Design of a Bio-Compatible Drug Delivery System Based on Gold Nanoparticles for RNA Aptamer as an Anti HIV-1 Drug: Molecular DynamicsSimulation

The interactions of nanoparticles with single stranded nucleic acids (NAs) have importantimplications ranged from drug and gene delivery to nano-machine building to bio-sensor designand productions [1]. Therefore, in this research work, we investigate the interactions of a goldnanosheet as drug carrier with RNA aptamer as anti-HIV drug acting as inhibitor for HIV-1protease by molecular dynamics simulation method.All molecular dynamics simulations were performed using the NAMD-2.12 software [2]and the visualizations and analyzing of MD trajectories were executed by VMD-1.9.2 package[3]. Three sequences families of RNA aptamers were selected. Recently, [4] studied these aptamersexperimentally and reported anti-HIV properties for them. The Second-generation RNAaptamers were selected from Kinefolde web server. The third structures predicted by SIMRNAweb server are in agreement with the experimental data.The interactions between GNP and considered aptamers have been studied by extractingthe structural and energetics results from the simulation trajectories. The structural data are likeRMSD, hydrogen bonds and center of mass distances were used for elucidation of the adsorptionand immobilization of aptamer on the gold nanosheets as well as its native folded structue.Enetrgerics of the interactions such as total inteaction energy and the contribution of van derWaals and electrostatic interactions in total energy were used for estimation of the adsorptionstrength of studied aptamers in the binded fashion. These results could give insights into theflexibility of aptamer sequences the qualitative information about the conformational changes ofthe aptamer’s backbone along the simulation time. These values were in a reasonable range andindicated the native structure of aptamer remained along the simulation. The intraction residueswere verifed by the help of the averaged RMSF values for intraction and nonintraction aptamersaccompanying conventional visual analysis of trajectories. Our study provides useful guides fordesigning/modifying nanomaterials to interact with aptamers for their bio-applications.

Keywords:

HIV , Gold Nanosheets , Molecular Dynamics , RNA Aptamer