2D-SAR, Topomer CoMFA and molecular docking studies on avian influenza neuraminidase inhibitors
Avian influenza is a serious zoonotic infectious disease with huge negative impacts on local poultry farming, human health and social stability. Therefore, the design of new compounds against avian influenza has been the focus in this field. In this study, computational methods were applied to inves...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2019-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037018301235 |
| _version_ | 1818158375662256128 |
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| author | Bing Niu Yi Lu Jianying Wang Yan Hu Jiahui Chen Qin Chen Guangwu He Linfeng Zheng |
| author_facet | Bing Niu Yi Lu Jianying Wang Yan Hu Jiahui Chen Qin Chen Guangwu He Linfeng Zheng |
| author_sort | Bing Niu |
| collection | DOAJ |
| description | Avian influenza is a serious zoonotic infectious disease with huge negative impacts on local poultry farming, human health and social stability. Therefore, the design of new compounds against avian influenza has been the focus in this field. In this study, computational methods were applied to investigate the compounds with neuraminidase inhibitory activity. First, 2D-SAR model was built to recognize neuraminidase inhibitors (NAIs). As a result, the accuracy of 10 cross-validation and independent tests is 96.84% and 98.97%, respectively. Then, the Topomer CoMFA model was constructed to predict the inhibitory activity and analyses molecular fields. Two models were obtained by changing the cutting methods. The second model is employed to predict the activity (q2 = 0.784 and r2 = 0.982). Molecular docking was also used to further analyze the binding sites between NAIs and neuraminidase from human and avian virus. As a result, it is found that same binding Total Score has some differences, but the binding sites are basically the same. At last, some potential NAIs were screened and some optimal opinions were taken. It is expected that our study can assist to study and develop new types of NAIs. Keywords: Avian influenza, Neuraminidase, 2D-SAR, Topomer CoMFA, Molecular docking |
| first_indexed | 2024-12-11T15:29:06Z |
| format | Article |
| id | doaj.art-5e59d64d06434e7eb717b585ecd4f111 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-12-11T15:29:06Z |
| publishDate | 2019-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-5e59d64d06434e7eb717b585ecd4f1112022-12-22T01:00:07ZengElsevierComputational and Structural Biotechnology Journal2001-03702019-01-011739482D-SAR, Topomer CoMFA and molecular docking studies on avian influenza neuraminidase inhibitorsBing Niu0Yi Lu1Jianying Wang2Yan Hu3Jiahui Chen4Qin Chen5Guangwu He6Linfeng Zheng7School of Life Sciences, Shanghai University, Shanghai 200444, China; Corresponding authors.School of Life Sciences, Shanghai University, Shanghai 200444, ChinaSchool of Life Sciences, Shanghai University, Shanghai 200444, ChinaSchool of Life Sciences, Shanghai University, Shanghai 200444, ChinaSchool of Life Sciences, Shanghai University, Shanghai 200444, ChinaSchool of Life Sciences, Shanghai University, Shanghai 200444, China; Corresponding authors.Department of Radiology, Shanghai First People's Hospital, Baoshan Branch, Shanghai 200940, China; Corresponding authors.Department of Radiology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, China; Department of Radiology, Shanghai First People's Hospital, Baoshan Branch, Shanghai 200940, China; Corresponding author at: Department of Radiology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, ChinaAvian influenza is a serious zoonotic infectious disease with huge negative impacts on local poultry farming, human health and social stability. Therefore, the design of new compounds against avian influenza has been the focus in this field. In this study, computational methods were applied to investigate the compounds with neuraminidase inhibitory activity. First, 2D-SAR model was built to recognize neuraminidase inhibitors (NAIs). As a result, the accuracy of 10 cross-validation and independent tests is 96.84% and 98.97%, respectively. Then, the Topomer CoMFA model was constructed to predict the inhibitory activity and analyses molecular fields. Two models were obtained by changing the cutting methods. The second model is employed to predict the activity (q2 = 0.784 and r2 = 0.982). Molecular docking was also used to further analyze the binding sites between NAIs and neuraminidase from human and avian virus. As a result, it is found that same binding Total Score has some differences, but the binding sites are basically the same. At last, some potential NAIs were screened and some optimal opinions were taken. It is expected that our study can assist to study and develop new types of NAIs. Keywords: Avian influenza, Neuraminidase, 2D-SAR, Topomer CoMFA, Molecular dockinghttp://www.sciencedirect.com/science/article/pii/S2001037018301235 |
| spellingShingle | Bing Niu Yi Lu Jianying Wang Yan Hu Jiahui Chen Qin Chen Guangwu He Linfeng Zheng 2D-SAR, Topomer CoMFA and molecular docking studies on avian influenza neuraminidase inhibitors Computational and Structural Biotechnology Journal |
| title | 2D-SAR, Topomer CoMFA and molecular docking studies on avian influenza neuraminidase inhibitors |
| title_full | 2D-SAR, Topomer CoMFA and molecular docking studies on avian influenza neuraminidase inhibitors |
| title_fullStr | 2D-SAR, Topomer CoMFA and molecular docking studies on avian influenza neuraminidase inhibitors |
| title_full_unstemmed | 2D-SAR, Topomer CoMFA and molecular docking studies on avian influenza neuraminidase inhibitors |
| title_short | 2D-SAR, Topomer CoMFA and molecular docking studies on avian influenza neuraminidase inhibitors |
| title_sort | 2d sar topomer comfa and molecular docking studies on avian influenza neuraminidase inhibitors |
| url | http://www.sciencedirect.com/science/article/pii/S2001037018301235 |
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