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

Abstract

Aptamers are nucleic acids that can bind with high affinity and specificity to a range of target molecules. However, their functionality relies on their secondary and tertiary structures such that the combination of nucleotides determines their three-dimensional conformation. In this study, the binding mechanisms of candidate aptamers and their interactions with selected target proteins found in the cell surface of Leptospira were predicted to select high-affinity aptamers. Four aptamers were evaluated through molecular modeling and docking using available software and web-based tools, following the workflow previously designed for in silico evaluation of DNA aptamers. The most predominant and highly conserved surface-exposed proteins among pathogenic Leptospira species were used as aptamer targets. The highest number of interactions was seen in aptamers AP5 and AP1. Hydrogen bonds, along with a few hydrophobic interactions, occur in most aptamer–protein complexes. Further analysis revealed serine, threonine, glutamine, and lysine as main protein residues. H-bond interactions occur mostly with polar amino acids, as reflected in the predicted interaction profiles of aptamer–protein complexes. In silico strategies allowed the identification of key residues crucial in aptamer–target interaction during aptamer screening. Such information can be used in aptamer modification for improved binding affinity and accuracy for diagnostics application.

Aptamer–Protein Interactions: From Regulation to Biomolecular Detection

“…The phosphate groups in aptamers generally act as hydrogen bond acceptors, and the side chains of proteins serve as hydrogen bond donors. 46,47 Besides, owing to the negatively charged phosphate backbones, aptamers can attract the positively charged surface of target proteins, thereby inducing electrostatic interactions. 48,49 The hydrophobic interaction of aromatic rings with the aliphatic side chains of proteins is reported to be another force responsible for aptamer−target protein interactions.…”

“…In addition to nucleic acid bases, phosphate groups also play an important role in the formation of hydrogen bonding. The phosphate groups in aptamers generally act as hydrogen bond acceptors, and the side chains of proteins serve as hydrogen bond donors. , Besides, owing to the negatively charged phosphate backbones, aptamers can attract the positively charged surface of target proteins, thereby inducing electrostatic interactions. , The hydrophobic interaction of aromatic rings with the aliphatic side chains of proteins is reported to be another force responsible for aptamer–target protein interactions. , In addition, aromatic rings are also confirmed to participate in π–π stacking, mainly due to the overlapping of π orbitals. − The final important binding interaction is the van der Waals force arising from the mutual attraction of dipoles and induced dipoles . It has been reported that the strength of van der Waals forces heavily depends on the dimension of the interacting interface .…”