ArticleScientific reports2024
Targeting the receptor binding domain and heparan sulfate binding for antiviral drug development against SARS-CoV-2 variants.
Article in Scientific reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 10 citations in OpenAlex.
- SARS-CoV-2 Evolution in Humans Enables Its Transmission to Nonhuman Primates.Molecular biology and evolution · 2025Article
- Heparan sulfate proteoglycans remodel SARS-CoV-2 spike conformation to allow integrin interaction and infection of endothelial cells.Frontiers in cellular and infection microbiology · 2025Article
- Docking heparan sulfate-based ligands as a promising inhibitor for SARS-CoV-2.Journal of molecular modeling · 2024Article
- Review
- In Silico Discovery of a Novel PI3Kδ Inhibitor Incorporating 3,5,7-Trihydroxychroman-4-one Targeting Diffuse Large B-Cell Lymphoma.International journal of molecular sciences · 2024Article
- Enterocin DD14 can inhibit the infection of eukaryotic cells with enveloped viruses.Archives of microbiology · 2024Article
- Most accurate mutations in SARS-CoV-2 genomes identified in Uzbek patients show novel amino acid changes.Frontiers in medicine · 2024Article
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Authors and funding
5 authors at 4 institutions in 1 country.
Funding
Abstract
The emergence of SARS-CoV-2 variants diminished the efficacy of current antiviral drugs and vaccines. Hence, identifying highly conserved sequences and potentially druggable pockets for drug development was a promising strategy against SARS-CoV-2 variants. In viral infection, the receptor-binding domain (RBD) proteins are essential in binding to the host receptor. Others, Heparan sulfate (HS), widely distributed on the surface of host cells, is thought to play a central role in the viral infection cycle of SARS-CoV-2. Therefore, it might be a reasonable strategy for antiviral drug design to interfere with the RBD in the HS binding site. In this study, we used computational approaches to analyze multiple sequences of coronaviruses and reveal important information about the binding of HS to RBD in the SARS-CoV-2 spike protein. Our results showed that the potential hot-spots, including R454 and E471, in RBD, exhibited strong interactions in the HS-RBD binding region. Therefore, we screened different compounds in the natural product database towards these hot-spots to find potential antiviral candidates using LibDock, Autodock vina and furthermore applying the MD simulation in AMBER20. The results showed three potential natural compounds, including Acetoside (ACE), Hyperoside (HYP), and Isoquercitrin (ISO), had a strong affinity to the RBD. Our results demonstrate a feasible approach to identify potential antiviral agents by evaluating the binding interaction between viral glycoproteins and host receptors. The present study provided the applications of the structure-based computational approach for designing and developing of new antiviral drugs against SARS-CoV-2 variants.
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