In Silico Approaches for the Identification of Aptamer Binding Interactions to <i>Leptospira</i> spp. Cell Surface Proteins
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 bind...
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MDPI AG
2023-02-01
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| Series: | Tropical Medicine and Infectious Disease |
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| Online Access: | https://www.mdpi.com/2414-6366/8/2/125 |
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| author | Chembie A. Almazar Marjo V. Mendoza Windell L. Rivera |
| author_facet | Chembie A. Almazar Marjo V. Mendoza Windell L. Rivera |
| author_sort | Chembie A. Almazar |
| collection | DOAJ |
| description | 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 <i>Leptospira</i> 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 <i>Leptospira</i> 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. |
| first_indexed | 2024-03-11T08:03:25Z |
| format | Article |
| id | doaj.art-fe309021cf044d309fa78056b4bf5a1d |
| institution | Directory Open Access Journal |
| issn | 2414-6366 |
| language | English |
| last_indexed | 2024-03-11T08:03:25Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Tropical Medicine and Infectious Disease |
| spelling | doaj.art-fe309021cf044d309fa78056b4bf5a1d2023-11-16T23:40:16ZengMDPI AGTropical Medicine and Infectious Disease2414-63662023-02-018212510.3390/tropicalmed8020125In Silico Approaches for the Identification of Aptamer Binding Interactions to <i>Leptospira</i> spp. Cell Surface ProteinsChembie A. Almazar0Marjo V. Mendoza1Windell L. Rivera2Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, PhilippinesPathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, PhilippinesPathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, PhilippinesAptamers 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 <i>Leptospira</i> 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 <i>Leptospira</i> 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.https://www.mdpi.com/2414-6366/8/2/125<i>Leptospira</i>in silicoaptamermolecular dockingbinding interactions |
| spellingShingle | Chembie A. Almazar Marjo V. Mendoza Windell L. Rivera In Silico Approaches for the Identification of Aptamer Binding Interactions to <i>Leptospira</i> spp. Cell Surface Proteins Tropical Medicine and Infectious Disease <i>Leptospira</i> in silico aptamer molecular docking binding interactions |
| title | In Silico Approaches for the Identification of Aptamer Binding Interactions to <i>Leptospira</i> spp. Cell Surface Proteins |
| title_full | In Silico Approaches for the Identification of Aptamer Binding Interactions to <i>Leptospira</i> spp. Cell Surface Proteins |
| title_fullStr | In Silico Approaches for the Identification of Aptamer Binding Interactions to <i>Leptospira</i> spp. Cell Surface Proteins |
| title_full_unstemmed | In Silico Approaches for the Identification of Aptamer Binding Interactions to <i>Leptospira</i> spp. Cell Surface Proteins |
| title_short | In Silico Approaches for the Identification of Aptamer Binding Interactions to <i>Leptospira</i> spp. Cell Surface Proteins |
| title_sort | in silico approaches for the identification of aptamer binding interactions to i leptospira i spp cell surface proteins |
| topic | <i>Leptospira</i> in silico aptamer molecular docking binding interactions |
| url | https://www.mdpi.com/2414-6366/8/2/125 |
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