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Molecular docking and 3D-QSAR studies on the binding mechanism of statine-based peptidomimetics with beta-secretase.
Bioorg Med Chem. 2005 Mar 15; 13(6):2121-31.BM

Abstract

beta-Secretase is an important protease in the pathogenesis of Alzheimer's disease. Some statine-based peptidomimetics show inhibitory activities to the beta-secretase. To explore the inhibitory mechanism, molecular docking and three-dimensional quantitative structure-activity relationship (3D-QSAR) studies on these analogues were performed. The Lamarckian Genetic Algorithm (LGA) was applied to locate the binding orientations and conformations of the peptidomimetics with the beta-secretase. A good correlation between the calculated binding free energies and the experimental inhibitory activities suggests that the identified binding conformations of these potential inhibitors are reliable. Based on the binding conformations, highly predictive 3D-QSAR models were developed with q(2) values of 0.582 and 0.622 for CoMFA and CoMSIA, respectively. The predictive abilities of these models were validated by some compounds that were not included in the training set. Furthermore, the 3D-QSAR models were mapped back to the binding site of the beta-secretase, to get a better understanding of vital interactions between the statine-based peptidomimetics and the protease. Both the CoMFA and the CoMSIA field distributions are in well agreement with the structural characteristics of the binding groove of the beta-secretase. Therefore, the final 3D-QSAR models and the information of the inhibitor-enzyme interaction would be useful in developing new drug leads against Alzheimer's disease.

Authors+Show Affiliations

Zuo Z
Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.
Luo X
No affiliation info available
Zhu W
No affiliation info available
Shen J
No affiliation info available
Shen X
No affiliation info available
Jiang H
No affiliation info available
Chen K
No affiliation info available

MeSH

AlgorithmsAmyloid Precursor Protein SecretasesBinding SitesBiomimetic MaterialsEndopeptidasesInhibitory Concentration 50Models, MolecularProtease InhibitorsProtein Structure, TertiaryQuantitative Structure-Activity RelationshipThermodynamics

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

15727865

Citation

Zuo, Zhili, et al. "Molecular Docking and 3D-QSAR Studies On the Binding Mechanism of Statine-based Peptidomimetics With Beta-secretase." Bioorganic & Medicinal Chemistry, vol. 13, no. 6, 2005, pp. 2121-31.
Zuo Z, Luo X, Zhu W, et al. Molecular docking and 3D-QSAR studies on the binding mechanism of statine-based peptidomimetics with beta-secretase. Bioorg Med Chem. 2005;13(6):2121-31.
Zuo, Z., Luo, X., Zhu, W., Shen, J., Shen, X., Jiang, H., & Chen, K. (2005). Molecular docking and 3D-QSAR studies on the binding mechanism of statine-based peptidomimetics with beta-secretase. Bioorganic & Medicinal Chemistry, 13(6), 2121-31.
Zuo Z, et al. Molecular Docking and 3D-QSAR Studies On the Binding Mechanism of Statine-based Peptidomimetics With Beta-secretase. Bioorg Med Chem. 2005 Mar 15;13(6):2121-31. PubMed PMID: 15727865.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Molecular docking and 3D-QSAR studies on the binding mechanism of statine-based peptidomimetics with beta-secretase. AU - Zuo,Zhili, AU - Luo,Xiaomin, AU - Zhu,Weiliang, AU - Shen,Jianhua, AU - Shen,Xu, AU - Jiang,Hualiang, AU - Chen,Kaixian, PY - 2004/11/23/received PY - 2005/01/04/revised PY - 2005/01/04/accepted PY - 2005/2/25/pubmed PY - 2005/8/3/medline PY - 2005/2/25/entrez SP - 2121 EP - 31 JF - Bioorganic & medicinal chemistry JO - Bioorg Med Chem VL - 13 IS - 6 N2 - beta-Secretase is an important protease in the pathogenesis of Alzheimer's disease. Some statine-based peptidomimetics show inhibitory activities to the beta-secretase. To explore the inhibitory mechanism, molecular docking and three-dimensional quantitative structure-activity relationship (3D-QSAR) studies on these analogues were performed. The Lamarckian Genetic Algorithm (LGA) was applied to locate the binding orientations and conformations of the peptidomimetics with the beta-secretase. A good correlation between the calculated binding free energies and the experimental inhibitory activities suggests that the identified binding conformations of these potential inhibitors are reliable. Based on the binding conformations, highly predictive 3D-QSAR models were developed with q(2) values of 0.582 and 0.622 for CoMFA and CoMSIA, respectively. The predictive abilities of these models were validated by some compounds that were not included in the training set. Furthermore, the 3D-QSAR models were mapped back to the binding site of the beta-secretase, to get a better understanding of vital interactions between the statine-based peptidomimetics and the protease. Both the CoMFA and the CoMSIA field distributions are in well agreement with the structural characteristics of the binding groove of the beta-secretase. Therefore, the final 3D-QSAR models and the information of the inhibitor-enzyme interaction would be useful in developing new drug leads against Alzheimer's disease. SN - 0968-0896 UR - https://www.unboundmedicine.com/medline/citation/15727865/Molecular_docking_and_3D_QSAR_studies_on_the_binding_mechanism_of_statine_based_peptidomimetics_with_beta_secretase_ DB - PRIME DP - Unbound Medicine ER -