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

• Published in: Tropical medicine and infectious disease Vol. 8; no. 2
• Main Authors: Almazar, Chembie A, Mendoza, Marjo V, Rivera, Windell L
• Format: Journal Article
• Language: English
• Published: MDPI AG 01.02.2023
• Subjects: Analysis; Gram-negative bacteria; Hydrogen; Organic acids; Protein binding; Proteins
• ISSN: 2414-6366; 2414-6366
• DOI: 10.3390/tropicalmed8020125

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.