In Silico study of a group of antibiotics affinity toward aptamers for biosensor development: Molecular Dynamics Simulations and Molecular Docking Studies

Aptamers are short single-stranded DNA (ssDNA) or nucleotide sequences prepared by a random library through an iterative in vitro process called SELEX (systematic evolution of ligands via exponential enrichment), which that can bind with high affinity and specificity to various targets, such as drugs, proteins or other organic or inorganic compounds. These single chains have many advantages such as cost effectiveness, flexibility, easy modification and high stability [1]. In this study, the affinity of sequences of specific aptamers for various antibiotics was studied using molecular dynamics simulations (MDs) method and molecular docking studies [2]. The desired sequences structures were generated and went through molecular dynamics simulations, using GROMACS 5.1.5, to investigate the molecules conformational and obtain a stable structure at the desired conditions. The target antibiotics affinity and tendency to interact with the aptamers was computed with the aid of molecular docking methodology, employing Schrodinger maestro software (version 12.5). The stability of the antibiotic-aptamer complexes interactions was further investigated using molecular dynamics simulations. The aptamers that the target antibiotics predicted to have more tendency to interact with were selected to design aptasensors to detect the antibiotics in different samples.