Novel Delivery System for Novel Therapeutic Agent: Molecular Dynamics Simulation of Interaction of Non-Coding RNA Aptamer with Boron-Nitride Nanotube

RNA aptamers have been attractively attentioned in the recent years by researchers. Incomparison to the antibodies they have numerous advantages such as high specificity and affinity thatmade them an excellent agent in order to identify and decrease diseased cells in the blood stream[1].Molecular information such as energetics of the interaction and structure of the drug-nanoparticlecomplex have critical importance in design smart delivery systems for cancer therapy [2]. Here, we haveinvestigated the molecular interaction of RNA aptamer with (12,12) boron-nitride nanotube (BNNTs),excellent biocompatible and non-toxic nanotube [3]. We prepared complexes composed from aRNA aptamer that has been selected and tested experimentally by Na Li et all[4] as an bindingagent to Epidermal Growth Factor Receptor (EGFR) and (12,12) BNNT. Then we simulated them byNAMD package[5] with CHARMM-36 force field along 60 simulation time with 1 fs time steps. Theresults of the simulation were analyzed as structural parameters like differences of the centers of mass,the radial distribution functions, the radius of gyration, the root mean square deviation and so on. Alongwith the structural analysis, we carried on the energetics analysis including the non-boning interactionenergies and the contributions of electrostatic and van der Waals interactions between aptamer andBNNT. The results show that the adsorption of aptamer on BNNT has not destructive effect on theaptamer structure and its configuration restore in adsorbed state. On the other hand, the release of aptamerfrom BNNT is not probably a difficult process, because the interaction energies (adsorption energies, inother terms) are not so large. Therefor the studied BNNT can be used as a delivery system for consideredRNA aptamer at the studied conditions.

Keywords:

Drug Delivery , RNA Aptamer , BNNT , Biocompatible , Molecular Dynamics Simulation