Month: July 2020

Generation of stable mammalian cell lines for the expression of proteins related to COVID-19 through random integration

Posted onAuthorJong FuLeave a comment

Background: Scientists centred around University of Oxford came together in the current COVID-19 pandemic to contribute to relevant studies collaboratively. Researchers with no prior experience in virology studies, myself included, had volunteered our time to contribute whichever way we can based on our field of expertise. The Biotech team of SGC Oxford, headed by Nicola Read More …

Predicting the effect of all possible mutations at nsp3-Mac1 ADPr-binding site on ADPr binding – Post 16

Posted onAuthorSetayesh YazdaniLeave a comment

In my last post, I showed you the genetic variants at the ADP-ribose (ADPr) binding site of SARS-CoV-2 nsp3-Mac1 and the predicted effects of those mutations on ADPr binding with Mac1. Next, we wanted to assess the effect of all possible mutations at the sidechains lining the ADPr binding site of nsp3-Mac1 and how that Read More …

Genetic variability at the ADP-ribose Binding Site of the SARS-CoV-2 nsp3-Mac1 and predicted effects of mutations on ADP-ribose binding – Post 15

Posted onAuthorSetayesh YazdaniLeave a comment

In two of my previous posts 13 and 14, I showed how we found the residues lining the ADP ribose (ADPr) binding site of SARS-CoV-2 nsp3-Mac1 and we looked at the variability of this site across Alpha- and Betacoronavirus entries from UniProt. In addition to the UniPro sequences, we were interested in looking at variants Read More …

Mapping the genetic variations of Alpha- and Betacoronavirus UniProt entries onto SARS-CoV-2 nsp3-Mac1 crystal structure – Post 14

Posted onAuthorSetayesh YazdaniLeave a comment

In my last post, I showed how we found the residues lining the ADP-ribose (ADPr) binding site of SARS-CoV-2 nsp3-Mac1 using its crystal structure (PDB: 6w02). In this post, I will show the sequence diversity across UniProt entries from the Alpha- and Betacoronavirus genera and map that to the Mac1’s ADPr binding site using the Read More …

WDR5 and histone H3 interaction cell assay report

Posted onAuthorMagdalena SzewczykLeave a comment

  Background WDR5 belongs to the WD-repeat protein family and is an important component of various complexes, including SET1/MLL, NuRD, and NSL complex. It interacts with several binding partners via the “WDR5-interacting” (Win) site (e.g. symmetrically dimethylated histone H3R2, MLL1-4, SET1-2) or “WDR5-binding motif” (WBM) site (e.g. c,l,n-MYC, RBBP5). WDR5 emerged as a prime target Read More …

L3MBTL1 and histone H3 interaction cellular assay

Posted onAuthorMagdalena SzewczykLeave a comment

Background Malignant-Brain-Tumor (MBT) protein L3MBTL1 contains three tandem MBT repeats (3xMBT), which interact with mono- and dimethylated lysines of histone H4, H3 and H1.4 resulting in transcriptional repression. The interaction requires conserved aspartic acid (D355) in the second MBT repeat (PMID:17540172, 18408754, 20870725, 18408754). Assay validation Assay measuring the interaction of L3MBTL1 to histone H3 was Read More …

Evaluating the inhibition of ALK2 phosphorylation of SMAD1/5 by M4K lead compounds in DIPG patient-derived cells (SU-DIPG-IV, HSJD-DIPG-007, HSJD-DIPG-018 and SU-DIPG-XXI)

Posted onAuthorJong FuLeave a comment

Background: The binding potency of M4K compounds to ALK2 has been assayed in biochemical assay and cellular assays in HEK293 or C2C12 myoblast cell lines. However, the potency of ALK2 inhibition by M4K compounds has not determined directly in DIPG patient-derived cell lines. While no major deviation from existing assay data is expected, direct experimental Read More …

The next target: SARS-CoV-2 Macrodomain and Its Druggability – Post 13

Posted onAuthorSetayesh YazdaniLeave a comment

Previously we reported our analysis on the structural diversity of binding pockets found on the SARS-CoV-2 Main protease, methyltransferase, and papain-like protease. We then shifted our focus on the SARS-CoV-2 macrodomain (nsp3-Mac1). There are six macrodomain classes based on structural similarity. Most viral macrodomains fall into the MacroD-like family the same as human homologs MacroD1 Read More …