In silico screening of lactic acid bacteria methanolic extract for potential antiviral activity against Japanese encephalitis virus
This study aimed to predict potential interactions between compounds produced by lactic acid bacteria (LAB) and Japanese encephalitis virus (JEV) to identify potential targets for anti-JEV drugs. Virtual screening was conducted by blind docking fourteen selected compounds extracted from 20 LAB strai...
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| Language: | English |
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Elsevier
2025-07-01
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| Series: | Results in Chemistry |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211715625003017 |
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| author | Suria Marlina Mansor Pouya Hassandarvish Siau Xuan Chong Phui Chyng Yap Sazaly Abubakar Wei Lim Chong Vannajan Sanghiran Lee Hai Yen Lee |
| author_facet | Suria Marlina Mansor Pouya Hassandarvish Siau Xuan Chong Phui Chyng Yap Sazaly Abubakar Wei Lim Chong Vannajan Sanghiran Lee Hai Yen Lee |
| author_sort | Suria Marlina Mansor |
| collection | DOAJ |
| description | This study aimed to predict potential interactions between compounds produced by lactic acid bacteria (LAB) and Japanese encephalitis virus (JEV) to identify potential targets for anti-JEV drugs. Virtual screening was conducted by blind docking fourteen selected compounds extracted from 20 LAB strains using Autodock Vina. The interaction between the most commonly produced compounds, namely 3-isobutyl-2,3,6,7,8,8a-hexahydropyrrolo [1,2] pyrazine-1,4-dione (Comp-A), Pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro-3-(phenylmethyl)- (Comp-B), and 2,4-ditert-butylphenol (Comp-C), towards the JEV proteins, was investigated through molecular docking supported by other analyses such as ADMET prediction and binding free energy calculation. AutoDock (version 4.2) and Vina predicted the optimal drug binding sites using the number of hydrogen bonds and other important interactions established with the target amino acids and the affinity of the active pockets based on binding energy. The findings demonstrated good affinity of the selected compounds against JEV protein, such as Comp-A (−7.3 kcal/mol), Comp-B (−7.8 kcal/mol), and Comp-C (−8.1 kcal/mol). Molecular dynamics simulations were performed for 100 ns, and a binding affinity weaker than −20 kcal/mol (less negative) suggests that the protein-ligand complex is less active, potentially limiting its contribution to the desired biological activity. In-silico pharmacological evaluation shows that these compounds exhibit the compounds exhibit the binding affinity for drug-like and ADMET properties in micromolar range. Therefore, this analysis anticipated that all three compounds would have antiviral activity against JEV protein, and it is possible to use these findings to direct the development of other antiviral drugs. |
| format | Article |
| id | doaj-art-bd84d66be92c4979bebf0737fce474e2 |
| institution | DOAJ |
| issn | 2211-7156 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Results in Chemistry |
| spelling | doaj-art-bd84d66be92c4979bebf0737fce474e22025-08-20T03:02:36ZengElsevierResults in Chemistry2211-71562025-07-011610231810.1016/j.rechem.2025.102318In silico screening of lactic acid bacteria methanolic extract for potential antiviral activity against Japanese encephalitis virusSuria Marlina Mansor0Pouya Hassandarvish1Siau Xuan Chong2Phui Chyng Yap3Sazaly Abubakar4Wei Lim Chong5Vannajan Sanghiran Lee6Hai Yen Lee7Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HiCOE), Universiti Malaya, 50603 Kuala Lumpur, MalaysiaTropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HiCOE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia; Corresponding authors.Tropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HiCOE), Universiti Malaya, 50603 Kuala Lumpur, MalaysiaTropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HiCOE), Universiti Malaya, 50603 Kuala Lumpur, MalaysiaTropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HiCOE), Universiti Malaya, 50603 Kuala Lumpur, MalaysiaDepartment of Chemistry, Centre of Excellence in Quantum Information Science and Technology (QIST), Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, MalaysiaDepartment of Chemistry, Centre of Excellence in Quantum Information Science and Technology (QIST), Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, MalaysiaTropical Infectious Diseases Research and Education Centre (TIDREC), Higher Institution Centre of Excellence (HiCOE), Universiti Malaya, 50603 Kuala Lumpur, Malaysia; Corresponding authors.This study aimed to predict potential interactions between compounds produced by lactic acid bacteria (LAB) and Japanese encephalitis virus (JEV) to identify potential targets for anti-JEV drugs. Virtual screening was conducted by blind docking fourteen selected compounds extracted from 20 LAB strains using Autodock Vina. The interaction between the most commonly produced compounds, namely 3-isobutyl-2,3,6,7,8,8a-hexahydropyrrolo [1,2] pyrazine-1,4-dione (Comp-A), Pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro-3-(phenylmethyl)- (Comp-B), and 2,4-ditert-butylphenol (Comp-C), towards the JEV proteins, was investigated through molecular docking supported by other analyses such as ADMET prediction and binding free energy calculation. AutoDock (version 4.2) and Vina predicted the optimal drug binding sites using the number of hydrogen bonds and other important interactions established with the target amino acids and the affinity of the active pockets based on binding energy. The findings demonstrated good affinity of the selected compounds against JEV protein, such as Comp-A (−7.3 kcal/mol), Comp-B (−7.8 kcal/mol), and Comp-C (−8.1 kcal/mol). Molecular dynamics simulations were performed for 100 ns, and a binding affinity weaker than −20 kcal/mol (less negative) suggests that the protein-ligand complex is less active, potentially limiting its contribution to the desired biological activity. In-silico pharmacological evaluation shows that these compounds exhibit the compounds exhibit the binding affinity for drug-like and ADMET properties in micromolar range. Therefore, this analysis anticipated that all three compounds would have antiviral activity against JEV protein, and it is possible to use these findings to direct the development of other antiviral drugs.http://www.sciencedirect.com/science/article/pii/S2211715625003017Japanese encephalitis virusLactic acid bacteriaIn silicoMolecular docking, molecular dynamics simulations |
| spellingShingle | Suria Marlina Mansor Pouya Hassandarvish Siau Xuan Chong Phui Chyng Yap Sazaly Abubakar Wei Lim Chong Vannajan Sanghiran Lee Hai Yen Lee In silico screening of lactic acid bacteria methanolic extract for potential antiviral activity against Japanese encephalitis virus Results in Chemistry Japanese encephalitis virus Lactic acid bacteria In silico Molecular docking, molecular dynamics simulations |
| title | In silico screening of lactic acid bacteria methanolic extract for potential antiviral activity against Japanese encephalitis virus |
| title_full | In silico screening of lactic acid bacteria methanolic extract for potential antiviral activity against Japanese encephalitis virus |
| title_fullStr | In silico screening of lactic acid bacteria methanolic extract for potential antiviral activity against Japanese encephalitis virus |
| title_full_unstemmed | In silico screening of lactic acid bacteria methanolic extract for potential antiviral activity against Japanese encephalitis virus |
| title_short | In silico screening of lactic acid bacteria methanolic extract for potential antiviral activity against Japanese encephalitis virus |
| title_sort | in silico screening of lactic acid bacteria methanolic extract for potential antiviral activity against japanese encephalitis virus |
| topic | Japanese encephalitis virus Lactic acid bacteria In silico Molecular docking, molecular dynamics simulations |
| url | http://www.sciencedirect.com/science/article/pii/S2211715625003017 |
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