Computational Approach to Target SARS-CoV-2 Proteins Using Bioactives Derived from Nerium indicum
SARS-CoV-2 spreads through inhalation or contact with infected individuals, with its receptor-binding domain (RBD) facilitating cell entry and causing severe effects. In order to identify a better ailment for this disease, the current study has been made using In-silico tools to predict the interact...
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EDP Sciences
2025-01-01
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| Series: | BIO Web of Conferences |
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| Online Access: | https://www.bio-conferences.org/articles/bioconf/pdf/2025/23/bioconf_nittebio2025_02011.pdf |
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| author | Khader Syed Zameer Ahmed Syed Zameer Ahmed Sidhra Saravanan Priya Dharshini Rajan Preethi Ravichandran Kaviya Chandrasekaran Surya Sivakumar Vaishnavi |
| author_facet | Khader Syed Zameer Ahmed Syed Zameer Ahmed Sidhra Saravanan Priya Dharshini Rajan Preethi Ravichandran Kaviya Chandrasekaran Surya Sivakumar Vaishnavi |
| author_sort | Khader Syed Zameer Ahmed |
| collection | DOAJ |
| description | SARS-CoV-2 spreads through inhalation or contact with infected individuals, with its receptor-binding domain (RBD) facilitating cell entry and causing severe effects. In order to identify a better ailment for this disease, the current study has been made using In-silico tools to predict the interaction of SARS-CoV-2 with natural ligand C-1: N-(4-Hydroxyphenyl)-2-methoxy-2-phenyl-acetamide and C-2: N-(4-Hydroxy-phenyl)-2-phenyl-N-phenylacetyl-acetamide of Nerium indicum as it is concerned with the antiviral property. The target proteins such as Glycoprotein (2GHV), Spike S3 (6LVN) and Protease (5RE5, 5RE8, 5RE9, 5REA, 5REB, 5REE, 5REF, 5REK) were docked against ligands. The results reveals that C-1 and C-2 has the high binding from -4.2 Kcal/mol to -8.1 Kcal/mol than the standard (Fingolimod). The protein 5REA has a highest binding affinity of -8.1 Kcal/ mol with C-2, indicating significant potential for interaction. Further, Molecular Simulation studies were conducted to determine the stability of proteins based on physiological conditions such as potential, temperature, pressure and density. The obtained values ranging from -2.20971E+06 kJ/mol to -1.55E+11 kJ/mol, 299.943 K to 299.68 K, 3.25424 bar to -7.26344 bar to and 1014.98 kg/m³ to 1012.33 kg/m³ determines the flexibility of protein structures and proves that the N. indicum compounds can be a potential drug against SARS-CoV-2. |
| format | Article |
| id | doaj-art-e7fc713516834785b520a24de85e51d9 |
| institution | OA Journals |
| issn | 2117-4458 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | EDP Sciences |
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| series | BIO Web of Conferences |
| spelling | doaj-art-e7fc713516834785b520a24de85e51d92025-08-20T02:16:29ZengEDP SciencesBIO Web of Conferences2117-44582025-01-011720201110.1051/bioconf/202517202011bioconf_nittebio2025_02011Computational Approach to Target SARS-CoV-2 Proteins Using Bioactives Derived from Nerium indicumKhader Syed Zameer Ahmed0Syed Zameer Ahmed Sidhra1Saravanan Priya Dharshini2Rajan Preethi3Ravichandran Kaviya4Chandrasekaran Surya5Sivakumar Vaishnavi6Department of Biotechnology, K.S.Rangasamy College of TechnologyDepartment of Biotechnology, K.S.Rangasamy College of TechnologyDepartment of Biotechnology, K.S.Rangasamy College of TechnologyDepartment of Biotechnology, K.S.Rangasamy College of TechnologyDepartment of Biotechnology, K.S.Rangasamy College of TechnologyDepartment of Biotechnology, K.S.Rangasamy College of TechnologyDepartment of Biotechnology, K.S.Rangasamy College of TechnologySARS-CoV-2 spreads through inhalation or contact with infected individuals, with its receptor-binding domain (RBD) facilitating cell entry and causing severe effects. In order to identify a better ailment for this disease, the current study has been made using In-silico tools to predict the interaction of SARS-CoV-2 with natural ligand C-1: N-(4-Hydroxyphenyl)-2-methoxy-2-phenyl-acetamide and C-2: N-(4-Hydroxy-phenyl)-2-phenyl-N-phenylacetyl-acetamide of Nerium indicum as it is concerned with the antiviral property. The target proteins such as Glycoprotein (2GHV), Spike S3 (6LVN) and Protease (5RE5, 5RE8, 5RE9, 5REA, 5REB, 5REE, 5REF, 5REK) were docked against ligands. The results reveals that C-1 and C-2 has the high binding from -4.2 Kcal/mol to -8.1 Kcal/mol than the standard (Fingolimod). The protein 5REA has a highest binding affinity of -8.1 Kcal/ mol with C-2, indicating significant potential for interaction. Further, Molecular Simulation studies were conducted to determine the stability of proteins based on physiological conditions such as potential, temperature, pressure and density. The obtained values ranging from -2.20971E+06 kJ/mol to -1.55E+11 kJ/mol, 299.943 K to 299.68 K, 3.25424 bar to -7.26344 bar to and 1014.98 kg/m³ to 1012.33 kg/m³ determines the flexibility of protein structures and proves that the N. indicum compounds can be a potential drug against SARS-CoV-2.https://www.bio-conferences.org/articles/bioconf/pdf/2025/23/bioconf_nittebio2025_02011.pdfsars-cov-2coronavirusswiss admet analysismolecular dockingenergy minimization on gromacs |
| spellingShingle | Khader Syed Zameer Ahmed Syed Zameer Ahmed Sidhra Saravanan Priya Dharshini Rajan Preethi Ravichandran Kaviya Chandrasekaran Surya Sivakumar Vaishnavi Computational Approach to Target SARS-CoV-2 Proteins Using Bioactives Derived from Nerium indicum BIO Web of Conferences sars-cov-2 coronavirus swiss admet analysis molecular docking energy minimization on gromacs |
| title | Computational Approach to Target SARS-CoV-2 Proteins Using Bioactives Derived from Nerium indicum |
| title_full | Computational Approach to Target SARS-CoV-2 Proteins Using Bioactives Derived from Nerium indicum |
| title_fullStr | Computational Approach to Target SARS-CoV-2 Proteins Using Bioactives Derived from Nerium indicum |
| title_full_unstemmed | Computational Approach to Target SARS-CoV-2 Proteins Using Bioactives Derived from Nerium indicum |
| title_short | Computational Approach to Target SARS-CoV-2 Proteins Using Bioactives Derived from Nerium indicum |
| title_sort | computational approach to target sars cov 2 proteins using bioactives derived from nerium indicum |
| topic | sars-cov-2 coronavirus swiss admet analysis molecular docking energy minimization on gromacs |
| url | https://www.bio-conferences.org/articles/bioconf/pdf/2025/23/bioconf_nittebio2025_02011.pdf |
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