Theoretical Study of the Interactions Involved in the Inhibition of Mycobacterium Tuberculosis Methionine Aminopeptidase by Several Molecules

Boucherit Hanane; Chikhi Abdelouahab; Bensegueni Abderrahmane; Merzoug Amina; Hioual khadidja Soulef; Mokrani El Hassen

doi:doi:10.11648/j.cbb.20140205.11

| Peer-Reviewed

Theoretical Study of the Interactions Involved in the Inhibition of Mycobacterium Tuberculosis Methionine Aminopeptidase by Several Molecules

Boucherit Hanane, Chikhi Abdelouahab, Bensegueni Abderrahmane, Merzoug Amina, Hioual khadidja Soulef, Mokrani El Hassen

Published in Computational Biology and Bioinformatics (Volume 2, Issue 5)

Received: 23 October 2014 Accepted: 7 November 2014 Published: 20 November 2014

Views: Downloads:

Download PDF

Share This Article

Twitter
Linked In
Facebook

Abstract

With the development of computer tools in the past 20 years, molecular modeling and more precisely molecular docking has quickly entered the area of biological research. Two programs of molecular docking, Surflex and GOLD (Genetic Optimization for Ligand Docking), have been developed to assist in the development of molecules with therapeutic activity. With the RMSD (Root Mean Square Deviation) values lower than 2 Å and the coefficient of correlation close to 1, the performances of Surflex and GOLD software’s are clearly proven and perfectly adapted to the different molecular structures used in this study. They have been used to study the inhibition of 3IU7, a methionine aminopeptidase belonging to Mycobacterium tuberculosis, by various molecules of ligands from the literature aimed to find new anti-tuberculosis drugs. The evaluation of the affinity and the energy of interaction of these molecules made it possible to release those presenting the best inhibiting effect, in accordance with IC50 values obtained from the literature. It is the compound TO7, which the values of Fitness and Affinity are respectively 57.35 and 3.10 M-1. The interactions types responsible for the stability of the various complexes are Van der Waals and hydrogen bonds.

Published in	Computational Biology and Bioinformatics (Volume 2, Issue 5)
DOI	10.11648/j.cbb.20140205.11
Page(s)	63-73
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

Protein-Ligand Interactions, Molecular Docking, Surflex, GOLD, RMSD, the Coefficient of Correlation, Methionine Aminopeptidase

