ArticleComputers in biology and medicine2021
Mechanistic insight on the remdesivir binding to RNA-Dependent RNA polymerase (RdRp) of SARS-cov-2.
Article in Computers in biology and medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 41 citations in OpenAlex.
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- Dynamical Fragment Molecular Orbital Interaction Analysis of SARS-CoV‑2 RNA-Dependent RNA Polymerase and Remdesivir.ACS omega · 2025Article
- Screening and discovery of an antiviral candidate inhibiting the SARS-CoV-2 envelope (2-E) channel.Current research in microbial sciences · 2025Article
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- Spiro heterocycles bearing piperidine moiety as potential scaffold for antileishmanial activity: synthesis, biological evaluation, andJournal of enzyme inhibition and medicinal chemistry · 2023Article
- Insights into targeting SARS-CoV-2: design, synthesis,RSC medicinal chemistry · 2023Article
- New pyrazolylpyrazoline derivatives as dual acting antimalarial-antileishamanial agents: synthesis, biological evaluation and molecular modelling simulations.Journal of enzyme inhibition and medicinal chemistry · 2022Article
- Structure-guided approach on the role of substitution on amide-linked bipyrazoles and its effect on their anti-inflammatory activity.Journal of enzyme inhibition and medicinal chemistry · 2022Article
- Discovering new potential inhibitors to SARS-CoV-2 RNA dependent RNA polymerase (RdRp) using high throughput virtual screening and molecular dynamics simulations.Scientific reports · 2022Article
- On the Recognition of Natural Substrate CTP and Endogenous Inhibitor ddhCTP of SARS-CoV-2 RNA-Dependent RNA Polymerase: A Molecular Dynamics Study.Journal of chemical information and modeling · 2022Article
- Virtual screening of substances used in the treatment of SARS-CoV-2 infection and analysis of compounds with known action on structurally similar proteins from other viruses.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2022Review
- Unraveling the binding mechanism of the active form of Remdesivir to RdRp of SARS-CoV-2 and designing new potential analogues: Insights from molecular dynamics simulations.Chemical physics letters · 2022Article
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- The Search for Cyclooxygenase-2 (COX-2) Inhibitors for the Treatment of Inflammation Disease: An in-silico Study.Journal of multidisciplinary healthcare · 2022Article
- Effectiveness of Natural Antioxidants against SARS-CoV-2? Insights from theAntibiotics (Basel, Switzerland) · 2021Article
- A review on the interaction of nucleoside analogues with SARS-CoV-2 RNA dependent RNA polymerase.International journal of biological macromolecules · 2021Review
- Modeling the Binding Mechanism of Remdesivir, Favilavir, and Ribavirin to SARS-CoV-2 RNA-Dependent RNA Polymerase.ACS central science · 2021Article
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The RNA-dependent RNA polymerase (RdRp) is a key enzyme which regulates the viral replication of SARS-CoV-2. Remdesivir (RDV) is clinically used drug which targets RdRp, however its mechanism of action remains elusive. This study aims to find out the binding dynamics of active Remdesivir-triphosphate (RDV-TP) to RdRp by means of molecular dynamics (MD) simulation. We built a homology model of RdRp along with RNA and manganese ion using RdRp hepatitis C virus and recent SARS-CoV-2 structures. We determined that the model was stable during the 500 ns MD simulations. We then employed the model to study the binding of RDV-TP to RdRp during three independent 500 ns MD simulations. It was revealed that the interactions of protein and template-primer RNA were dominated by salt bridge interactions with phosphate groups of RNA, while interactions with base pairs of template-primer RNA were minimal. The binding of RDV-TP showed that the position of phosphate groups was at the entry of the NTP channel and it was stabilized by the interactions with K551, R553, and K621, while the adenosine group on RDV-TP was pairing with U2 of the template strand. The manganese ion was located close to D618, D760, and D761, and helps in stabilization of the phosphate groups of RDV-TP. Further we identified three hits from the natural product database that pose similar to RDV-TP while having lower binding energies than that of RDV-TP, and that SN00359915 had binding free energy about three times lower than that of RDV-TP.
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