COVID-19

In my last post, I showed you the genetic variants at SARS-CoV-2 SAM-dependent m7GpppA-specific 2’-O-methyltransferase (2’-O-MTase). Also, we predicted the effects of SARS-CoV-2 samples mutations on SAM- and RNA-binding to the 2’-O-MTase (NSP16) catalytic site using the change in Gibbs free energy (ddGbind) values. Next, we wanted to assess the effect of all possible mutations Read More …

In two of my previous posts 5 and 6, I showed how we found the residues lining the catalytic pockets of SARS-CoV-2 SAM-dependent m7GpppA-specific 2’-O-methyltransferase (2’-O-MTase) which I refer to as NSP16. In this post, I show the energy calculations corresponding to the variants from SARS-CoV-2 patient samples at the catalytic site of 2’-O-MTase. Alongside Read More …

In my last post, I showed how we found the residues lining the catalytic site of SARS-CoV-2 SAM-dependent m7GpppA-specific 2’-O-methyltransferase (2’-O-MTase), which I refer to as NSP16. In this post, I will share with the diversity dendrograms corresponding to the reviewed entries of the Alpha- and Betacoronavirus genera from the UniProt database. I use a Read More …

Following the work on the SARS-CoV-2 main protease, we selected NSP16 as the next target of interest. But what is NSP16? The coronavirus genome size is large, about 30 kb single-stranded positive RNA. The RNA molecule is 5’-capped and has 3’-poly-A tail. The viral RNA is the molecular template that is translated to make viral Read More …

In my previous posts (post 1 and post 2), I explained how we found the neighboring residues of the SARS-CoV-2 main protease (MPro) catalytic site, then created a diversity dendrogram of the residues, and looked at three examples of coronavirus MPro structures (SARS-CoV, SARS-CoV-2, MERS). In this post, I explain how we looked at hundreds Read More …

In my previous post, I explained how we found the surrounding residues lining the catalytic site of the SARS-CoV-2 main protease (MPro) using the available crystal structure from the protein databank (PDB code: 7bqy). Following that step, we wanted to zoom in on a few MPro’s structures bound to inhibitors. We looked at MERS, SARS-CoV, Read More …

Many people have spent a few months in quarantine because of the emergence of a novel coronavirus, SARS-CoV-2, the pathogen that causes COVID-19. (1) More people around the globe are fighting this virus as the number of cases increase. As of today, May 19, 2020, the number of confirmed cases globally almost reach five million, Read More …