Designing Anti-Influenza Aptamers: Novel Quantitative Structure Activity Relationship Approach Gives Insights into Aptamer – Virus Interaction
| Autor: | Silvia Noiman, Boaz Musafia, Rony Oren-Banaroya |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
Quantitative structure–activity relationship
Viral Diseases Drug Research and Development Viral protein Aptamer Hemagglutinin (influenza) lcsh:Medicine Computational biology medicine.disease_cause Biochemistry Antiviral Agents Virus Madin Darby Canine Kidney Cells Structure-Activity Relationship Computational Chemistry Dogs Influenza A Virus H1N1 Subtype Orthomyxoviridae Infections Nucleic Acids Molecular Cell Biology Drug Discovery medicine Influenza A virus Medicine and Health Sciences Animals Structural motif lcsh:Science Pharmacology Multidisciplinary biology Oligonucleotide Nucleotides Influenza A Virus H3N2 Subtype lcsh:R Biology and Life Sciences Computational Biology DNA Cell Biology Aptamers Nucleotide Virology Influenza Chemistry Infectious Diseases Drug Design Physical Sciences biology.protein lcsh:Q Research Article Biotechnology |
| Zdroj: | PLoS ONE PLoS ONE, Vol 9, Iss 5, p e97696 (2014) |
| ISSN: | 1932-6203 |
| Popis: | This study describes the development of aptamers as a therapy against influenza virus infection. Aptamers are oligonucleotides (like ssDNA or RNA) that are capable of binding to a variety of molecular targets with high affinity and specificity. We have studied the ssDNA aptamer BV02, which was designed to inhibit influenza infection by targeting the hemagglutinin viral protein, a protein that facilitates the first stage of the virus' infection. While testing other aptamers and during lead optimization, we realized that the dominant characteristics that determine the aptamer's binding to the influenza virus may not necessarily be sequence-specific, as with other known aptamers, but rather depend on general 2D structural motifs. We adopted QSAR (quantitative structure activity relationship) tool and developed computational algorithm that correlate six calculated structural and physicochemical properties to the aptamers' binding affinity to the virus. The QSAR study provided us with a predictive tool of the binding potential of an aptamer to the influenza virus. The correlation between the calculated and actual binding was R2 = 0.702 for the training set, and R2 = 0.66 for the independent test set. Moreover, in the test set the model's sensitivity was 89%, and the specificity was 87%, in selecting aptamers with enhanced viral binding. The most important properties that positively correlated with the aptamer's binding were the aptamer length, 2D-loops and repeating sequences of C nucleotides. Based on the structure-activity study, we have managed to produce aptamers having viral affinity that was more than 20 times higher than that of the original BV02 aptamer. Further testing of influenza infection in cell culture and animal models yielded aptamers with 10 to 15 times greater anti-viral activity than the BV02 aptamer. Our insights concerning the mechanism of action and the structural and physicochemical properties that govern the interaction with the influenza virus are discussed. |
| Databáze: | OpenAIRE |
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