Assessing Molecular Dynamics in Predicting Aptamer–Ligand Binding Thermodynamics: Insights from the OTA Binding Aptamers

The targeting of nucleic acid platforms is of particular interest in biochemistry and pharmaceutical applications. Among nucleic-based structures, aptamers, short, synthetic oligonucleotides, stand out because of their tunable sequences, enabling highly selective recognition of molecules of different sizes. However, an accurate evaluation of aptamers' affinity toward their targets remains elusive, as results obtained from different experimental techniques are often inconsistent. In this context, computational methods provide an appealing alternative for characterizing aptamer binding and structure. To this end, we selected two ochratoxin A binding aptamers as a case study to assess the ability of molecular dynamics simulations and alchemical free energy calculations to model the conformational dynamics and binding thermodynamics of these systems. Extensive classical molecular dynamics simulations were performed to characterize the aptamers' structures in the absence of their ligand, which could not be determined experimentally due to the intrinsic flexibility of these sequences. Additional simulations on aptamer-ligand complexes provided atomistic details of the interactions underlying the corresponding aptamers' preferential binding to their target compared with an analogue ligand that differs by a single atom. Lastly, alchemical free energy calculations were employed to estimate aptamers' selectivity for the target over its analogue, expressed as relative binding free energy. Our estimates are in good agreement with experimental data. We expect these computational strategies to contribute to future protocols for aptamer design and evaluation, enabling a more rigorous assessment of their binding to biochemically relevant molecules.