Clinical Pharmacology & Biopharmaceutics
Open Access

Abstract

Riboswitches are cis acting riboregulaters usually located at 5â�?�? untranslated region of mRNAs. Discovery of the contribution of FMN, TPP and lysine riboswitches in antibiotic targeting was a milestone in the history of riboswitches. Some studies revealed the interaction between aminoglycosides and artificial riboswitches. In this study, the binding potential of different types of aminglycosides with various classes of riboswitches using molecular docking methods was elucidated. To achieve this goal, the affinity between each aminoglycoside and its target â�?�?16S rRNA A siteâ�? was studied. The affinity of riboswitches/natural ligands was used as the positive control and the interactions of riboswitches/ ampicillin and 5S rRNA/aminoglycosides were employed as negative controls. Applying AutoDock vina, it was showed that the binding energy of each kind of riboswitches with different types of aminoglycosides is almost the same or sometimes more than the binding energy of the aminoglycoside with the corresponding binding cage of â�?�?16S rRNA A siteâ�? as aminoglycosidesâ�?�? target site. Accordingly, lysine, glycine and SAM-I riboswitches were recognized as the best RNA targets for all of the aminoglycosides with average binding energy of -10 kcal/mol whereas the mean binding energy of 16S rRNA A site/aminoglysides and riboswitches/ampicillin was -8 kcal/mol and -4 kcal/mol, respectively. In the next step, docking results were validated through rDock program. According to total scores, all of the studied riboswitches showed considerable affinity to paromomycin in the range of -16.83 â�?�? -55.16 for c-d-GMP-II and lysine riboswitches, respectively. Furthermore, it was indicated that hydrogen binding makes a key role in the binding energy between aminoglycosides and riboswitches. Moreover, simulation studies on riboswitch/aminoglycoside complex approved the strong interaction and stability of the docked structure in the solvent containing ions. In conclusion, computational findings support the hypothesis of possible role of riboswitches as aminoglycoside targets.

Biography

Email: msaeidhejazi@yahoo.com