In silico exploration of phytocompounds from AYUSH-64 medicinal plants against SARS CoV-2 RNA-dependent RNA polymerase
Background: The AYUSH 64 formulation helps to treat mild to moderate cases of COVID-19. Although several drugs have been proposed to combat COVID-19, no medication is available for SARS-CoV-2 infection. The RNA-dependent RNA polymerase (RdRp) is the pivotal enzyme of SARS-CoV-2 replication, so it co...
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Elsevier
2024-11-01
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| Series: | Journal of Ayurveda and Integrative Medicine |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0975947624001414 |
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| author | Srinivasulu Cheemanapalli Ramanjaneyulu Golla Sudhakar Pagidi Seshapani Pantangi |
| author_facet | Srinivasulu Cheemanapalli Ramanjaneyulu Golla Sudhakar Pagidi Seshapani Pantangi |
| author_sort | Srinivasulu Cheemanapalli |
| collection | DOAJ |
| description | Background: The AYUSH 64 formulation helps to treat mild to moderate cases of COVID-19. Although several drugs have been proposed to combat COVID-19, no medication is available for SARS-CoV-2 infection. The RNA-dependent RNA polymerase (RdRp) is the pivotal enzyme of SARS-CoV-2 replication, so it could be considered a better drug target for experimental studies. Objective: The AYUSH-64 formulation plants exhibited multiple therapeutic properties; thus, the present study aims to screen the phytocompounds of these plants against SARS CoV2 RdRp to identify specific compounds that could potentially affect COVID-19 infection. Materials and methods: PatchDock and AutoDock tools were used for docking experiments. MD simulations and Density Functional Theory (DFT) calculations of protein-ligand Picroside-I and Remdesivir complexes were carried out in GROMACS v2019.4 and Gaussian 09 software, respectively. Results: Among the tested, five phytocompounds (Picroside I, Oleanolic acid, Arvenin I, II, and III) from AYUSH-64 medicinal plants showed possible binding with RdRp catalytic residues (Ser759, Asp760, and Asp761). Of these, Picroside I exhibited hydrogen bond interactions with NTP entry channel residues (Arg553 and Arg555). The MM-PBSA free energy, RMSD, Rg, PCA, and RMSF analysis suggested that the Picroside I complex showed stable binding interactions with RdRp in the 50 ns simulation. In addition to this, Picroside I revealed its robust and attractive nature toward the target protein, as confirmed by DFT. Conclusion: The results of this study have proposed that Picroside I from AYUSH 64 medicinal plant compounds was the selective binder of catalytic and NTP entry channel residues of SARS-CoV2 RdRp thereby; it may considered as a potential inhibitor of SARS-CoV2 RdRp. |
| format | Article |
| id | doaj-art-cabfcbd55f6f44b09e17eb83f71c99a7 |
| institution | Kabale University |
| issn | 0975-9476 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Ayurveda and Integrative Medicine |
| spelling | doaj-art-cabfcbd55f6f44b09e17eb83f71c99a72024-12-23T04:19:05ZengElsevierJournal of Ayurveda and Integrative Medicine0975-94762024-11-01156101026In silico exploration of phytocompounds from AYUSH-64 medicinal plants against SARS CoV-2 RNA-dependent RNA polymeraseSrinivasulu Cheemanapalli0Ramanjaneyulu Golla1Sudhakar Pagidi2Seshapani Pantangi3Survey of Medicinal Plants Unit, CCRAS - Regional Ayurveda Research Institute, Itanagar, Arunachal Pradesh, IndiaDepartment of Biochemistry, School of Allied Health Science, REVA University, Bangalore, India; Corresponding author. Department of Biochemistry, School of Allied Health Science, REVA University, Bangalore, India.Department of Chemical Sciences, Indian Institute of Science, Bangalore, IndiaDepartment of Microbiology, Sri Venkateswara University, Tirupati, IndiaBackground: The AYUSH 64 formulation helps to treat mild to moderate cases of COVID-19. Although several drugs have been proposed to combat COVID-19, no medication is available for SARS-CoV-2 infection. The RNA-dependent RNA polymerase (RdRp) is the pivotal enzyme of SARS-CoV-2 replication, so it could be considered a better drug target for experimental studies. Objective: The AYUSH-64 formulation plants exhibited multiple therapeutic properties; thus, the present study aims to screen the phytocompounds of these plants against SARS CoV2 RdRp to identify specific compounds that could potentially affect COVID-19 infection. Materials and methods: PatchDock and AutoDock tools were used for docking experiments. MD simulations and Density Functional Theory (DFT) calculations of protein-ligand Picroside-I and Remdesivir complexes were carried out in GROMACS v2019.4 and Gaussian 09 software, respectively. Results: Among the tested, five phytocompounds (Picroside I, Oleanolic acid, Arvenin I, II, and III) from AYUSH-64 medicinal plants showed possible binding with RdRp catalytic residues (Ser759, Asp760, and Asp761). Of these, Picroside I exhibited hydrogen bond interactions with NTP entry channel residues (Arg553 and Arg555). The MM-PBSA free energy, RMSD, Rg, PCA, and RMSF analysis suggested that the Picroside I complex showed stable binding interactions with RdRp in the 50 ns simulation. In addition to this, Picroside I revealed its robust and attractive nature toward the target protein, as confirmed by DFT. Conclusion: The results of this study have proposed that Picroside I from AYUSH 64 medicinal plant compounds was the selective binder of catalytic and NTP entry channel residues of SARS-CoV2 RdRp thereby; it may considered as a potential inhibitor of SARS-CoV2 RdRp.http://www.sciencedirect.com/science/article/pii/S0975947624001414SARS-CoV2RNA-Dependent RNA polymeraseAYUSH-64DockingMD simulationsPicroside I |
| spellingShingle | Srinivasulu Cheemanapalli Ramanjaneyulu Golla Sudhakar Pagidi Seshapani Pantangi In silico exploration of phytocompounds from AYUSH-64 medicinal plants against SARS CoV-2 RNA-dependent RNA polymerase Journal of Ayurveda and Integrative Medicine SARS-CoV2 RNA-Dependent RNA polymerase AYUSH-64 Docking MD simulations Picroside I |
| title | In silico exploration of phytocompounds from AYUSH-64 medicinal plants against SARS CoV-2 RNA-dependent RNA polymerase |
| title_full | In silico exploration of phytocompounds from AYUSH-64 medicinal plants against SARS CoV-2 RNA-dependent RNA polymerase |
| title_fullStr | In silico exploration of phytocompounds from AYUSH-64 medicinal plants against SARS CoV-2 RNA-dependent RNA polymerase |
| title_full_unstemmed | In silico exploration of phytocompounds from AYUSH-64 medicinal plants against SARS CoV-2 RNA-dependent RNA polymerase |
| title_short | In silico exploration of phytocompounds from AYUSH-64 medicinal plants against SARS CoV-2 RNA-dependent RNA polymerase |
| title_sort | in silico exploration of phytocompounds from ayush 64 medicinal plants against sars cov 2 rna dependent rna polymerase |
| topic | SARS-CoV2 RNA-Dependent RNA polymerase AYUSH-64 Docking MD simulations Picroside I |
| url | http://www.sciencedirect.com/science/article/pii/S0975947624001414 |
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