Multi-group structure analysis and molecular docking of aptamers and small molecules: A case study of chloramphenicol

Aptamers, a kind of short nucleotide sequences with high specificity and affinity with targets, have attracted extensive attention in recent years. Molecular docking method (MDM) is the most common method to explore the binding mode and recognition mechanism of aptamers and small molecules, which generally use the target to dock with the highest scoring tertiary structural model of the aptamer, and the highest scoring result is used as the predicted model. However, this prediction results may miss out the true interaction pattern due to the fact that aptamers are not completely rigid and the natural aptamers conformations are not in a single state. Thus, evaluation of the binding pattern from two or more tertiary structural modes might be more accurate. The use of chloramphenicol (CAP) has been banned because it causes myelosuppression and aplastic anemia in humans. However, CAP is still abused and is often studied as a target for detection. Two CAP aptamers (Apt-11 and Apt-16) were used as cases in this study. All secondary structures of these two aptamers were predicted using the UNAFold Web Server tool, and then the corresponding tertiary structure models were built using the RNA Composer tool and Discovery Studio 4.5 Client software. The resulted six tertiary structure models were docked with CAP respectively. By optimizing the docking conditions, multiple groups of docking outcomes were obtained, including the tertiary structure, its binding free energy, and the binding site. The results suggested that there may be multiple binding sites in the same tertiary structure, and the binding energy of the same tertiary structure as well as the proportion of multiple binding sites vary greatly. In addition, it was found that Autodock4 works well in analyzing the binding mode between screened aptamers with its defined target, but cannot be used to identify that whether an aptamer could bind well with other molecule with big structural difference from the target. The CAP aptamer was tailored according to the molecular docking results, and the potential binding sites with CAP were verified by a colloidal gold colorimetry assay. In conclusion, we propose a method to explore the binding patterns between aptamer and its targets by using multiple optimized docking data from different tertiary structures of the aptamer, which provides a theoretical basis for the study of the binding mode of aptamers and targets, as well as the optimization and modification of aptamers.