Cited Article: Hummer, G. Water conduction through the hydrophobic channel of a carbon nanotube
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Title:
Combined 3D-QSAR, Molecular Docking and Molecular Dynamics Study on Derivatives of Peptide Epoxyketone and Tyropeptin-Boronic Acid as Inhibitors Against the beta 5 Subunit of Human 20S Proteasome
Authors:
Liu, JL; Zhang, H; Xiao, ZT; Wang, FF; Wang, X; Wang, YH
Author Full Names:
Liu, Jianling; Zhang, Hong; Xiao, Zhengtao; Wang, Fangfang; Wang, Xia; Wang, Yonghua
Source:
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 12 (3): 1807-1835 MAR 2011
Language:
English
Document Type:
Article
Author Keywords:
ubiquitin-proteasome; 3D-QSAR; CoMFA; CoMSIA; homology modeling; molecular docking; molecular dynamics
KeyWords Plus:
CRYSTAL-STRUCTURE; SWISS-MODEL; ANGSTROM RESOLUTION; MULTIPLE-MYELOMA; COMSIA METHODS; CORE PARTICLE; SYSTEM; BORTEZOMIB; BINDING; DESIGN
Abstract:
An abnormal ubiquitin-proteasome is found in many human diseases, especially in cancer, and has received extensive attention as a promising therapeutic target in recent years. In this work, several in silico models have been built with two classes of proteasome inhibitors (PIs) by using 3D-QSAR, homology modeling, molecular docking and molecular dynamics (MD) simulations. The study resulted in two types of satisfactory 3D-QSAR models, i.e., the CoMFA model (Q(2) = 0.462, R-pred(2) = 0.820) for epoxyketone inhibitors (EPK) and the CoMSIA model (Q(2) = 0.622, R-pred(2) = 0.821) for tyropeptin-boronic acid derivatives (TBA). From the contour maps, some key structural factors responsible for the activity of these two series of PIs are revealed. For EPK inhibitors, the N-cap part should have higher electropositivity; a large substituent such as a benzene ring is favored at the C6-position. In terms of TBA inhibitors, hydrophobic substituents with a larger size anisole group are pr
eferential at the C8-position; higher electropositive substituents like a naphthalene group at the C3-position can enhance the activity of the drug by providing hydrogen bond interaction with the protein target. Molecular docking disclosed that residues Thr60, Thr80, Gly106 and Ser189 play a pivotal role in maintaining the drug-target interactions, which are consistent with the contour maps. MD simulations further indicated that the binding modes of each conformation derived from docking is stable and in accord with the corresponding structure extracted from MD simulation overall. These results can offer useful theoretical references for designing more potent PIs.
Reprint Address:
Wang, YH, NW A&F Univ, Ctr Bioinformat, Yangling 712100, Shaanxi, Peoples R China.
Research Institution addresses:
[Xiao, Zhengtao; Wang, Yonghua] NW A&F Univ, Ctr Bioinformat, Yangling 712100, Shaanxi, Peoples R China; [Liu, Jianling; Zhang, Hong; Wang, Fangfang] NW Univ Xian, Coll Life Sci, Xian 710069, Shaanxi, Peoples R China; [Wang, Xia] Dalian Univ Technol, Sch Chem Engn, Dalian 116012, Peoples R China
E-mail Address:
yh_wang@nwsuaf.edu.cn
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Cited Reference Count:
66
Times Cited:
0
Publisher:
MDPI AG; KANDERERSTRASSE 25, CH-4057 BASEL, SWITZERLAND
Subject Category:
Chemistry, Multidisciplinary
ISSN:
1422-0067
DOI:
10.3390/ijms12031807
IDS Number:
740HZ
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