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Etminani F, Etminani A, Fazeli-Nasab B. Bioinformatic Study of the Antiviral Properties of Thyme and Eucalyptus Against the Coat Protein of Mimosa Yellow Vein Virus. pbp 2025; 7 (In press)
URL: http://pbp.medilam.ac.ir/article-1-305-en.html
URL: http://pbp.medilam.ac.ir/article-1-305-en.html
1- Department of Plant Production, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
2- Young Researchers and Elite Clubs, Sanandaj Branch, Islamic Azad University of Sanandaj, Sanandaj, Iran
3- Department of Agronomy and Plant Breeding, Agriculture Institute, Research Institute of Zabol, Zabol, Iran ,bfazelinasab@gmail.com
2- Young Researchers and Elite Clubs, Sanandaj Branch, Islamic Azad University of Sanandaj, Sanandaj, Iran
3- Department of Agronomy and Plant Breeding, Agriculture Institute, Research Institute of Zabol, Zabol, Iran ,
Abstract: (120 Views)
Objective: The Geminiviridae family comprises significant plant pathogens causing severe economic losses worldwide. Among them, Begomovirus species, like Mimosa yellow leaf curl virus (MiYLCV), threaten crops and ornamental plants. Natural compounds, such as thyme and eucalyptus essential oils, may offer antiviral solutions. This study investigates the inhibitory potential of thyme and eucalyptus essential oils against MiYLCV coat protein using molecular docking, providing insights into eco-friendly antiviral strategies.
Methods: In this study, first, the three-dimensional structure of phytochemical compounds present in the two medicinal plants, Thymus vulgaris and Eucalyptus grandis, was obtained from the PubChem database. Next, the three-dimensional structure of the virus coat protein was optimized using the Swiss-MODEL online tool. The ability of the selected chemical compounds to inhibit the coat protein associated with pathogen virulence was explored using the molecular docking method using the specialized software autodock4.2.6.
Results: Phylogenetic analysis of Mimosa yellow vein virus coat protein revealed close relationships between some Begomovirus sequences (e.g., NP_808548.1 and NP_803540.1), while others (YP_00358491.1, ADW83758.1) showed divergence. The 3D protein model exhibited stable Ramachandran plot angles. Among thyme compounds, β-Myrcene had the highest permeability (logP=2.89), while γ-Terpinene showed the highest solubility (logS=-3.45). In eucalyptus, Isoamyl isovalerate (logP=3.05) and alpha-Terpinene (logS=-3.30) exhibited extreme values. Molecular docking identified strong binding interactions: Endo-borneol (-4.75 kcal/mol), α-Terpineol (-4.96 kcal/mol), and Terpinen-4-ol (-4.78 kcal/mol) from thyme, and beta-Terpineol (-5.14 kcal/mol), trans-Carveol (-5.15 kcal/mol), and Carvotanacetone (-5.21 kcal/mol) from eucalyptus exhibited the highest affinity for the viral coat protein. These findings suggest potential antiviral activity against Mimosa yellow vein virus.
Conclusion: The results revealed that the combination of a-Terpineol and Carvotanacetone act as the strongest binding molecules in thyme and eucalyptus plants, respectively. These compounds can be proposed as potent antagonists targeting the coat protein of Mimosa yellow vein virus, effectively impeding its function.
Methods: In this study, first, the three-dimensional structure of phytochemical compounds present in the two medicinal plants, Thymus vulgaris and Eucalyptus grandis, was obtained from the PubChem database. Next, the three-dimensional structure of the virus coat protein was optimized using the Swiss-MODEL online tool. The ability of the selected chemical compounds to inhibit the coat protein associated with pathogen virulence was explored using the molecular docking method using the specialized software autodock4.2.6.
Results: Phylogenetic analysis of Mimosa yellow vein virus coat protein revealed close relationships between some Begomovirus sequences (e.g., NP_808548.1 and NP_803540.1), while others (YP_00358491.1, ADW83758.1) showed divergence. The 3D protein model exhibited stable Ramachandran plot angles. Among thyme compounds, β-Myrcene had the highest permeability (logP=2.89), while γ-Terpinene showed the highest solubility (logS=-3.45). In eucalyptus, Isoamyl isovalerate (logP=3.05) and alpha-Terpinene (logS=-3.30) exhibited extreme values. Molecular docking identified strong binding interactions: Endo-borneol (-4.75 kcal/mol), α-Terpineol (-4.96 kcal/mol), and Terpinen-4-ol (-4.78 kcal/mol) from thyme, and beta-Terpineol (-5.14 kcal/mol), trans-Carveol (-5.15 kcal/mol), and Carvotanacetone (-5.21 kcal/mol) from eucalyptus exhibited the highest affinity for the viral coat protein. These findings suggest potential antiviral activity against Mimosa yellow vein virus.
Conclusion: The results revealed that the combination of a-Terpineol and Carvotanacetone act as the strongest binding molecules in thyme and eucalyptus plants, respectively. These compounds can be proposed as potent antagonists targeting the coat protein of Mimosa yellow vein virus, effectively impeding its function.
Type of Study: Research |
Subject:
Biotechnology
Received: 2025/05/24 | Accepted: 2025/06/2 | Published: 2025/12/1
Received: 2025/05/24 | Accepted: 2025/06/2 | Published: 2025/12/1
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