In silico screening and experimental validation identify riboflavin as an RNA-targeted antiviral against SARS-CoV-2
Abstract This study explored drug repurposing strategies against conserved RNA structures in the SARS-CoV-2 genome to address viral mutation challenges. Conserved RNA elements were computationally identified by aligning 283 SARS-CoV-2 genomes from Korean patients. RNA secondary structures were predi...
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Nature Portfolio
2025-08-01
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| Online Access: | https://doi.org/10.1038/s41598-025-16949-8 |
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| author | Chae-Hong Jeong Yoo Jin Na Tae Yong Kim So Young Lee Jungyeon Kim Sangmi Ryou |
| author_facet | Chae-Hong Jeong Yoo Jin Na Tae Yong Kim So Young Lee Jungyeon Kim Sangmi Ryou |
| author_sort | Chae-Hong Jeong |
| collection | DOAJ |
| description | Abstract This study explored drug repurposing strategies against conserved RNA structures in the SARS-CoV-2 genome to address viral mutation challenges. Conserved RNA elements were computationally identified by aligning 283 SARS-CoV-2 genomes from Korean patients. RNA secondary structures were predicted using RNAfold and RNAstructure, followed by virtual screening of 11 compounds using the RNALigands database (binding energy threshold: -6.0 kcal/mol). The antiviral activity and cytotoxicity of riboflavin were experimentally validated in vitro using Vero E6 cells infected with SARS-CoV-2 (MOI 0.01). Riboflavin exhibited selective antiviral activity against SARS-CoV-2 (IC50 = 59.41 µM), showing no cytotoxicity at concentrations < 100 µM. Riboflavin treatment during viral inoculation significantly reduced viral replication, whereas riboflavin treatment pre- or post-inoculation had no effect. The other screened compounds lacked antiviral efficacy. In terms of antiviral activity, riboflavin was less potent than remdesivir (IC50 = 25.81 µM). Riboflavin is a potential RNA-targeted therapeutic agent against SARS-CoV-2. This study established a framework for integrating computational and experimental methods to identify conserved RNA targets, thus offering a strategy applicable to other RNA viruses. This result indicates the potential of riboflavin as a broad-spectrum antiviral agent against SARS-CoV-2 and highlights the importance of considering nutritional factors in the context of viral infections. |
| format | Article |
| id | doaj-art-b5afe68fdb2047a1bde5068ed2a1e203 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-08-01 |
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| spelling | doaj-art-b5afe68fdb2047a1bde5068ed2a1e2032025-08-24T11:24:04ZengNature PortfolioScientific Reports2045-23222025-08-011511810.1038/s41598-025-16949-8In silico screening and experimental validation identify riboflavin as an RNA-targeted antiviral against SARS-CoV-2Chae-Hong Jeong0Yoo Jin Na1Tae Yong Kim2So Young Lee3Jungyeon Kim4Sangmi Ryou5Division of Clinical Research, Center for Emerging Virus Research, National Institute of Infectious Diseases, Korea National Institute of HealthDivision of Clinical Research, Center for Emerging Virus Research, National Institute of Infectious Diseases, Korea National Institute of HealthDivision of Clinical Research, Center for Emerging Virus Research, National Institute of Infectious Diseases, Korea National Institute of HealthDivision of Clinical Research, Center for Emerging Virus Research, National Institute of Infectious Diseases, Korea National Institute of HealthDivision of Clinical Research, Center for Emerging Virus Research, National Institute of Infectious Diseases, Korea National Institute of HealthDivision of Clinical Research, Center for Emerging Virus Research, National Institute of Infectious Diseases, Korea National Institute of HealthAbstract This study explored drug repurposing strategies against conserved RNA structures in the SARS-CoV-2 genome to address viral mutation challenges. Conserved RNA elements were computationally identified by aligning 283 SARS-CoV-2 genomes from Korean patients. RNA secondary structures were predicted using RNAfold and RNAstructure, followed by virtual screening of 11 compounds using the RNALigands database (binding energy threshold: -6.0 kcal/mol). The antiviral activity and cytotoxicity of riboflavin were experimentally validated in vitro using Vero E6 cells infected with SARS-CoV-2 (MOI 0.01). Riboflavin exhibited selective antiviral activity against SARS-CoV-2 (IC50 = 59.41 µM), showing no cytotoxicity at concentrations < 100 µM. Riboflavin treatment during viral inoculation significantly reduced viral replication, whereas riboflavin treatment pre- or post-inoculation had no effect. The other screened compounds lacked antiviral efficacy. In terms of antiviral activity, riboflavin was less potent than remdesivir (IC50 = 25.81 µM). Riboflavin is a potential RNA-targeted therapeutic agent against SARS-CoV-2. This study established a framework for integrating computational and experimental methods to identify conserved RNA targets, thus offering a strategy applicable to other RNA viruses. This result indicates the potential of riboflavin as a broad-spectrum antiviral agent against SARS-CoV-2 and highlights the importance of considering nutritional factors in the context of viral infections.https://doi.org/10.1038/s41598-025-16949-8Drug repurposingAntiretroviralRNA secondary structureIn silicoRiboflavinSARS-CoV-2 |
| spellingShingle | Chae-Hong Jeong Yoo Jin Na Tae Yong Kim So Young Lee Jungyeon Kim Sangmi Ryou In silico screening and experimental validation identify riboflavin as an RNA-targeted antiviral against SARS-CoV-2 Scientific Reports Drug repurposing Antiretroviral RNA secondary structure In silico Riboflavin SARS-CoV-2 |
| title | In silico screening and experimental validation identify riboflavin as an RNA-targeted antiviral against SARS-CoV-2 |
| title_full | In silico screening and experimental validation identify riboflavin as an RNA-targeted antiviral against SARS-CoV-2 |
| title_fullStr | In silico screening and experimental validation identify riboflavin as an RNA-targeted antiviral against SARS-CoV-2 |
| title_full_unstemmed | In silico screening and experimental validation identify riboflavin as an RNA-targeted antiviral against SARS-CoV-2 |
| title_short | In silico screening and experimental validation identify riboflavin as an RNA-targeted antiviral against SARS-CoV-2 |
| title_sort | in silico screening and experimental validation identify riboflavin as an rna targeted antiviral against sars cov 2 |
| topic | Drug repurposing Antiretroviral RNA secondary structure In silico Riboflavin SARS-CoV-2 |
| url | https://doi.org/10.1038/s41598-025-16949-8 |
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