ArticleJournal of chemical theory and computation2025
Comparing Force Field Treatments in QM/MM Studies of the SARS-CoV-2 RNA-Dependent RNA Polymerase (RdRp) Mechanism.
Article in Journal of chemical theory and computation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Systematically Improvable and Locality Accelerated Enzymatic Reactivity Modeling: Toward Chemical Accuracy at Affordable Cost.Journal of chemical theory and computation · 2026Article
- Drugs against broad-spectrum of coronaviruses.Frontiers in immunology · 2026Review
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Authors and funding
5 authors.
Funding
Abstract
Molecular simulations have been instrumental in elucidating the SARS-CoV-2 lifecycle, thereby supporting the design and development of antiviral therapies and diagnostic tools for COVID-19. Here, the molecular mechanism of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), a potential target for antiviral drugs to treat COVID-19, was explored based on QM/MM simulations with fixed-charge and polarizable force fields (cFF and pFF, respectively). The free energy perturbation (FEP) method allowed exploring the free energy landscape of the enzymatic reaction mechanism, addressing key questions about the initial deprotonation of the 3'-OH group of the terminal nucleotide before a nucleophilic attack on the incoming nucleotide takes place. Indeed, among the five mechanisms explored, the most favorable was identified as a three-step process. The first step consists of a proton transfer from the 3'-OH group of the terminal nucleotide to a hydroxide group coordinated with an Mg
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