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Vitamin B12 may inhibit RNA‐dependent‐RNA polymerase activity of nsp12 from the SARS‐CoV‐2 virus

Authors: Narayanan, Naveen; Nair, Deepak T.;

Vitamin B12 may inhibit RNA‐dependent‐RNA polymerase activity of nsp12 from the SARS‐CoV‐2 virus

Abstract

AbstractSARS‐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 Food and Drug Administration‐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.

Keywords

Protein Conformation, alpha-Helical, Prescription Drugs, COVID19, Clinical Biochemistry, Genome, Viral, Molecular Dynamics Simulation, Biochemistry, Antiviral Agents, Substrate Specificity, User-Computer Interface, Genetics, Medicine and Health Sciences, Protein Interaction Domains and Motifs, Amino Acid Sequence, Molecular Biology, inhbitior, Binding Sites, Coronavirus RNA-Dependent RNA Polymerase, bepress|Medicine and Health Sciences|Chemicals and Drugs|Other Chemicals and Drugs, Sequence Homology, Amino Acid, SARS-CoV-2, other, Cell Biology, bepress|Medicine and Health Sciences, bepress|Medicine and Health Sciences|Chemicals and Drugs, Chemicals and Drugs, High-Throughput Screening Assays, Molecular Docking Simulation, Vitamin B 12, nsp12, Thermodynamics, Protein Conformation, beta-Strand, Sequence Alignment, Other Chemicals and Drugs, Protein Binding

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    influence
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
53
Top 1%
Top 10%
Top 1%
Green
hybrid