Structure of the virus capsid protein VP1 of enterovirus 71 predicted by some homology modeling and molecular docking studies
Identifieur interne : 004167 ( Main/Exploration ); précédent : 004166; suivant : 004168Structure of the virus capsid protein VP1 of enterovirus 71 predicted by some homology modeling and molecular docking studies
Auteurs : Yi-Yu Ke [Taïwan] ; Yun-Chu Chen [Taïwan] ; Thy-Hou Lin [Taïwan]Source :
- Journal of Computational Chemistry [ 0192-8651 ] ; 2006-10.
English descriptors
- Teeft :
- 1eah, 1piv, Active site, Activity data, Amber force, Amino, Amino acid residues, Antimicrob agents chemother, Best energy score, Binding pocket, Capsid, Capsid protein, Chem, Chemical scores, Computational, Computational chemistry, Computational chemistry figure, Corresponding prosa energy, Dock program, Docking, Docking parameters, Docking scores, Docking study, Energy minimization, Enterovirus, Errat, Errat server, Homology, Homology model, Homology modeling, Hydrophobic, Hydrophobic nature, Inhibitor, Ligand, Minimization, Mod1, Mod2, Model system, Modeling, Overall quality factor, Pleconaril, Protein, Protein model, Protein model mod1, Protein model mod2, Protein models, Protein structures, Ramachandran plot, Secondary structures, Server, Shia, Simulation, Simulation steps, Standard values, Structure mod1, Target sequence, Template, Template 1piv, Template structure, Template structures, Virus capsid protein.
Abstract
The homology modeling technique has been used to construct the structure of enterovirus 71 (EV 71) capsid protein VP1. The protein is consisted of 297 amino acid residues and treated as the target. The amino acid sequence identity between the target protein and sequences of template proteins 1EAH, 1PIV, and 1D4M searched from NCBI protein BLAST and WorkBench protein tools were 38, 37, and 36%, respectively. Based on these template structures, the protein model was constructed by using the InsightII/Homology program. The protein model was briefly refined by energy minimization and molecular dynamics (MD) simulation steps. The protein model was validated using some web available servers such as ERRAT, PROCHECK, PROVE, and PROSA2003. However, an inconsistency between the docking scores and the measured activity was observed for a series of EV 71 VP1 inhibitors synthesized by Shia et al. (J Med Chem 2002, 45, 1644) and docked into the binding pocket of the protein model using the DOCK 4.0.2 program. The protein model with an EV 71 VP1 inhibitor docked and engulfed was then refined further by some MD simulation steps in the presence of water molecules. The docking scores obtained for these inhibitors after such a MD refinement were well correlated with the activities. The structure–activity relationships for the ligand–protein model system was also analyzed using the GRID‐VOLSURF programs and the corresponding noncrossvalidated and crossvalidated (by leave‐one‐out) r2 and q2 were 0.99 and 0.61, respectively. The hydrophobic nature of the binding pocket of the protein model was also examined using the GRID21 program. The possibility of improving the potency of the current series of EV 71 VP1 inhibitors was discussed based on all the studies presented. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1556–1570, 2006
Url:
DOI: 10.1002/jcc.20460
Affiliations:
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<term>Best energy score</term>
<term>Binding pocket</term>
<term>Capsid</term>
<term>Capsid protein</term>
<term>Chem</term>
<term>Chemical scores</term>
<term>Computational</term>
<term>Computational chemistry</term>
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<term>Docking</term>
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<term>Errat</term>
<term>Errat server</term>
<term>Homology</term>
<term>Homology model</term>
<term>Homology modeling</term>
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<term>Minimization</term>
<term>Mod1</term>
<term>Mod2</term>
<term>Model system</term>
<term>Modeling</term>
<term>Overall quality factor</term>
<term>Pleconaril</term>
<term>Protein</term>
<term>Protein model</term>
<term>Protein model mod1</term>
<term>Protein model mod2</term>
<term>Protein models</term>
<term>Protein structures</term>
<term>Ramachandran plot</term>
<term>Secondary structures</term>
<term>Server</term>
<term>Shia</term>
<term>Simulation</term>
<term>Simulation steps</term>
<term>Standard values</term>
<term>Structure mod1</term>
<term>Target sequence</term>
<term>Template</term>
<term>Template 1piv</term>
<term>Template structure</term>
<term>Template structures</term>
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<front><div type="abstract" xml:lang="fr">The homology modeling technique has been used to construct the structure of enterovirus 71 (EV 71) capsid protein VP1. The protein is consisted of 297 amino acid residues and treated as the target. The amino acid sequence identity between the target protein and sequences of template proteins 1EAH, 1PIV, and 1D4M searched from NCBI protein BLAST and WorkBench protein tools were 38, 37, and 36%, respectively. Based on these template structures, the protein model was constructed by using the InsightII/Homology program. The protein model was briefly refined by energy minimization and molecular dynamics (MD) simulation steps. The protein model was validated using some web available servers such as ERRAT, PROCHECK, PROVE, and PROSA2003. However, an inconsistency between the docking scores and the measured activity was observed for a series of EV 71 VP1 inhibitors synthesized by Shia et al. (J Med Chem 2002, 45, 1644) and docked into the binding pocket of the protein model using the DOCK 4.0.2 program. The protein model with an EV 71 VP1 inhibitor docked and engulfed was then refined further by some MD simulation steps in the presence of water molecules. The docking scores obtained for these inhibitors after such a MD refinement were well correlated with the activities. The structure–activity relationships for the ligand–protein model system was also analyzed using the GRID‐VOLSURF programs and the corresponding noncrossvalidated and crossvalidated (by leave‐one‐out) r2 and q2 were 0.99 and 0.61, respectively. The hydrophobic nature of the binding pocket of the protein model was also examined using the GRID21 program. The possibility of improving the potency of the current series of EV 71 VP1 inhibitors was discussed based on all the studies presented. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1556–1570, 2006</div>
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