Druggability and Amino Acid Variability of the Catalytic Site of SARS-CoV-2 Nsp15 Across Coronaviruses and SARS-CoV-2 Samples – Post 26

Today’s post focuses on another protein encoded by many coronaviruses, the non-structural protein 15 (nsp15), an endoribonuclease. Nsp15 is a nidoviral RNA uridylate-specific endoribonuclease (NendoU) with C-terminal catalytic activity. This protein belongs to the EndoU family, and they all carry an RNA endonuclease activity to produce 2’-3’ cyclic phosphodiester and 5’-hydroxyl termini. (Kim et al. Read More …

Druggability and Genetic Variability at nsp9 Peptide-bound Pockets and Beta-barrel Pockets Across Coronaviruses and SARS-CoV-2 Samples – Post 25

Today’s post focuses on another protein encoded in open reading frame 1a (ORF1a) of many coronaviruses, the non-structural protein 9 (nsp9). Nsp9 is thought to mediate viral replication. In SARS-CoV-1, nsp9’s role has been highlighted as a single-stranded RNA-binding subunit. (Egloff et al., 2004) The structure of SARS-CoV-2 nsp9 was solved in both apo and Read More …

Druggability and Genetic Variability of the Catalytic and Allosteric Sites of SARS-CoV-2 nsp14 Across Coronaviruses and SARS-CoV-2 Samples – Post 24

Hello and happy new year! I am back from my winter break and starting to get back to research. If you have followed my previous posts, you know that I have posted the druggability and genetic variability analysis of several protein targets of SARS-CoV-2. There are a few targets that I will be posting in Read More …

Druggability and Genetic Variability of the ATPase Site and Central Channel of SARS-CoV-2 nsp13 Helicase Across Coronaviruses and SARS-CoV-2 Samples – Post 23

One of the important enzymes in the replication cycle of the SARS-CoV-2 virus is the helicase, which is also known as non-structural protein 13 (nsp13). During the viral life cycle, the holo-RNA-dependent RNA polymerase, also known as nsp12, is thought to coordinate with several additional factors, including the nsp13 helicase (Snijder et al., 2016; Sola Read More …

Druggability and Genetic Variability of the ADP-bound Pocket of SARS-CoV-2 RNA-dependent RNA polymerase NiRAN domain Across Coronaviruses and SARS-CoV-2 Samples – Post 22

The RNA-dependent RNA-polymerase (RdRp) also known as non-structural protein 12 (nsp12) is the target of antiviral agent remdesivir. Nsp12 has an important role in viral genome replication and transcription. (Chen et al., 2020)  Chen et al. identified a new pocket on the N-terminal extension of nsp12 occupied by ADP-Mg2+ after solving the structure of the helicase-polymerase complex. This ADP-bound pocket is on the N-terminal nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain which Read More …

Genetic Variability at An Allosteric site of SARS-CoV-2 RNA-dependent RNA polymerase Across Coronaviruses and SARS-CoV-2 Samples – Post 21

SARS-CoV-2 is a positive-strand RNA virus, depending on its multi-subunit machinery to replicate its RNA. This machinery is known as RNA-dependent RNA polymerase (RdRp). The catalytic subunit of RdRp, which is the core component of this machinery, is called nsp12. Nsp12 has little catalytic activity on its own and relies on accessory subunits to have Read More …

Genetic Variability at the Remdesivir-binding Pocket of SARS-CoV-2 RNA-dependent RNA polymerase Across Coronaviruses and SARS-CoV-2 Samples – Post 20

In my previous post 19, I showed how we assessed the druggability of the remdesivir-binding site of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and determined the residues lining that site. In this post, we analyze the genetic diversity of RdRp catalytic site across Alpha- and Betacoronavirus entries from UniProt and among SARS-CoV-2 samples. In the context Read More …

Calculating the change in Gibbs free energy (ddGbind) of an improved alpha-ketoamide inhibitor binding associated with genetic variations of SARS-CoV-2 main protease – post18

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 …

Calculating the change in Gibbs free energy (ddGbind) of inhibitor binding associated with genetic variations of SARS-CoV-2 Main Protease – Post 4

In my last post, I briefly mentioned our work in collaboration with Nicola de Maio from Nick Goldman’s lab, at EMBL’s European Bioinformatics Institute (EBI). What Nicola is doing is filtering out unreliable sequences of SARS-CoV-2 samples before analyzing them for genetic variability at the drug-binding sites of SARS-CoV-2 proteins that we want to investigate. First, Read More …

Genetic diversity at the catalytic site of the main SARS-CoV-2 protease

We investigated genetic variation of SARS-CoV-2 at the catalytic site of the main SARS-CoV-2 protease, following the work of Setayesh Yazdani (see https://zenodo.org/record/3834875#.Xs1IHsZ7nyk and https://openlabnotebooks.org/mapping-the-genetic-variations-of-sars-cov-2-onto-its-proteins-crystal-structures-post-1/ ). We collected information from more than 15,000 genomic sequences available from GISAID (https://www.epicov.org/) available on the 17th of May 2020, givig us considerable power to detect viral genetic variation Read More …