期刊
TROPICAL MEDICINE AND INFECTIOUS DISEASE
卷 8, 期 2, 页码 -出版社
MDPI
DOI: 10.3390/tropicalmed8020125
关键词
Leptospira; in silico; aptamer; molecular docking; binding interactions
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. AP5 and AP1 showed the highest number of interactions. Hydrogen bonds and a few hydrophobic interactions were observed in most aptamer-protein complexes. Serine, threonine, glutamine, and lysine were identified as the main protein residues. This study provides insights for improving the binding affinity and accuracy of aptamers.
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.
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