Mandeep Mann

You may recall I was in Montreal for the last three months doing an internship with Molecular Forecaster Inc. (MFI), a computational chemistry company. I’m back in Toronto from my internship, ready to jump back into my research, but first I’ll summarize the virtual screening work I did at MFI for USP5. In a previous Read More …

In a previous post, I tested hit analogues and found compound XSR00035795a (Figure 1) had increased potency and ligand efficiency; however, compound XSR00035795a was also found to bind to HDAC6 Zf-UBD, so it was not selective towards USP5. Figure 1. XSR00035795a We hypothesized that it was possible to extend the aliphatic group on the carboxylic Read More …

In my last post, I mentioned I would be doing an internship at a biotech company in Montreal, Molecular Forecaster Inc as a part of a NSERC ChemNet CREATE grant. I’ve been in Montreal for about three weeks now and have had a chance to play around with the Forecaster software. I did preliminary docking Read More …

In a previous post, I tested hit analogues against USP5 Zf-UBD using a SPR assay. Compound AE-641/11456811, now aptly re-named XSR00035795a (an SGC global ID- since our database infrastructure is finally re-vamped), had a binding affinity of approximately 60 µM. The addition of a methyl group on the carboxylic chain of the compound increased potency Read More …

In a previous post, I described using hit expansion tools such as commercial substructure searches, docking, and free energy perturbation (FEP) simulations to explore the structure activity relationship (SAR) of the chemical series focused on the Zf-UBD of USP5. The first batch of commercially ordered compounds arrived just before the Christmas holidays. I decided to Read More …

In a previous post, I described the importance of solving the structure of other USPs that have a Zf-UBD for the rational design of selective compounds. The last post described the design, cloning, E.coli expression, growth and purification of some of the USP Zf-UBD constructs. As a continuation in my quest to try and crystallize Read More …

Now that I’ve got my biophysical screening assays developed (19F NMR, SPR), as well as my hit expansion campaign started for small molecule inhibitors against the USP5 Zf-UBD, I need to be able to test if these small molecule inhibitors will antagonize the catalytic activity of USP5. It has been speculated in literature that the Read More …

Molecular dynamic simulations are a powerful tool for modeling biomolecular systems such as ligand binding to proteins. In a previous post I was able to get co-crystal structures of ligands which bind to the USP5 zinc finger ubiquitin binding domain (Zf-UBD). In order to explore the structure activity relationship (SAR) of the chemical series, so Read More …

X-ray crystallography is a tool used for the structural determination of proteins and biological molecules. My specific project focuses on the zinc finger ubiquitin binding domain (Zf-UBD) of USP5; however, USP5 is just one of many USPs that contain a Zf-UBD. Table 1 shows a list of the USP Zf-UBDs and their available structures in Read More …

I used a surface plasmon resonance assay to determine the binding affinities of hit compounds that were identified in 19F NMR spectroscopy screens against the zinc finger ubiquitin binding domain of USP5. To see how these assays work, check out some of my previous posts! You can see details of the SPR experiment on Zenodo. Read More …