ArticleJournal of molecular graphics & modelling2020
Intermolecular interaction among Remdesivir, RNA and RNA-dependent RNA polymerase of SARS-CoV-2 analyzed by fragment molecular orbital calculation.
Article in Journal of molecular graphics & modelling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 34 citations in OpenAlex.
- Applications of Integrated Molecular Dynamics and Fragment Molecular Orbital (MD+FMO) Calculations in Drug Discovery and Structural Biology.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Dynamical Fragment Molecular Orbital Interaction Analysis of SARS-CoV‑2 RNA-Dependent RNA Polymerase and Remdesivir.ACS omega · 2025Article
- Design, Synthesis, and Antiviral Activity of 8‑Aza Fluoroneplanocin Derivatives Targeting SAH Hydrolase and Viral RdRp.ACS medicinal chemistry letters · 2025Article
- Quantitative Structure-Activity Relationships for Human Galectin-3 Inhibitors: Insights from Quantum Chemical Interaction Energy Terms.Journal of chemical information and modeling · 2025Article
- FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses.Journal of chemical information and modeling · 2024Article
- Probing RNA-Small Molecule Interactions Using Biophysical and Computational Approaches.ACS chemical biology · 2023Article
- 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
- Targeting and ultrabroad insight into molecular basis of Resistance-nodulation-cell division efflux pumps.Scientific reports · 2022Article
- Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design.Chemical science · 2021Article
- Human endeavor for anti-SARS-CoV-2 pharmacotherapy: A major strategy to fight the pandemic.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2021Review
- Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses.Chemical science · 2021Article
- Mechanistic insight on the remdesivir binding to RNA-Dependent RNA polymerase (RdRp) of SARS-cov-2.Computers in biology and medicine · 2021Article
- Discovery of potential inhibitors against New Delhi metallo-β-lactamase-1 from natural compounds: in silico-based methods.Scientific reports · 2021Article
- Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations.RSC advances · 2021Article
- Molecular Dynamics Simulations Reveal the Interaction Fingerprint of Remdesivir Triphosphate Pivotal in Allosteric Regulation of SARS-CoV-2 RdRp.Frontiers in molecular biosciences · 2021Article
- Non-conventional interactions of N3 inhibitor with the main protease of SARS-CoV and SARS-CoV-2.Computational and structural biotechnology journal · 2021Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
COVID-19, a disease caused by a new strain of coronavirus (SARS-CoV-2) originating from Wuhan, China, has now spread around the world, triggering a global pandemic, leaving the public eagerly awaiting the development of a specific medicine and vaccine. In response, aggressive efforts are underway around the world to overcome COVID-19. In this study, referencing the data published on the Protein Data Bank (PDB ID: 7BV2) on April 22, we conducted a detailed analysis of the interaction between the complex structures of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 and Remdesivir, an antiviral drug, from the quantum chemical perspective based on the fragment molecular orbital (FMO) method. In addition to the hydrogen bonding and intra-strand stacking between complementary strands as seen in normal base pairs, Remdesivir bound to the terminus of an primer-RNA strand was further stabilized by diagonal π-π stacking with the -1A' base of the complementary strand and an additional hydrogen bond with an intra-strand base, due to the effect of chemically modified functional group. Moreover, stable OH/π interaction is also formed with Thr687 of the RdRp. We quantitatively revealed the exhaustive interaction within the complex among Remdesivir, template-primer-RNA, RdRp and co-factors, and published the results in the FMODB database.
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