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Abstract
Abstract
XIII
Abstract:
Aims: Structural demystifying of some viral polymerases by using sofosbuvir
as a nucleotide inhibitor that has promising results in terms of its efficacy
against different viral polymerases. Materials and Methods: In this study,
molecular docking and dynamics simulation studies are used for the
comparison of the effect of sofosbuvir (a clinically approved drug) on the
treatment of different viral protein RNA-dependent RNA polymerase (RdRp).
This drug was docked onto the three-dimensional structure of the nsp12
protein of SARS-CoV-2 (COVID-19) and MERS-CoV (Middle East
Respiratory Syndrome), which controls the polymerization process and
considered as one of the primary therapeutic targets for human coronaviruses,
and docked also onto the three-dimensional structure of the NS5 protein of
ZIKV, which controls the polymerization process and considered as one of the
primary therapeutic targets for ZIKV. Sofosbuvir is a drug that is currently
used for HCV treatment; therefore, HCV RdRp is used as a positive control
target. The dynamics of the protein are simulated for 100 ns, while the binding
is tested during different dynamics states of the MERS-CoV RdRp, SARSCoV-
2 RdRp and ZIKV RdRp. Key findings: The interaction of SARS-CoV-
2, MERS-CoV and ZIKV RdRps as a target with the active form of sofosbuvir
as a ligand demonstrates the effectiveness of binding. One of the FDAapproved
antiviral drugs such as sofosbuvir can help us in this mission, aiming
to limit the danger of these viruses.
Keywords:
SARS-CoV-2 (COVID-19); MERS-COV; ZIKV; RdRp; Sofosbuvir;
Docking; Molecular Dynamics Simulation; Drug repurposing.