References

[1]	Chikhi A and Bensegueni A. Comparative Study of the Efficiency of Three Protein-Ligand Docking Programs. Journal of Proteomics & Bioinformatics, 1, 161-165. 2008
[2]	Olaleye A. O., Bishaie W. R., Liua J. O. Targeting the role of N-terminal methionine processing enzymes in Mycobacterium Tuberculosis. Tuberculosis89, S1, S55- S59. 2009
[3]	Olaleye O., Raghunand T. R., Bhat S., He J., Tyagi S., Lamichhane G., Gu P., Zhou J., Zhang Y., Grosset J., Bishai W. R., Liu J. O.Methionine Aminopeptidases from Mycobacterium tuberculosis as Novel Antimycobacterial Targets. Chemistry & Biology, 17, 86-97. 2010
[4]	Kramer B., Rarey M., Lengauer T. Evaluation of the FLEXX Incremental Construction Algorithm for Protein–Ligand Docking. Proteins: Structure, Function, and Genetics, 37, 228-241.1999
[5]	Kellenberger E., Rodrigo J., Muller P., Rognan D. Comparative Evaluation of Eight Docking Tools for Docking and Virtual Screening Accuracy. Proteins: Structure, Function, and Bioinformatics, 57, 225-242. 2004
[6]	Fox W. Statistiques Sociales. 3éme édition. France: De Boeck. 1999. 374 p.
[7]	Evdokimov A. G., Pokross M., Walter R. L., Mekel M., Barnett B. L., Amburgey J., Seibel W. L., Soper S. J., Djung J. F., Fairweather N., Diven C., Rastogi V., Grinius L., Klanke C., Siehnel R., Twinem T., Andrews R., Curnow A. Serendipitous Discovery of Novel Bacterial Methionine Aminopeptidase Inhibitors. Proteins: Structure, Function, and Bioinformatics, 66, 538-546. 2007
[8]	Altmeyer M. A., Marschner A., Schiffmann R., Klein C. D. 2010. Subtype-selectivity of metal-dependent methionine aminopeptidase inhibitors. Bioorganic & Medicinal Chemistry Letters, 20, 4038-4044. 2010
[9]	Huang Q. Q., Huang M., Nana F. J., Ye Q. Z. Metalloform-selective inhibition: Synthesis and structure–activity analysis of Mn(II)-form-selective inhibitors of Escherichia coli methionine aminopeptidase. Bioorganic & Medicinal Chemistry Letters, 15, 5386-5391. 2005
[10]	Berman H. M. The Protein Data Bank: a historical perspective. ActaCryst, A64, 88-95. 2008
[11]	Protein Data Bank (PDB). Biological Macromolecular Resource. [En ligne]. http://www.pdb.org/pdb/home.
[12]	Mark A. ArgusLab (version 4.0.1). Thompson. Planaria software LLC. Seattle. http://www.ArgusLab.com.
[13]	BioPharmics LLC. 2005.Surflex Manual: Docking and Similarity (version 1.3).
[14]	Lipinski C. A., Lombardo F., Dominy B. W., Feeney P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings.Advanced Drug Delivery Reviews, 46, 3-26. 2001
[15]	Gabb H. A, Jackson R. M, Sternberg M. J. Modelling protein docking using shape complementarity,electrostatics and biochemical information. J Mol Biol, 272, 106-120.1997
[16]	Zaheer-ul-Haq, Halim S. A, Uddin R, Madura J. D. Benchmarking docking and scoring protocol for the identification of potential acetyl cholinesterase inhibitors. J Mol Graph Model, 28, 870-882.2010
[17]	Lape M, Elam C, Paula S. Comparison of current docking tools for the simulation of inhibitor binding by the transmembrane domain of the sarco/ endoplasmic reticulum calcium ATPase. Biophys Chem, 150, 88-97.2010
[18]	Bensegueni A. Etude théorique des métabolites secondaires des végétaux et des composés de synthèse sur le plan de l’activité biologique : simulation par docking (arrimage) moléculaire sur la lipoxygénase et la cyclooxygénase. Thèse de doctorat en Biochimie Appliquée. Constantine : Université Mentouri Constantine. Algérie. 2007. 76p.
[19]	Chikhi A., Bensegueni A. In Silico Study of the Selective Inhibition of Bacterial Peptide Deformylases by Several Drugs. Journal of Proteomics and Bioinformatics, 3, 061-065. 2010
[20]	Kamel M. M., Ali H. I., Anwar M. M., Mohameda N. A., Soliman A. M. Synthesis, antitumor activity and molecular docking study of novel Sulfonamide-Schiff’s bases, thiazolidinones, benzothiazinones and their C-nucleoside derivatives. European Journal of Medicinal Chemistry, 45, 572-580. 2010
[21]	Maouche A. T., Maouche B., Kellou S. T., El-Aoufi S., Martínez M. M., Muñiz R. G., Fourmy D., Maigret G. Exploring the binding pocket for pyridopyrimidine ligands at the CCK1 receptor by molecular docking. Journal of MolecularModeling, 14, 303-314. 2008
[22]	Molinspiration. [En ligne]. http://www.molinspiration.com/.

Cite This Article

Plain Text BibTeX RIS

APA Style

Boucherit Hanane, Chikhi Abdelouahab, Bensegueni Abderrahmane, Merzoug Amina, Hioual khadidja Soulef, et al. (2014). Theoretical Study of the Interactions Involved in the Inhibition of Mycobacterium Tuberculosis Methionine Aminopeptidase by Several Molecules. Computational Biology and Bioinformatics, 2(5), 63-73. https://doi.org/10.11648/j.cbb.20140205.11

Copy | Download

ACS Style

Boucherit Hanane; Chikhi Abdelouahab; Bensegueni Abderrahmane; Merzoug Amina; Hioual khadidja Soulef, et al. Theoretical Study of the Interactions Involved in the Inhibition of Mycobacterium Tuberculosis Methionine Aminopeptidase by Several Molecules. Comput. Biol. Bioinform. 2014, 2(5), 63-73. doi: 10.11648/j.cbb.20140205.11

Copy | Download

AMA Style

Boucherit Hanane, Chikhi Abdelouahab, Bensegueni Abderrahmane, Merzoug Amina, Hioual khadidja Soulef, et al. Theoretical Study of the Interactions Involved in the Inhibition of Mycobacterium Tuberculosis Methionine Aminopeptidase by Several Molecules. Comput Biol Bioinform. 2014;2(5):63-73. doi: 10.11648/j.cbb.20140205.11

