Indexing
All Issues
Submission
Author Guidelines
Reviewers
Editorial Members
Publication Fee
Vol.1 , No. 1, Publication Date: Jul. 7, 2014, Page: 11-14
 . Although, these tools have a wide scope in the process of searching for new drugs, we limit ourselves to the description of the methods used for this work, namely molecular docking, or " docking". The in silico molecular docking aims to predict the structure of a molecular complex from the isolated molecules, which is easier to implement, cheaper and faster than the use of experimental methods. Our goal is first to test the reliability of the docking software FlexX1.3.0 via RMSD (Root Mean Square Deviation), then to search for new inhibitors of neuraminidase (NA) which is one of the therapeutic targets of the influenza virus using zanamivir similars; one of the NA inhibitors, obtained from the PubChem.&picture=http://www.aascit.org/aascit/decorators/img/journal/903.jpg)
| [1] | Hioual K. S , Department of Biochemistry and Microbiology, Faculty of natural and life Sciences , Mentouri University, Constantine, Algeria. |
| [2] | Chikhi A , Department of Biochemistry and Microbiology, Faculty of natural and life Sciences , Mentouri University, Constantine, Algeria. |
| [3] | Bensegueni A , Department of Biochemistry and Microbiology, Faculty of natural and life Sciences , Mentouri University, Constantine, Algeria. |
| [4] | Merzoug A , Department of Biochemistry and Microbiology, Faculty of natural and life Sciences , Mentouri University, Constantine, Algeria. |
| [5] | Boucherit H , Department of Biochemistry and Microbiology, Faculty of natural and life Sciences , Mentouri University, Constantine, Algeria. |
| [6] | Mokrani El H , Department of Biochemistry and Microbiology, Faculty of natural and life Sciences , Mentouri University, Constantine, Algeria. |
| [7] | Teniou S , Department of Biochemistry and Microbiology, Faculty of natural and life Sciences , Mentouri University, Constantine, Algeria. |
| [8] | Merabti B , Department of Biochemistry and Microbiology, Faculty of natural and life Sciences , Mentouri University, Constantine, Algeria. |
The design molecules of therapeutic interest has benefited in recent decades developments from various scientific disciplines such as biology, medicinal chemistry and computer science and research, which once was to synthesize and test compounds selected on the basis of intuition and experience of the chemist medicinal, has radically changed. The development of computers has changed the particular given, leading to the emergence of a new discipline can participate in step initials of pharmaceutical research in addition to experimental methods already recognized. This is referred to in silico drug design - that is to say, assisted by computer - which corresponds to a specific set of information technology often designated by the acronym CADD (for "Computer Aided Drug Design" ) . Although, these tools have a wide scope in the process of searching for new drugs, we limit ourselves to the description of the methods used for this work, namely molecular docking, or " docking". The in silico molecular docking aims to predict the structure of a molecular complex from the isolated molecules, which is easier to implement, cheaper and faster than the use of experimental methods. Our goal is first to test the reliability of the docking software FlexX1.3.0 via RMSD (Root Mean Square Deviation), then to search for new inhibitors of neuraminidase (NA) which is one of the therapeutic targets of the influenza virus using zanamivir similars; one of the NA inhibitors, obtained from the PubChem.
Keywords
Molecular Docking, Flexx, Influenza Virus, Neuraminidase, Zanamivir
Reference
| [01] | Brooijmans N, Kuntz ID. 2003, Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct; 32:335–373. |
| [02] | Kramer B, Rarey M, Lengauer T. 1999, Evaluation of the FLEXX incremental construction algorithm for protein– ligand docking. Proteins; 37:228–241. |
| [03] | Venkatachalam C. M., Jiang X., Oldfield T., Waldman M., 2003, LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graph. Model, 21 (4), 289-307. |
| [04] | McGann M.R., Almond H.R, Nicholls A., Grant J.A., Brown F.K., 2003, Gaussian Docking Functions. Biopolymers, 68, 76-90. |
| [05] | Welch W., Ruppert J., Jain A.N., 1996, Hammerhead: Fast, Fully Automated Docking of Flexible Ligands to Protein Binding Sites, Chem Biol, 3, 449-462. |
| [06] | Jones G., Willett P., Glen R.C., Leach A.R., Taylor R., 1997, Development and validation of genetic algorithm for flexible docking. J. Mol. Biol, 267, 727-748. |
| [07] | Baxter C.A., Murray C.W., Clark D.E., Westhead D.R., Eldridge M.D., 1998. Flexible Docking Using Tabu Search and an Empirical Estimate of Binding Affinity. Proteins, 33, 367-382. |
| [08] | Gohlke.H., Hendlich. M., Klebe.G., 2000, Knowledge-based scoring function to predict protein-ligand interactions. J. Mol. Biol, 295 (2), 337-356. |
| [09] | Gohlke H.; Klebe G., 2002, Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. Angew. Chem., Int. Ed. Engl, 41 (15), 2644-2676. |
| [10] | Baxter C.A., Murray C.W., Clark D.E., Westhead D.R., Eldridge M.D., 1998. Flexible Docking Using Tabu Search and an Empirical Estimate of Binding Affinity. Proteins, 33, 367-382. |
| [11] | Bissantz C., Folkers G., Rognan D., 2000, Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J. Med. Chem, 43, 4759- 4767. |
| [12] | Clark R. D., Strizhev A., Leonard J. M., Blake J. F., Matthew J. B., 2002, Consensus scoring for ligand/protein interactions. J. Mol. Graph. Model, 20, 281-295. |
| [13] | Stahl M., Rarey M., 2001, Detailed analysis of scoring functions for virtual screening. J. Med. Chem, 44, 1035-1042. |
| [14] | Charifson P. S., Corkery J. J., Murcko M. A., Walters W. P., 1999, Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J. Med. Chem, 42 (25), 5100-5109. |
| [15] | Venkatachalam C. M., Jiang X., Oldfield T., Waldman M., 2003, LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graph. Model, 21 (4), 289-307. |
| [16] | Bissantz C., Folkers G., Rognan D., 2000, Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J. Med. Chem, 43, 4759- 4767. |
| [17] | Stahl M., Rarey M., 2001, Detailed analysis of scoring functions for virtual screening. J. Med. Chem, 44, 1035-1042. |
| [18] | Michael L., Christopher E., Stefan P, 2010, 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. |
| [19] | Zaheer U.H., Sobia A.H, Reaz U., Jeffry D., Madurab B., 2010, Benchmarking docking and scoring protocol for the identification of potential acetyl cholinesterase inhibitors, J. Mol. Graph. Model, 28, 870–882. |
| [20] | Figeys D., 2003, Novel approaches to map protein interactions. Curr. Opin. Biotechol, 14, 119- 125. |
| [21] | Oakley A. J, Barrett S, Peat T. S, Newman J, Streltsov V. A, Waddington L, Saito T, Tashiro M, McKimm-Breschkin J. L. Structural and functional basis of resistance to neuraminidase inhibitors of influenza B viruses. J Med Chem, 2010, 53(17): 6421-31. |
| [22] | Bernstein F, Koetzle T, Williams G, Meyer J.r E, Brice M, Rodgers J, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. FEBS J, 2008; 10: 1432-1033. |
| [23] | An J, Lee DC, Law AH, Yang CL, Poon L.L, Lau A.S, Jones S.J.A novel small molecule inhibitor of the avian influenza H5N1 virus determined through computational screening against the neuraminidase. J. Med. Chem. 2009; 52: 2667–2672. |
| [24] | Moscona A. Neuraminidase inhibitors for influenza. N Engl J Med, 2005; 73: 353-1363. |
