Document Detail


Homology modeling and docking mechanism of the mercaptosuccinate and methotrexate to P. falciparum 1-Cys peroxiredoxin: a preliminary molecular study.
MedLine Citation:
PMID:  12144348     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
A three-dimensional (3-D) model of 1-Cys peroxiredoxin from P. falciparum (Pf-Prx) has been constructed by homology modeling. The model building was based on a structural alignment with the human 1-Cys peroxiredoxin ray structure. First, mercaptosuccinate was docked by Molecular and Quantum Mechanics at the active site in both isozymes, evidencing the role of different residues in the ligand-protein interaction. Stable conformation of the inhibitor in the active site was obtained from the conformational analysis by molecular dynamics. Next, The complex was reoptimized by semiempirical molecular orbital AM1 method. Conformational and frontier orbitals analyses of the ligand-protein complex were carried out in an attempt to obtain structural insight into the inhibition mechanism. Finally, the docking study of the methotrexate (MTX), an anticancer drug also used as an antimalarial inhibitor, into the modes binding site was performed. From the resulting stable complex structure, it was found that the glutamate ring of MTX fits the active site with high complementarity. The glutamate ring formed two hydrogen bonds to the imidazol group of His41 and the amino groups of Arg129. The side-chain of glutamate was in close proximity to the sulfur atom of the catalytic residue, Cys47. This binding mode suggests a possible inhibition mechanism, whereby the cysteine residue is covered with the glutamate ring of the MTX inhibitor, forming an enzyme-ligand adduct. In addition, the higher interaction energies and the molecular orbitals localization between the Pf-Prx active site and the inhibitors alluded to the probable binding sites of the ligand nucleophilic ring.
Authors:
A Hamza
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Journal of biomolecular structure & dynamics     Volume:  20     ISSN:  0739-1102     ISO Abbreviation:  J. Biomol. Struct. Dyn.     Publication Date:  2002 Aug 
Date Detail:
Created Date:  2002-07-29     Completed Date:  2003-02-26     Revised Date:  2007-11-15    
Medline Journal Info:
Nlm Unique ID:  8404176     Medline TA:  J Biomol Struct Dyn     Country:  United States    
Other Details:
Languages:  eng     Pagination:  7-20     Citation Subset:  IM    
Affiliation:
Unité Modélisation Moculaire, Institut Pasteur de Tunis 13, Place Pasteur 1002 Tunis-Belvédère, Tunisia. adel.hamza@pasteur.rns.tn
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MeSH Terms
Descriptor/Qualifier:
Amino Acid Sequence
Animals
Methotrexate / chemistry*
Models, Molecular
Molecular Sequence Data
Peroxidases / chemistry*
Peroxiredoxins
Plasmodium falciparum / metabolism*
Protein Binding
Protein Structure, Tertiary
Sequence Homology, Amino Acid
Software
Thermodynamics
Thiomalates / chemistry*
Time Factors
Chemical
Reg. No./Substance:
0/Thiomalates; 59-05-2/Methotrexate; 70-49-5/2-thiomalic acid; EC 1.11.1.-/Peroxidases; EC 1.11.1.15/Peroxiredoxins

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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