alexa Riboswitches as Potential Targets for Aminoglycosides Compared with rRNA Molecules: In Silico Study
ISSN: 1948-5948

Journal of Microbial & Biochemical Technology
Open Access

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Research Article

Riboswitches as Potential Targets for Aminoglycosides Compared with rRNA Molecules: In Silico Study

Elnaz Mehdizadeh Aghdam1,2, Mohammad Esmaeil Hejazi3, Mohammad Saeid Hejazi1* and Abolfazl Barzegar4*

1Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran

2Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran

3Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.

4Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran

*Corresponding Author:
Mohammad Saeid Hejazi
Department of Pharmaceutical Biotechnology
Faculty of Pharmacy, Tabriz University of Medical
Sciences, Tabriz, Iran
Tel: +98 41 33372256
Fax: +98 41 33344798
E-mail: [email protected]; [email protected]

Abolfazl Barzegar
Research Institute for Fundamental Sciences (RIFS)
University of Tabriz, Tabriz, Iran
Tel: +98 4113294114
Fax: +98 411 294113
E-mail: [email protected]

Received Date: July 29, 2014; Accepted Date:November 21, 2014;s Published date: November 28, 2014

Citation: Mehdizadeh Aghdam E, Esmaeil Hejazi M, Hejazi MS, Barzegar A (2014) Riboswitches as Potential Targets for Aminoglycosides Compared with rRNA Molecules: In Silico Study. J Microb Biochem Technol S9:002. doi:10.4172/1948-5948.S9-002

Copyright: © 2014 Mehdizadeh Aghdam E, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Abstract

Riboswitches are cis acting riboregulaters in non-coding region of the mRNAs. Their possible contribution in antibiotic targeting especially for FMN, TPP and lysine riboswitches in bacteria has been revealed since a decade ago. Regarding some studies on the possibility of the interaction between aminoglycosides and the artificial riboswitches, in this study we attempted to evaluate the binding potential of different types of aminoglycosides including gentamicin, amikacin, kanamycin, neomycin, tobramaycin, sisomicin and paromomycin with various classes of riboswitches using computational methods. Applying Auto Dock vina, it was shown that the binding energy of each kind of riboswitches with different types of aminoglycosides (riboswitches/aminoglycosides) is almost similar or sometimes more than the binding energy of the aminoglycoside with the corresponding binding cage of “16S rRNA A site” (16S rRNA A site/aminoglycosides) as aminoglycosides’ target site. The affinity between riboswitches and aminoglycosides is almost the same or higher than the affinity of riboswitches/natural ligands. In this study ampicillin was used as the negative control antibiotic and 5S rRNA was employed as the negative control RNA. Results showed that the binding energies of riboswitches/ampicillin and 5S rRNA/aminoglycosides are usually lower than the energy of riboswitches/aminoglycosides. Accordingly, lysine, glycine and SAM-I riboswitches were recognized as the best RNA targets for all of the aminoglycosides because of their higher binding energy. In the next step, docking results were further validated by rDock program. Furthermore, it was shown that hydrogen binding makes a key role in the binding energy between aminoglycosides and riboswitches. Moreover, MD simulation studies on lysine riboswitch/paromomycin complex confirmed the stability of the docked structure in the solvent containing magnesium and chloride ions.

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