scholarly journals Vitamin B12 may inhibit RNA-dependent-RNA polymerase activity of nsp12 from the COVID-19 Virus

2020 ◽  
Author(s):  
deepak t nair ◽  
naveen narayanan
Keyword(s):  
Rna Polymerase ◽  
Vitamin B12 ◽  
Active Site ◽  
Protein A ◽  
Homology Model ◽  
Polymerase Activity ◽  
Rdrp Activity ◽  
Rna Dependent Rna Polymerase ◽  
Rna Polymerase Activity ◽  
Approved Drugs

COVID-19 is the causative agent for the ongoing pandemic, and this virus belongs to the Coronaviridae family. Like other members of this family, the virus possesses a positive-sense single-stranded RNA genome. The genome encodes for the nsp12 protein, which houses the RNA-dependent-RNA polymerase (RdRP) activity responsible for the replication of the viral genome. A homology model of nsp12 was prepared using the structure of the SARS nsp12 (6NUR) as a model. The model was used to carry out in silico screening to identify molecules among natural products, or FDA approved drugs that can potentially inhibit the activity of nsp12. This exercise showed that vitamin B12 (methylcobalamin) may bind to the active site of the nsp12 protein. A model of the nsp12 in complex with substrate RNA and incoming NTP showed that Vitamin B12 binding site overlaps with that of the incoming nucleotide. A comparison of the calculated energies of binding for RNA plus NTP and methylcobalamin suggested that the vitamin may bind to the active site of nsp12 with significant affinity. It is, therefore, possible that methylcobalamin binding may prevent association with RNA and NTP and thus inhibit the RdRP activity of nsp12. Overall, our computational studies suggest that methylcobalamin form of vitamin B12 may serve as an effective inhibitor of the nsp12 protein.

scholarly journals Vitamin B12 May Inhibit RNA-Dependent-RNA Polymerase Activity of nsp12 from the SARS-CoV-2 Virus

2020 ◽  
Author(s):  
Naveen Narayanan ◽  
Deepak T. Nair
Keyword(s):  
Rna Polymerase ◽  
Vitamin B12 ◽  
Active Site ◽  
Protein A ◽  
Homology Model ◽  
Polymerase Activity ◽  
Rdrp Activity ◽  
Rna Dependent Rna Polymerase ◽  
Rna Polymerase Activity ◽  
Approved Drugs

SARS-CoV-2 is the causative agent for the ongoing COVID19 pandemic, and this virus belongs to the Coronaviridae family. Like other members of this family, the virus possesses a positive-sense single-stranded RNA genome. The genome encodes for the nsp12 protein, which houses the RNA-dependent-RNA polymerase (RdRP) activity responsible for the replication of the viral genome. A homology model of nsp12 was prepared using the structure of the SARS nsp12 (6NUR) as a model. The model was used to carry out in silico screening to identify molecules among natural products, or FDA approved drugs that can potentially inhibit the activity of nsp12. This exercise showed that vitamin B12 (methylcobalamin) may bind to the active site of the nsp12 protein. A model of the nsp12 in complex with substrate RNA and incoming NTP showed that Vitamin B12 binding site overlaps with that of the incoming nucleotide. A comparison of the calculated energies of binding for RNA plus NTP and methylcobalamin suggested that the vitamin may bind to the active site of nsp12 with significant affinity. It is, therefore, possible that methylcobalamin binding may prevent association with RNA and NTP and thus inhibit the RdRP activity of nsp12. Overall, our computational studies suggest that methylcobalamin form of vitamin B12 may serve as an effective inhibitor of the nsp12 protein.

scholarly journals Poly(A)- and Primer-Independent RNA Polymerase of Norovirus

2004 ◽  
Vol 78 (8) ◽  
pp. 3889-3896 ◽  
Author(s):  
Shuetsu Fukushi ◽  
Shigeyuki Kojima ◽  
Reiko Takai ◽  
Fuminori B. Hoshino ◽  
Tomoichiro Oka ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Enzymatic Activity ◽  
Recombinant Baculovirus ◽  
Polymerase Activity ◽  
Genomic Region ◽  
Rdrp Activity ◽  
Rna Dependent Rna Polymerase ◽  
The Family ◽  
Baculovirus System ◽  
Rna Polymerase Activity

ABSTRACT Replication of positive-strand caliciviruses is mediated by a virus-encoded RNA-dependent RNA polymerase (RdRp). To study the replication of Norovirus (NV), a member of the family Caliciviridae, we used a recombinant baculovirus system to express an enzymatically active RdRp protein from the 3D region of the NV genome and defined conditions for optimum enzymatic activity. Using an RNA template from the NV 3′ genomic region, we observed similar levels of enzymatic activity in assays with and without a poly(A) tail. RdRp activity was not significantly affected by the addition of an RNA primer to the reaction mixture. Thus, the NV RdRp exhibited primer- and poly(A)-independent RNA polymerase activity. While the RdRp inhibitor phosphonoacetic acid inhibited NV RdRp activity, another gliotoxin did not. The active recombinant NV RdRp will be of benefit to studies of NV replication and will facilitate the development of specific inhibitors of NV proliferation.

scholarly journals Thermolabile L-A virus-like particles from pet18 mutants of Saccharomyces cerevisiae.

1986 ◽  
Vol 6 (2) ◽  
pp. 404-410 ◽  
Author(s):  
T Fujimura ◽  
R B Wickner
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase ◽  
Polymerase Activity ◽  
Nonpermissive Temperature ◽  
Wild Type ◽  
Rna Dependent Rna Polymerase ◽  
Virus Like Particles ◽  
Rna Polymerase Activity ◽  
Lines Of Evidence

pet18 mutations in Saccharomyces cerevisiae confer on the cell the inability to maintain either L-A or M double-stranded RNAs (dsRNAs) at the nonpermissive temperature. In in vitro experiments, we examined the effects of pet18 mutations on the RNA-dependent RNA polymerase activity associated with virus-like particles (VLPs). pet18 mutations caused thermolabile RNA polymerase activity of L-A VLPs, and this thermolability was found to be due to the instability of the L-A VLP structure. The pet18 mutations did not affect RNA polymerase activity of M VLPs. Furthermore, the temperature sensitivity of wild-type L-A RNA polymerase differed substantially from that of M RNA polymerase. From these results, and from other genetic and biochemical lines of evidence which suggest that replication of M dsRNA requires the presence of L-A dsRNA, we propose that the primary effect of the pet18 mutation is on the L-A VLP structure and that the inability of pet18 mutants to maintain M dsRNA comes from the loss of L-A dsRNA.

An Assay for RNA-Dependent RNA Polymerase Activity

2006 ◽  
Vol 2006 (1) ◽  
pp. pdb.prot4322
Author(s):  
Luyun Huang ◽  
John Gledhill ◽  
Craig E. Cameron
Keyword(s):  
Rna Polymerase ◽  
Polymerase Activity ◽  
Rna Dependent Rna Polymerase ◽  
Rna Polymerase Activity

scholarly journals High-throughput identification of compounds targeting influenza RNA-dependent RNA polymerase activity

2010 ◽  
Vol 107 (45) ◽  
pp. 19151-19156 ◽  
Author(s):  
C.-Y. Su ◽  
T.-J. R. Cheng ◽  
M.-I. Lin ◽  
S.-Y. Wang ◽  
W.-I. Huang ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
High Throughput ◽  
Polymerase Activity ◽  
Rna Dependent Rna Polymerase ◽  
Rna Polymerase Activity
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