Identification of potential AMPK activator by pharmacophore modeling, molecular docking and QSAR study
Li, Yingying1,2; Peng, Jiale1; Li, Penghua1; Du, Haibo1; Li, Yaping1; Liu, Xingyong1; Zhang, Li1; Wang, Liang-Liang2; Zuo, Zhili1,2
Corresponding AuthorZhang, Li(zhangli19700554@163.com) ; Wang, Liang-Liang(wangliangliang@mail.kib.ac.cn)
2019-04-01
Source PublicationCOMPUTATIONAL BIOLOGY AND CHEMISTRY
ISSN1476-9271
Volume79Pages:165-176
AbstractAMP-activated protein kinase (AMPK) plays a major role in maintaining cellular energy homeostasis by sensing and responding to AMP/ADP concentrations relative to ATP. AMPK has attracted widespread attention as a potential therapeutic target for metabolic diseases such as cancer and cardiovascular diseases. The structure-based 3D pharmacophore model was developed based on the training set. The best pharmacophore model Hypo5 was proposed and validated using a decoy set, an external test set. Hypo5, with the correlation coefficient value of 0.936, cost difference value of 112.08 and low RMS value of 1.63, includes a ionizable positive, a hydrogen bond donor, a hydrogen bond acceptor and two hydrophobic features, which showed a high goodness of fit and enrichment factor. Thus it was used as a 3D query to find potential activator from the SPECS Database. Then the ADMET descriptors were used to filter all of 158 screening molecules. The 41 filtering compounds were subsequently subjected to molecular docking and Quantitative structure activity relationship (QSAR) analysis. Finally, the compound H2 was picked out from those filtering compounds based on the receptor-ligand interaction analysis and the prediction of the QSAR models. And then it was submitted for molecular dynamics (MD) simulations to explore the stability of complex. The result indicates that the candidate could be considered a potential AMPK activator.
KeywordPharmacophore modeling Molecular docking Quantitative structure activity relationship (QSAR) Molecular dynamics AMPK Activator
DOI10.1016/j.compbiolchem.2019.02.007
Indexed BySCI
Language英语
WOS Research AreaLife Sciences & Biomedicine - Other Topics ; Computer Science
WOS SubjectBiology ; Computer Science, Interdisciplinary Applications
WOS IDWOS:000463124100019
Citation statistics
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/67653
Collection植物化学与西部植物资源持续利用国家重点实验室
Corresponding AuthorZhang, Li; Wang, Liang-Liang
Affiliation1.Sichuan Univ Sci & Engn, Sch Chem Engn, Zigong 643000, Peoples R China
2.Chinese Acad Sci, Kunming Inst Bot, State Key Lab Phytochem & Plant Resources West Ch, Kunming 650201, Yunnan, Peoples R China
Recommended Citation
GB/T 7714
Li, Yingying,Peng, Jiale,Li, Penghua,et al. Identification of potential AMPK activator by pharmacophore modeling, molecular docking and QSAR study[J]. COMPUTATIONAL BIOLOGY AND CHEMISTRY,2019,79:165-176.
APA Li, Yingying.,Peng, Jiale.,Li, Penghua.,Du, Haibo.,Li, Yaping.,...&Zuo, Zhili.(2019).Identification of potential AMPK activator by pharmacophore modeling, molecular docking and QSAR study.COMPUTATIONAL BIOLOGY AND CHEMISTRY,79,165-176.
MLA Li, Yingying,et al."Identification of potential AMPK activator by pharmacophore modeling, molecular docking and QSAR study".COMPUTATIONAL BIOLOGY AND CHEMISTRY 79(2019):165-176.
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