Pea eggplant (Solanum torvum Swartz) is a source of plant food polyphenols with SARS-CoV inhibiting potential
Background Pea eggplant (Solanum torvum Swartz) commonly known as turkey berry or ‘terung pipit’ in Malay is a vegetable plant widely consumed by the local community in Malaysia. The shrub bears pea-like turkey berry fruits (TBFs), rich in phytochemicals of medicinal interest. The TBF phytochemicals...
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PeerJ Inc.
2022-11-01
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| Online Access: | https://peerj.com/articles/14168.pdf |
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| author | Nisha Govender Norazura Syazlin Zulkifli Nurul Farhana Badrul Hisham Nur Syatila Ab Ghani Zeti-Azura Mohamed-Hussein |
| author_facet | Nisha Govender Norazura Syazlin Zulkifli Nurul Farhana Badrul Hisham Nur Syatila Ab Ghani Zeti-Azura Mohamed-Hussein |
| author_sort | Nisha Govender |
| collection | DOAJ |
| description | Background Pea eggplant (Solanum torvum Swartz) commonly known as turkey berry or ‘terung pipit’ in Malay is a vegetable plant widely consumed by the local community in Malaysia. The shrub bears pea-like turkey berry fruits (TBFs), rich in phytochemicals of medicinal interest. The TBF phytochemicals hold a wide spectrum of pharmacological properties. In this study, the TBF phytochemicals’ potential inhibitory properties were evaluated against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) of the Coronavirus disease 2019 (COVID-19). The TBF polyphenols were screened against SARS-CoV receptors via molecular docking and the best receptor-ligand complex was validated further by molecular dynamics (MD) simulation. Method The SARS-CoV receptor structure files (viral structural components) were retrieved from the Protein Data Bank (PDB) database: membrane protein (PDB ID: 3I6G), main protease (PDB ID: 5RE4), and spike glycoproteins (PDB ID: 6VXX and 6VYB). The receptor binding pocket regions were identified by Discovery Studio (BIOVIA) for targeted docking with TBF polyphenols (genistin, kaempferol, mellein, rhoifolin and scutellarein). The ligand and SARS-CoV family receptor structure files were pre-processed using the AutoDock tools. Molecular docking was performed with the Lamarckian genetic algorithm using AutoDock Vina 4.2 software. The best pose (ligand-receptor complex) from the molecular docking analysis was selected based on the minimum binding energy (MBE) and extent of structural interactions, as indicated by BIOVIA visualization tool. The selected complex was validated by a 100 ns MD simulation run using the GROMACS software. The dynamic behaviour and stability of the receptor-ligand complex were evaluated by the root mean square displacement (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), solvent accessible surface volume (SASV) and number of hydrogen bonds. Results At RMSD = 0, the TBF polyphenols showed fairly strong physical interactions with SARS-CoV receptors under all possible combinations. The MBE of TBF polyphenol-bound SARS CoV complexes ranged from −4.6 to −8.3 kcal/mol. Analysis of the structural interactions showed the presence of hydrogen bonds, electrostatic and hydrophobic interactions between the receptor residues (RR) and ligands atoms. Based on the MBE values, the 3I6G-rhoifolin (MBE = −8.3 kcal/mol) and 5RE4-genistin (MBE = −7.6 kcal/mol) complexes were ranked with the least value. However, the latter showed a greater extent of interactions between the RRs and the ligand atoms and thus was further validated by MD simulation. The MD simulation parameters of the 5RE4-genistin complex over a 100 ns run indicated good structural stability with minimal flexibility within genistin binding pocket region. The findings suggest that S. torvum polyphenols hold good therapeutics potential in COVID-19 management. |
