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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 …
All great things come in threes, even quality control of synuclein fibrils
Someone pointed out a funny quirk of mine the other day. I love things that come in threes. I never realized it before, but then I started thinking about it, and before you could say thirty-three, I was contemplating all the threes I like. Maybe its because the house I lived in growing up was Read More …
Purifications of HTT and HTT-HAP40 from insect (Sf9) and mammalian (EXPI293F) expression systems
Purifications of HTT and HTT-HAP40 from insect (Sf9) and mammalian (EXPI293F) expression systems
Summer travels showcasing the huntingtin protein toolkit
Summer travels showcasing the huntingtin protein toolkit
Evaluating the effect of 8 M4K compounds on the viability of DIPG patient-derived cells (SU-DIPG-VI, HSJD-DIPG-007 and SU-DIPG-IV)
Background: I have been characterising the cellular potency of many M4K compounds against ALK2 and ALK5. Compounds that targets ALK2 and not ALK5 should be further evaluated for their ability to reduce the viability of cells derived from DIPG patients. Although these cultured cells might not reflect what actually happens in a DIPG patient’s brain, Read More …