4K project was to look at the structure of potentially interesting molecules bound to the protein ALK2 and use that to try and design better molecules that might be useful in the treatment of the rare childhood brain cancer, DIPG. Ros did a lot of work on this Read More …

HDAC11 cellular assay development- histones deacetylation

In my previous post I mentioned that there is controversy if HDAC11 can deacetylate histones. I decided to look at the effect of overexpression of HDAC11 on exogenous histone acetylation in cells. In my preliminary results I noticed that exogenous GFP-tagged histones, one day post transfection, have very low levels of acetylation; therefore I decided Read More …

More GS loop mutations – purification of ALK2 proteins.

I’ve been getting my stocks in order recently and catching up on some other work which has been both busy but not the most thrilling in terms of experimental results. As such I’ve not had much time to write up a blog post so I’ll try and get back on top of that although it’s Read More …

Synthesis and biological evaluation of H-8 analogues as PKN3 inhibitors

The protein kinase N3 (PKN3) represents one of the understudied kinases in the human kinome and therefore one of the kinases SGC-UNC wants to target. As part of the UNC-SOLAR program, a summer program for students, Guillermo Correa Otero was working with me in the lab for 9 weeks. Under the supervision of David Drewry, Read More …

Scaffold hopping for selectivity

Scaffold hopping is a strategy utilized in medicinal chemistry where the core chemical structure of a promising drug candidate is replaced isosterically, which leads to structurally novel compounds. There are many reasons for undertaking this exercise including; improving potency, changing physiochemical properties such as solubility and clogP, enhance ADME properties and to move into new Read More …

2D or not 2D: 3D is the answer

Well the summer has come and gone and after 9 blogs, I am ready for the big finale- Blog number 10. I did tell you when I started I was going to give you ten blogs over 2 months with multiple protocols to be published  online and now we are at the end. So, what shall we talk Read More …

Growth and Purification of Biotinylated USP5 Constructs & Testing ZnF-UBD Ligands in a Displacement Assay

Hi all, today’s post covers some concepts that I have previously described: expression and purification of protein constructs, and testing ligands in a displacement assay. If you’ll recall, I tried to develop and optimize a fluorescence polarization (FP) displacement assay for the ZnF-UBD of USP5 for some time but found that FP was a no Read More …

PROTAC Virtual Screening: A Retrospective Screening Exercise

In my previous post https://openlabnotebooks.org/protein-protein-docking-for-protac-discovery/ I showed that HADDOCK was the best protein-protein docking tool among those I tested to predict how E3 ligases interact with their protein substrates. Here, I ask whether docking virtual libraries of PROTAC candidates to these E3 ligase – substrate protein interfaces can be used to predict which PROTACs are active. Read More …