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| spelling | doaj.art-16de6c2b16d34490bbd8ad572dca23892023-12-03T11:36:53ZengPeerJ Inc.PeerJ2167-83592022-11-0110e1416810.7717/peerj.14168Pea eggplant (Solanum torvum Swartz) is a source of plant food polyphenols with SARS-CoV inhibiting potentialNisha Govender0Norazura Syazlin Zulkifli1Nurul Farhana Badrul Hisham2Nur Syatila Ab Ghani3Zeti-Azura Mohamed-Hussein4Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, MalaysiaInstitute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, MalaysiaInstitute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, MalaysiaInstitute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, MalaysiaInstitute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, MalaysiaBackground Pea eggplant (Solanum torvum Swartz) commonly known as turkey berry or ‘terung pipit’ in Malay is a vegetable plant widely consumed by the local community in Malaysia. The shrub bears pea-like turkey berry fruits (TBFs), rich in phytochemicals of medicinal interest. The TBF phytochemicals hold a wide spectrum of pharmacological properties. In this study, the TBF phytochemicals’ potential inhibitory properties were evaluated against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) of the Coronavirus disease 2019 (COVID-19). The TBF polyphenols were screened against SARS-CoV receptors via molecular docking and the best receptor-ligand complex was validated further by molecular dynamics (MD) simulation. Method The SARS-CoV receptor structure files (viral structural components) were retrieved from the Protein Data Bank (PDB) database: membrane protein (PDB ID: 3I6G), main protease (PDB ID: 5RE4), and spike glycoproteins (PDB ID: 6VXX and 6VYB). The receptor binding pocket regions were identified by Discovery Studio (BIOVIA) for targeted docking with TBF polyphenols (genistin, kaempferol, mellein, rhoifolin and scutellarein). The ligand and SARS-CoV family receptor structure files were pre-processed using the AutoDock tools. Molecular docking was performed with the Lamarckian genetic algorithm using AutoDock Vina 4.2 software. The best pose (ligand-receptor complex) from the molecular docking analysis was selected based on the minimum binding energy (MBE) and extent of structural interactions, as indicated by BIOVIA visualization tool. The selected complex was validated by a 100 ns MD simulation run using the GROMACS software. The dynamic behaviour and stability of the receptor-ligand complex were evaluated by the root mean square displacement (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), solvent accessible surface volume (SASV) and number of hydrogen bonds. Results At RMSD = 0, the TBF polyphenols showed fairly strong physical interactions with SARS-CoV receptors under all possible combinations. The MBE of TBF polyphenol-bound SARS CoV complexes ranged from −4.6 to −8.3 kcal/mol. Analysis of the structural interactions showed the presence of hydrogen bonds, electrostatic and hydrophobic interactions between the receptor residues (RR) and ligands atoms. Based on the MBE values, the 3I6G-rhoifolin (MBE = −8.3 kcal/mol) and 5RE4-genistin (MBE = −7.6 kcal/mol) complexes were ranked with the least value. However, the latter showed a greater extent of interactions between the RRs and the ligand atoms and thus was further validated by MD simulation. The MD simulation parameters of the 5RE4-genistin complex over a 100 ns run indicated good structural stability with minimal flexibility within genistin binding pocket region. The findings suggest that S. torvum polyphenols hold good therapeutics potential in COVID-19 management.https://peerj.com/articles/14168.pdfCOVID-19Pea eggplantMolecular dockingMolecular dynamics simulationSARS CoVPolyphenols |
| spellingShingle | Nisha Govender Norazura Syazlin Zulkifli Nurul Farhana Badrul Hisham Nur Syatila Ab Ghani Zeti-Azura Mohamed-Hussein Pea eggplant (Solanum torvum Swartz) is a source of plant food polyphenols with SARS-CoV inhibiting potential PeerJ COVID-19 Pea eggplant Molecular docking Molecular dynamics simulation SARS CoV Polyphenols |
| title | Pea eggplant (Solanum torvum Swartz) is a source of plant food polyphenols with SARS-CoV inhibiting potential |
| title_full | Pea eggplant (Solanum torvum Swartz) is a source of plant food polyphenols with SARS-CoV inhibiting potential |
| title_fullStr | Pea eggplant (Solanum torvum Swartz) is a source of plant food polyphenols with SARS-CoV inhibiting potential |
| title_full_unstemmed | Pea eggplant (Solanum torvum Swartz) is a source of plant food polyphenols with SARS-CoV inhibiting potential |
| title_short | Pea eggplant (Solanum torvum Swartz) is a source of plant food polyphenols with SARS-CoV inhibiting potential |
| title_sort | pea eggplant solanum torvum swartz is a source of plant food polyphenols with sars cov inhibiting potential |
| topic | COVID-19 Pea eggplant Molecular docking Molecular dynamics simulation SARS CoV Polyphenols |
| url | https://peerj.com/articles/14168.pdf |
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