Copy | Download

@article{10.11648/j.cbb.20140205.11,
  author = {Boucherit Hanane and Chikhi Abdelouahab and Bensegueni Abderrahmane and Merzoug Amina and Hioual khadidja Soulef and Mokrani El Hassen},
  title = {Theoretical Study of the Interactions Involved in the Inhibition of Mycobacterium Tuberculosis Methionine Aminopeptidase by Several Molecules},
  journal = {Computational Biology and Bioinformatics},
  volume = {2},
  number = {5},
  pages = {63-73},
  doi = {10.11648/j.cbb.20140205.11},
  url = {https://doi.org/10.11648/j.cbb.20140205.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20140205.11},
  abstract = {With the development of computer tools in the past 20 years, molecular modeling and more precisely molecular docking has quickly entered the area of biological research. Two programs of molecular docking, Surflex and GOLD (Genetic Optimization for Ligand Docking), have been developed to assist in the development of molecules with therapeutic activity. With the RMSD (Root Mean Square Deviation) values lower than 2 Å and the coefficient of correlation close to 1, the performances of Surflex and GOLD software’s are clearly proven and perfectly adapted to the different molecular structures used in this study. They have been used to study the inhibition of 3IU7, a methionine aminopeptidase belonging to Mycobacterium tuberculosis, by various molecules of ligands from the literature aimed to find new anti-tuberculosis drugs. The evaluation of the affinity and the energy of interaction of these molecules made it possible to release those presenting the best inhibiting effect, in accordance with IC50 values obtained from the literature. It is the compound TO7, which the values of Fitness and Affinity are respectively 57.35 and 3.10 M-1. The interactions types responsible for the stability of the various complexes are Van der Waals and hydrogen bonds.},
 year = {2014}
}

Copy | Download

TY  - JOUR
T1  - Theoretical Study of the Interactions Involved in the Inhibition of Mycobacterium Tuberculosis Methionine Aminopeptidase by Several Molecules
AU  - Boucherit Hanane
AU  - Chikhi Abdelouahab
AU  - Bensegueni Abderrahmane
AU  - Merzoug Amina
AU  - Hioual khadidja Soulef
AU  - Mokrani El Hassen
Y1  - 2014/11/20
PY  - 2014
N1  - https://doi.org/10.11648/j.cbb.20140205.11
DO  - 10.11648/j.cbb.20140205.11
T2  - Computational Biology and Bioinformatics
JF  - Computational Biology and Bioinformatics
JO  - Computational Biology and Bioinformatics
SP  - 63
EP  - 73
PB  - Science Publishing Group
SN  - 2330-8281
UR  - https://doi.org/10.11648/j.cbb.20140205.11
AB  - With the development of computer tools in the past 20 years, molecular modeling and more precisely molecular docking has quickly entered the area of biological research. Two programs of molecular docking, Surflex and GOLD (Genetic Optimization for Ligand Docking), have been developed to assist in the development of molecules with therapeutic activity. With the RMSD (Root Mean Square Deviation) values lower than 2 Å and the coefficient of correlation close to 1, the performances of Surflex and GOLD software’s are clearly proven and perfectly adapted to the different molecular structures used in this study. They have been used to study the inhibition of 3IU7, a methionine aminopeptidase belonging to Mycobacterium tuberculosis, by various molecules of ligands from the literature aimed to find new anti-tuberculosis drugs. The evaluation of the affinity and the energy of interaction of these molecules made it possible to release those presenting the best inhibiting effect, in accordance with IC50 values obtained from the literature. It is the compound TO7, which the values of Fitness and Affinity are respectively 57.35 and 3.10 M-1. The interactions types responsible for the stability of the various complexes are Van der Waals and hydrogen bonds.
VL  - 2
IS  - 5
ER  -

Copy | Download

Author Information

Boucherit Hanane

Laboratory of Applied Biology and Health, Department of Biochemistry-Microbiology, Faculty of Natural And Life Sciences, University of Constantine 1, Constantine, Algeria
Chikhi Abdelouahab

Laboratory of Applied Biology and Health, Department of Biochemistry-Microbiology, Faculty of Natural And Life Sciences, University of Constantine 1, Constantine, Algeria
Bensegueni Abderrahmane

Laboratory of Applied Biology and Health, Department of Biochemistry-Microbiology, Faculty of Natural And Life Sciences, University of Constantine 1, Constantine, Algeria
Merzoug Amina

Laboratory of Applied Biology and Health, Department of Biochemistry-Microbiology, Faculty of Natural And Life Sciences, University of Constantine 1, Constantine, Algeria
Hioual khadidja Soulef

Laboratory of Applied Biology and Health, Department of Biochemistry-Microbiology, Faculty of Natural And Life Sciences, University of Constantine 1, Constantine, Algeria
Mokrani El Hassen

Laboratory of Applied Biology and Health, Department of Biochemistry-Microbiology, Faculty of Natural And Life Sciences, University of Constantine 1, Constantine, Algeria

Download PDF

Sections

Plain Text BibTeX RIS

APA Style

Boucherit Hanane, Chikhi Abdelouahab, Bensegueni Abderrahmane, Merzoug Amina, Hioual khadidja Soulef, et al. (2014). Theoretical Study of the Interactions Involved in the Inhibition of Mycobacterium Tuberculosis Methionine Aminopeptidase by Several Molecules. Computational Biology and Bioinformatics, 2(5), 63-73. https://doi.org/10.11648/j.cbb.20140205.11

