Exploring Echinacea angustifolia for anti-viral compounds against Zika virus RNA-dependent RNA polymerase: a computational study
Abstract The Zika virus (ZIKV), a member of the Flaviviridae family, has caused multiple widespread outbreaks, posing significant challenges to global health. This study explores the potential of compounds from Echinacea angustifolia (E. angustifolia) to inhibit the activity of ZIKV’s RNA-dependent...
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Nature Portfolio
2025-02-01
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| Online Access: | https://doi.org/10.1038/s41598-025-88481-8 |
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| author | Mai M. El-Daly Leena H. Bajrai Thamir A. Alandijany Isra M. Alsaady Hattan S. Gattan Meshari M. Alhamdan Vivek Dhar Dwivedi Esam I. Azhar |
| author_facet | Mai M. El-Daly Leena H. Bajrai Thamir A. Alandijany Isra M. Alsaady Hattan S. Gattan Meshari M. Alhamdan Vivek Dhar Dwivedi Esam I. Azhar |
| author_sort | Mai M. El-Daly |
| collection | DOAJ |
| description | Abstract The Zika virus (ZIKV), a member of the Flaviviridae family, has caused multiple widespread outbreaks, posing significant challenges to global health. This study explores the potential of compounds from Echinacea angustifolia (E. angustifolia) to inhibit the activity of ZIKV’s RNA-dependent RNA polymerase (RDRP), a key enzyme in the viral replication process and an ideal candidate for antiviral therapy. Utilizing computational techniques, we conducted a thorough virtual examination using the MTi-OpenScreen tool to identify potential RDRP inhibitors among E. angustifolia compounds. The top four compounds were further examined through re-docking procedures. To assess the robustness and effectiveness of these interactions, we performed molecular dynamics simulations along with calculations of the binding free energy and PCA analysis. This investigation highlighted four naturally occurring compounds, viz., Echinacoside, Rutin, Echinacin, and Cynaroside, demonstrating a notable affinity for binding to the allosteric site of ZIKV RDRP. These compounds showed strong hydrogen bond formation with crucial residues of the RDRP and presented favorable binding free energies. Our research sheds light on the viability of these E. angustifolia compounds as ZIKV RDRP inhibitors, laying a foundation for further experimental research in developing novel antiviral treatments against ZIKV infections. |
| format | Article |
| id | doaj-art-a8bb3a547fb240d4acc447a624e08a36 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-a8bb3a547fb240d4acc447a624e08a362025-02-09T12:29:33ZengNature PortfolioScientific Reports2045-23222025-02-0115111910.1038/s41598-025-88481-8Exploring Echinacea angustifolia for anti-viral compounds against Zika virus RNA-dependent RNA polymerase: a computational studyMai M. El-Daly0Leena H. Bajrai1Thamir A. Alandijany2Isra M. Alsaady3Hattan S. Gattan4Meshari M. Alhamdan5Vivek Dhar Dwivedi6Esam I. Azhar7Special Infectious Agents Unit – BSL3, King Fahd Medical Research Center, King Abdulaziz UniversitySpecial Infectious Agents Unit – BSL3, King Fahd Medical Research Center, King Abdulaziz UniversitySpecial Infectious Agents Unit – BSL3, King Fahd Medical Research Center, King Abdulaziz UniversitySpecial Infectious Agents Unit – BSL3, King Fahd Medical Research Center, King Abdulaziz UniversitySpecial Infectious Agents Unit – BSL3, King Fahd Medical Research Center, King Abdulaziz UniversityFamily Medicine Department, Faculty of Medicine, King Abdulaziz UniversityCenter for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Saveetha Medical College and Hospitals, Saveetha UniversitySpecial Infectious Agents Unit – BSL3, King Fahd Medical Research Center, King Abdulaziz UniversityAbstract The Zika virus (ZIKV), a member of the Flaviviridae family, has caused multiple widespread outbreaks, posing significant challenges to global health. This study explores the potential of compounds from Echinacea angustifolia (E. angustifolia) to inhibit the activity of ZIKV’s RNA-dependent RNA polymerase (RDRP), a key enzyme in the viral replication process and an ideal candidate for antiviral therapy. Utilizing computational techniques, we conducted a thorough virtual examination using the MTi-OpenScreen tool to identify potential RDRP inhibitors among E. angustifolia compounds. The top four compounds were further examined through re-docking procedures. To assess the robustness and effectiveness of these interactions, we performed molecular dynamics simulations along with calculations of the binding free energy and PCA analysis. This investigation highlighted four naturally occurring compounds, viz., Echinacoside, Rutin, Echinacin, and Cynaroside, demonstrating a notable affinity for binding to the allosteric site of ZIKV RDRP. These compounds showed strong hydrogen bond formation with crucial residues of the RDRP and presented favorable binding free energies. Our research sheds light on the viability of these E. angustifolia compounds as ZIKV RDRP inhibitors, laying a foundation for further experimental research in developing novel antiviral treatments against ZIKV infections.https://doi.org/10.1038/s41598-025-88481-8Zika virusRNA-dependent RNA polymerase (RDRP)Echinacea angustifoliaMD simulation |
| spellingShingle | Mai M. El-Daly Leena H. Bajrai Thamir A. Alandijany Isra M. Alsaady Hattan S. Gattan Meshari M. Alhamdan Vivek Dhar Dwivedi Esam I. Azhar Exploring Echinacea angustifolia for anti-viral compounds against Zika virus RNA-dependent RNA polymerase: a computational study Scientific Reports Zika virus RNA-dependent RNA polymerase (RDRP) Echinacea angustifolia MD simulation |
| title | Exploring Echinacea angustifolia for anti-viral compounds against Zika virus RNA-dependent RNA polymerase: a computational study |
| title_full | Exploring Echinacea angustifolia for anti-viral compounds against Zika virus RNA-dependent RNA polymerase: a computational study |
| title_fullStr | Exploring Echinacea angustifolia for anti-viral compounds against Zika virus RNA-dependent RNA polymerase: a computational study |
| title_full_unstemmed | Exploring Echinacea angustifolia for anti-viral compounds against Zika virus RNA-dependent RNA polymerase: a computational study |
| title_short | Exploring Echinacea angustifolia for anti-viral compounds against Zika virus RNA-dependent RNA polymerase: a computational study |
| title_sort | exploring echinacea angustifolia for anti viral compounds against zika virus rna dependent rna polymerase a computational study |
| topic | Zika virus RNA-dependent RNA polymerase (RDRP) Echinacea angustifolia MD simulation |
| url | https://doi.org/10.1038/s41598-025-88481-8 |
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