Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking

Abstract

Aptamers are single-stranded oligonucleotides, formerly evolved by Systematic Evolution of Ligands by EXponential enrichment (SELEX), that fold into functional three-dimensional structures. Such conformation is crucial for aptamers’ ability to bind to a target with high affinity and specificity. Unnatural nucleotides have been used to develop nucleic acid mimic (NAM) aptamers with increased performance, such as biological stability. Prior knowledge of aptamer-target interactions is critical for applying post-SELEX modifications with unnatural nucleotides since it can affect aptamers’ structure and performance. Here, we describe an easy-to-apply in silico workflow using free available software / web servers to predict the tertiary conformation of NAM, DNA and RNA aptamers, as well as the docking with the target molecule. Representative 2ʹ-O-methyl (2ʹOMe), locked nucleic acid (LNA), DNA and RNA aptamers, with experimental data deposited in Protein Data Bank, were selected to validate the workflow. All aptamers’ tertiary structure and docking models were successfully predicted with good structural similarity to the experimental data. Thus, this workflow will boost the development of aptamers, particularly NAM aptamers, by assisting in the rational modification of specific nucleotides and avoiding trial-and-error approaches.

Prediction of Aptamer–Small-Molecule Interactions Using Metastable States from Multiple Independent Molecular Dynamics Simulations

“…Computational modeling of aptamer tertiary structures and molecular docking are available in silico methods to help elucidate DNA aptamer–small-molecule interactions. − Different workflows have been reported to model DNA oligonucleotides with different levels of accuracy compared to their characterized tertiary structure. − Generally, they involve the generation of an RNA three-dimensional (3D) model that is later mutated to DNA and subjected to energy minimization prior to molecular docking analysis. The approaches based on 3D prediction tools and servers, albeit computationally inexpensive and straightforward, output the most probable RNA conformation, that is, the most thermodynamically stable conformation.…”

“…The approaches based on 3D prediction tools and servers, albeit computationally inexpensive and straightforward, output the most probable RNA conformation, that is, the most thermodynamically stable conformation. Nevertheless, it is known that the most thermodynamically stable unbound aptamer conformation (apo state) is not necessarily the most favorable for binding (holo state) . Additionally, these methods assume that there is only one unbound conformation; when in reality, an unbound aptamer is an ensemble of metastable states that coexist in a system. − Therefore, accurate prediction of aptamer binding sites remains elusive.…”

“…Nevertheless, it is known that the most thermodynamically stable unbound aptamer conformation (apo state) is not necessarily the most favorable for binding (holo state). 19 Additionally, these methods assume that there is only one unbound conformation; when in reality, an unbound aptamer is an ensemble of metastable states that coexist in a system. 23−25 Therefore, accurate prediction of aptamer binding sites remains elusive.…”

An overview of structural approaches to study therapeutic RNAs

“…Also, the identification of key interaction residues and structural motifs is helpful for aptamer design modification ( Sharma et al, 2017 ). Actually, few in silico example are reported that determine the three-dimensional conformation of aptamers and the binding to their target ( Oliveira et al, 2022 ).…”

In Silico Approaches for the Identification of Aptamer Binding Interactions to Leptospira spp. Cell Surface Proteins

“…Development of specific and sensitive diagnostic tests is therefore imperative for appropriate patient management and treatment. Using aptamers selected against Leptospira from in vitro experiments, we derived their secondary and tertiary structures by adopting a previously described workflow for structural modeling [ 13 ]. Aptamer interactions with selected proteins were also predicted to determine possible binding residues.…”