ArticleMolecules (Basel, Switzerland)2024
Molecular Mechanism of Interaction between DNA Aptamer and Receptor-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus 2 Variants Revealed by Steered Molecular Dynamics Simulations.
Article in Molecules (Basel, Switzerland), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Mechanochemical and machine-intelligent design of programmable materials: From molecular interactions to macroscale functionality.Materials today. Bio · 2026Review
- In silico aptamer design: from sequence selection to structural optimization and computational modelling strategies.Journal of computer-aided molecular design · 2026Review
- A Novel Aptamer Selection Strategy forMolecules (Basel, Switzerland) · 2025Article
- Replication Features of SARS-CoV-2 and Advantages of Targeting S Protein with Aptamers to Block Viral Entry.ACS omega · 2025Review
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The ongoing SARS-CoV-2 pandemic has underscored the urgent need for versatile and rapidly deployable antiviral strategies. While vaccines have been pivotal in controlling the spread of the virus, the emergence of new variants continues to pose significant challenges to global health. Here, our study focuses on a novel approach to antiviral therapy using DNA aptamers, short oligonucleotides with high specificity and affinity for their targets, as potential inhibitors against the spike protein of SARS-CoV-2 variants Omicron and JN.1. Our research utilizes steered molecular dynamics (SMD) simulations to elucidate the binding mechanisms of a specifically designed DNA aptamer, AM032-4, to the receptor-binding domain (RBD) of the aforementioned variants. The simulations reveal detailed molecular insights into the aptamer-RBD interaction, demonstrating the aptamer's potential to maintain effective binding in the face of rapid viral evolution. Our work not only demonstrates the dynamic interaction between aptamer-RBD for possible antiviral therapy but also introduces a computational method to study aptamer-protein interactions.
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