Chemically modified aptamers for improving binding affinity to the target proteins via enhanced non-covalent bonding

Abstract

Nucleic acid aptamers are ssDNA or ssRNA fragments that specifically recognize targets. However, the pharmacodynamic properties of natural aptamers consisting of 4 naturally occurring nucleosides (A, G, C, T/U) are generally restricted for inferior binding affinity than the cognate antibodies. The development of high-affinity modification strategies has attracted extensive attention in aptamer applications. Chemically modified aptamers with stable three-dimensional shapes can tightly interact with the target proteins via enhanced non-covalent bonding, possibly resulting in hundreds of affinity enhancements. This review overviewed high-affinity modification strategies used in aptamers, including nucleobase modifications, fluorine modifications (2′-fluoro nucleic acid, 2′-fluoro arabino nucleic acid, 2′,2′-difluoro nucleic acid), structural alteration modifications (locked nucleic acid, unlocked nucleic acid), phosphate modifications (phosphorothioates, phosphorodithioates), and extended alphabets. The review emphasized how these high-affinity modifications function in effect as the interactions with target proteins, thereby refining the pharmacodynamic properties of aptamers.

Aptamer–Protein Interactions: From Regulation to Biomolecular Detection

“…Antibodies, conventional recognition molecules, are composed of 20 different amino acids with a variety of spatial structures. , In contrast, the limited components of natural nucleotides (A, G, C, T, or U) definitely restrict the structural and functional diversity of aptamers. , Introducing chemical groups not found in natural nucleotides not only allows the formation of aptamers with richer spatial conformations, but also provides additional interactions between aptamers and their target proteins. , Therefore, strategies regarding chemical modifications of aptamers are also well established for modulating aptamer–protein interactions. Many conceivable chemical modifications are not compatible with the conventional SELEX process involving RNA polymerase transcription and/or PCR depending on DNA polymerases .…”

“…Due to the introduction of hydrophobic interactions by sulfur substitution, PS2-modified aptamers had an approximately 1000-fold increase in affinity toward target proteins compared with unmodified aptamers. Indeed, some modifications not only bring remarkable enhancements in target affinity, but may also increase off-target affinities. , …”

“…Indeed, some modifications not only bring remarkable enhancements in target affinity, but may also increase offtarget affinities. 38,97 Modifications on bases, that is, base substitutions or addition of unnatural bases, are widely studied chemical modification strategies. In general, base substitutions refer to replacing the 5′-position of pyrimidines with hydrophobic, hydrophilic, or charged groups, thereby introducing additional interactions into aptamer−protein interactions.…”

“…95,96 In contrast, the limited components of natural nucleotides (A, G, C, T, or U) definitely restrict the structural and functional diversity of aptamers. 97,98 Introducing chemical groups not found in natural nucleotides not only allows the formation of aptamers with richer spatial conformations, but also provides additional interactions between aptamers and their target proteins. 99,100 Therefore, strategies regarding chemical modifications of aptamers are also well established for modulating aptamer−protein interactions.…”

Aptamers Targeting the PD-1/PD-L1 Axis: A Perspective

“…XA-PDL1-82 showed similar capacity as a PD-L1 antibody to bind PD-L1 expressing pancreatic tumor tissue. Alternatively to 3′ or 5′ modifications, locked and unlocked nucleic acids (Figure C, LNA, UNA) and non-ribose nucleic acid were developed to enhance plasma and thermal stability. Biologically stable threose-based aptamers (TNA) were proposed for targeting PD-L1 .…”