Copy | Download

ACS Style

Boucherit Hanane; Chikhi Abdelouahab; Bensegueni Abderrahmane; Merzoug Amina; Hioual khadidja Soulef, et al. Theoretical Study of the Interactions Involved in the Inhibition of Mycobacterium Tuberculosis Methionine Aminopeptidase by Several Molecules. Comput. Biol. Bioinform. 2014, 2(5), 63-73. doi: 10.11648/j.cbb.20140205.11

Copy | Download

AMA Style

Boucherit Hanane, Chikhi Abdelouahab, Bensegueni Abderrahmane, Merzoug Amina, Hioual khadidja Soulef, et al. Theoretical Study of the Interactions Involved in the Inhibition of Mycobacterium Tuberculosis Methionine Aminopeptidase by Several Molecules. Comput Biol Bioinform. 2014;2(5):63-73. doi: 10.11648/j.cbb.20140205.11

Copy | Download

@article{10.11648/j.cbb.20140205.11,
  author = {Boucherit Hanane and Chikhi Abdelouahab and Bensegueni Abderrahmane and Merzoug Amina and Hioual khadidja Soulef and Mokrani El Hassen},
  title = {Theoretical Study of the Interactions Involved in the Inhibition of Mycobacterium Tuberculosis Methionine Aminopeptidase by Several Molecules},
  journal = {Computational Biology and Bioinformatics},
  volume = {2},
  number = {5},
  pages = {63-73},
  doi = {10.11648/j.cbb.20140205.11},
  url = {https://doi.org/10.11648/j.cbb.20140205.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20140205.11},
  abstract = {With the development of computer tools in the past 20 years, molecular modeling and more precisely molecular docking has quickly entered the area of biological research. Two programs of molecular docking, Surflex and GOLD (Genetic Optimization for Ligand Docking), have been developed to assist in the development of molecules with therapeutic activity. With the RMSD (Root Mean Square Deviation) values lower than 2 Å and the coefficient of correlation close to 1, the performances of Surflex and GOLD software’s are clearly proven and perfectly adapted to the different molecular structures used in this study. They have been used to study the inhibition of 3IU7, a methionine aminopeptidase belonging to Mycobacterium tuberculosis, by various molecules of ligands from the literature aimed to find new anti-tuberculosis drugs. The evaluation of the affinity and the energy of interaction of these molecules made it possible to release those presenting the best inhibiting effect, in accordance with IC50 values obtained from the literature. It is the compound TO7, which the values of Fitness and Affinity are respectively 57.35 and 3.10 M-1. The interactions types responsible for the stability of the various complexes are Van der Waals and hydrogen bonds.},
 year = {2014}
}

Copy | Download

TY  - JOUR
T1  - Theoretical Study of the Interactions Involved in the Inhibition of Mycobacterium Tuberculosis Methionine Aminopeptidase by Several Molecules
AU  - Boucherit Hanane
AU  - Chikhi Abdelouahab
AU  - Bensegueni Abderrahmane
AU  - Merzoug Amina
AU  - Hioual khadidja Soulef
AU  - Mokrani El Hassen
Y1  - 2014/11/20
PY  - 2014
N1  - https://doi.org/10.11648/j.cbb.20140205.11
DO  - 10.11648/j.cbb.20140205.11
T2  - Computational Biology and Bioinformatics
JF  - Computational Biology and Bioinformatics
JO  - Computational Biology and Bioinformatics
SP  - 63
EP  - 73
PB  - Science Publishing Group
SN  - 2330-8281
UR  - https://doi.org/10.11648/j.cbb.20140205.11
AB  - With the development of computer tools in the past 20 years, molecular modeling and more precisely molecular docking has quickly entered the area of biological research. Two programs of molecular docking, Surflex and GOLD (Genetic Optimization for Ligand Docking), have been developed to assist in the development of molecules with therapeutic activity. With the RMSD (Root Mean Square Deviation) values lower than 2 Å and the coefficient of correlation close to 1, the performances of Surflex and GOLD software’s are clearly proven and perfectly adapted to the different molecular structures used in this study. They have been used to study the inhibition of 3IU7, a methionine aminopeptidase belonging to Mycobacterium tuberculosis, by various molecules of ligands from the literature aimed to find new anti-tuberculosis drugs. The evaluation of the affinity and the energy of interaction of these molecules made it possible to release those presenting the best inhibiting effect, in accordance with IC50 values obtained from the literature. It is the compound TO7, which the values of Fitness and Affinity are respectively 57.35 and 3.10 M-1. The interactions types responsible for the stability of the various complexes are Van der Waals and hydrogen bonds.
VL  - 2
IS  - 5
ER  -

Copy | Download