Evaluation of the binding performance of flavonoids to estrogen receptor alpha by Autodock, Autodock Vina and Surflex-Dock
文献类型：期刊论文
| 作者 | Xue, Qiao; Liu, Xian ; Russell, Paul; Li, Jin; Pan, Wenxiao; Fu, Jianjie; Zhang, Aiqian
|
| 刊名 | ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
 |
| 出版日期 | 2022-03-15 |
| 卷号 | 233期号:0页码:113323 |
| ISSN号 | 0147-6513 |
| 关键词 | PROTEIN-LIGAND DOCKING MOLECULAR DOCKING DISCOVERY FRAMEWORK DYNAMICS AFFINITY |
| 英文摘要 | Molecular docking is a widely used method to predict the binding modes of small-molecule ligands to the target binding site. However, it remains a challenge to identify the correct binding conformation and the corresponding binding affinity for a series of structurally similar ligands, especially those with weak binding. An understanding of the various relative attributes of popular docking programs is required to ensure a successful docking outcome. In this study, we systematically compared the performance of three popular docking programs, Autodock, Autodock Vina, and Surflex-Dock for a series of structurally similar weekly binding flavonoids (22) binding to the estrogen receptor alpha (ER alpha). For these flavonoids-ER alpha interactions, Surflex-Dock showed higher accuracy than Autodock and Autodock Vina. The hydrogen bond overweighting by Autodock and Autodock Vina led to incorrect binding results, while Surflex-Dock effectively balanced both hydrogen bond and hydrophobic interactions. Moreover, the selection of initial receptor structure is critical as it influences the docking conformations of flavonoids-ER alpha complexes. The flexible docking method failed to further improve the docking accuracy of the semi-flexible docking method for such chemicals. In addition, binding interaction analysis revealed that 8 residues, including Ala350, Glu353, Leu387, Arg394, Phe404, Gly521, His524, and Leu525, are the key residues in ER alpha-flavonoids complexes. This work provides reference for assessing molecular interactions between ER alpha and flavonoid-like chemicals and provides instructive information for other environmental chemicals. |
| 源URL | [https://ir.rcees.ac.cn/handle/311016/47532]  |
| 专题 | 生态环境研究中心_环境化学与生态毒理学国家重点实验室 |
| 通讯作者 | Fu, Jianjie |
| 作者单位 | 1.Unilever Safety & Environm Assurance Ctr, Colworth Sci Pk, Sharnbrook MK44 1LQ, Beds, England 2.Univ Chinese Acad Sci, Coll Resources & Environm, Beijing 100049, Peoples R China 3.Univ Chinese Acad Sci, Sch Environm, Hangzhou Inst Adv Study, Hangzhou 310024, Peoples R China 4.Chinese Acad Sci, Res Ctr Ecoenvironm Sci, State Key Lab Environm Chem & Ecotoxicol, Beijing 100085, Peoples R China |
| 推荐引用方式 GB/T 7714 | Xue, Qiao,Liu, Xian,Russell, Paul,et al. Evaluation of the binding performance of flavonoids to estrogen receptor alpha by Autodock, Autodock Vina and Surflex-Dock[J]. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY,2022,233(0):113323. |
| APA | Xue, Qiao.,Liu, Xian.,Russell, Paul.,Li, Jin.,Pan, Wenxiao.,...&Zhang, Aiqian.(2022).Evaluation of the binding performance of flavonoids to estrogen receptor alpha by Autodock, Autodock Vina and Surflex-Dock.ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY,233(0),113323. |
| MLA | Xue, Qiao,et al."Evaluation of the binding performance of flavonoids to estrogen receptor alpha by Autodock, Autodock Vina and Surflex-Dock".ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 233.0(2022):113323. |
入库方式： OAI收割
来源：生态环境研究中心
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