A growing team of groundbreaking scientists around the world are now sharing their lab notebooks online
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, macrodomain. We then shifted our focus on the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). SARS-CoV-2 is a positive-strand RNA virus, depending on its multi-subunit machinery to replicate its RNA. The catalytic subunit of RdRp Read More …
Since we posted our analysis of genetic variation of SARS-CoV-2 main protease (MPro) with inhibitor N3 (PDB: 7bqy), there have been other inhibitors co-crystallized with the MPro (PDB: 6lze, PDB: 6m0k, and PDB: 6y2f). In my last post, I talked about the two inhibitors, 11a and 11b (PDB: 6lze, PDB: 6m0k) and in today’s post, Read More …
My name is Joseph Newman and I have been working in Lab of Opher Gileadi at SGC Oxford since 2013 mainly on targeting DNA repair factors as synthetic lethal targets for early stage development of new cancer therapeutics. Like many scientists my normal laboratory based research activities were disrupted by the lockdown, and when Opher Read More …
Since we posted our analysis of genetic variation of SARS-CoV-2 main protease (MPro) with inhibitor N3 (PDB: 7bqy), there have been other inhibitors co-crystallized with the MPro (PDB: 6lze and PDB: 6m0k). MPro acts like a scissor by cutting SARS-CoV-2 polyproteins into functional pieces, making it a critical target for antiviral therapies against SARS-CoV-2. In Read More …
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 …
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 …
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 …
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 …
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 …
Following our work on SARS-CoV-2 NSP16, we shifted our focus on SARS-CoV-2 Papain-like protease (PLPro) which is a cysteine protease. A protease is an enzyme that breaks down proteins into smaller polypeptides or single amino acids. Similarly, PLPro recognizes specific tetrapeptide motif (LXGG) found in-between the fused viral proteins and cuts them at those particular Read More …
