Aminoglycoside antibiotics bind to the influenza A virus RNA promoter

Kim, Henna; Lee, Mi Kyung; Ko, Jong Soo; Park, Chin‐Ju; Kim, Meehyein; Jeong, Yujeong; Hong, Sungwoo; Varani, Gabriele; Choi, Byung-Seok

doi:10.1039/c2mb25333j

Cited by 18 publications

(27 citation statements)

References 27 publications

(27 reference statements)

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“…Based on examination of aminoglycoside binding to the hammerhead ribozyme, the positively charged amino groups of the aminoglycoside are thought to form electrostatic interactions with the negatively charged phosphate backbone of the nucleic acids. [36] Aminoglycosides have also been shown to bind to various types of RNA, including the influenza A virus RNA promoter[37], the HIV Rev RNA recognition element[38] and TAR RNA[39], and thymidylate synthase mRNA[40]. These molecules have prominent internal loops and bulges, as measured by a variety of biophysical and spectroscopy methods, which is consistent with our study that demonstrates aminoglycoside binding to internal stem loops in Ysr170 by SHAPE.…”

Section: Discussionsupporting

confidence: 86%

Functional and Structural Analysis of a Highly-Expressed Yersinia pestis Small RNA following Infection of Cultured Macrophages

Hennelly

Stubben

et al. 2016

PLoS ONE

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Non-coding small RNAs (sRNAs) are found in practically all bacterial genomes and play important roles in regulating gene expression to impact bacterial metabolism, growth, and virulence. We performed transcriptomics analysis to identify sRNAs that are differentially expressed in Yersinia pestis that invaded the human macrophage cell line THP-1, compared to pathogens that remained extracellular in the presence of host. Using ultra high-throughput sequencing, we identified 37 novel and 143 previously known sRNAs in Y. pestis. In particular, the sRNA Ysr170 was highly expressed in intracellular Yersinia and exhibited a log2 fold change ~3.6 higher levels compared to extracellular bacteria. We found that knock-down of Ysr170 expression attenuated infection efficiency in cell culture and growth rate in response to different stressors. In addition, we applied selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) analysis to determine the secondary structure of Ysr170 and observed structural changes resulting from interactions with the aminoglycoside antibiotic gentamycin and the RNA chaperone Hfq. Interestingly, gentamicin stabilized helix 4 of Ysr170, which structurally resembles the native gentamicin 16S ribosomal binding site. Finally, we modeled the tertiary structure of Ysr170 binding to gentamycin using RNA motif modeling. Integration of these experimental and structural methods can provide further insight into the design of small molecules that can inhibit function of sRNAs required for pathogen virulence.

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Section: Discussionsupporting

confidence: 86%

Functional and Structural Analysis of a Highly-Expressed Yersinia pestis Small RNA following Infection of Cultured Macrophages

Hennelly

Stubben

et al. 2016

PLoS ONE

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“…Hence, the binding affinity of TO‐PRO‐3 is one order of magnitude stronger than that of DPQ, which indicates that TO‐PRO‐3 shows the strongest binding reported, to date, among non‐aminoglycoside ligands. The K d value of TO‐PRO‐3 is almost comparable to that of neomycin ( K d =2.7 μ m ) . We note that strong RNA binders with K d values in the sub‐micromolar range for the RNA promoter region of influenza A virus were recently developed based on peptide nucleic acid (PNA) oligonucleotides .…”

Section: Figurementioning

confidence: 91%

Section: Figurementioning

confidence: 99%

“…In an early attempt, aminoglycosides antibiotics, typical RNA‐binding scaffolds, were examined for binding to the model RNA containing the promoter region of influenza A virus (Figure A) . Neomycin (Figure B) was found to strongly bind to the (A ⋅ A)−U internal loop structure (dissociation constant ( K d )=2.7 μ m ; I =0.18 m , pH 7.5) . However, given some inherent problems of aminoglycoside antibiotics, such as promiscuous binding to various RNA structures and the risk of adverse effects, their clinical use would be severely limited.…”

Section: Figurementioning

confidence: 99%

“…Alternatively, a FID assay has superior sensitivity to that of the NMR spectroscopy‐based screening assay. Carboxytetramethylrhodamine (TAMRA)‐tagged paromomycin (CRP) was used as a fluorescence indicator to target the influenza A virus RNA promoter, in which the change in the fluorescence anisotropy of the TAMRA moiety was analyzed to monitor the displacement event with test compounds. The emission wavelength of TO‐PRO‐3 ( λ em >650 nm) is much longer than that of the TAMRA moiety ( λ em =580 nm), which is of great importance to reduce “compound optical interference” that is frequently found in fluorescence‐based screening assays .…”

Section: Figurementioning

confidence: 99%

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Strong Binding and Off–On Signaling Functions of Deep‐Red Fluorescent TO‐PRO‐3 for Influenza A Virus RNA Promoter Region

et al. 2019

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The RNA promoter region of the influenza A virus has recently attracted much attention as an RNA target for the development of anti‐influenza drugs. However, there are very few reports on small RNA‐binding ligands targeting this region. In this work, it is reported that TO‐PRO‐3, a thiazole orange analogue with a trimethine bridge, exhibits strong and selective binding to the internal loop structure of the influenza A virus RNA promoter. This binding accompanies the remarkable light‐up response of TO‐PRO‐3 in the deep‐red spectral region. By virtue of these binding and fluorescence signaling functions, TO‐PRO‐3 can act as a useful indicator for the assessment of the binding capabilities of various test compounds for this RNA region, with a view toward the development of anti‐influenza drug candidates.

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Small molecules targeting viral RNA

2016

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Highly conserved noncoding RNA (ncRNA) elements in viral genomes and transcripts offer new opportunities to expand the repertoire of drug targets for the development of antiinfective therapy. Ligands binding to ncRNA architectures are able to affect interactions, structural stability or conformational changes and thereby block processes essential for viral replication. Proof of concept for targeting functional RNA by small molecule inhibitors has been demonstrated for multiple viruses with RNA genomes. Strategies to identify antiviral compounds as inhibitors of ncRNA are increasingly emphasizing consideration of drug-like properties of candidate molecules emerging from screening and ligand design. Recent efforts of antiviral lead discovery for RNA targets have provided drug-like small molecules that inhibit viral replication and include inhibitors of human immunodeficiency virus (HIV), hepatitis C virus (HCV), severe respiratory syndrome coronavirus (SARS CoV), and influenza A virus. While target selectivity remains a challenge for the discovery of useful RNA-binding compounds, a better understanding is emerging of properties that define RNA targets amenable for inhibition by small molecule ligands. Insight from successful approaches of targeting viral ncRNA in HIV, HCV, SARS CoV, and influenza A will provide a basis for the future exploration of RNA targets for therapeutic intervention in other viral pathogens which create urgent, unmet medical needs. Viruses for which targeting ncRNA components in the genome or transcripts may be promising include insect-borne flaviviruses (Dengue, Zika, and West Nile) and filoviruses (Ebola and Marburg). WIREs RNA 2016, 7:726-743. doi: 10.1002/wrna.1373 For further resources related to this article, please visit the WIREs website.

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Aminoglycoside antibiotics bind to the influenza A virus RNA promoter

Cited by 18 publications

References 27 publications

Functional and Structural Analysis of a Highly-Expressed Yersinia pestis Small RNA following Infection of Cultured Macrophages

Functional and Structural Analysis of a Highly-Expressed Yersinia pestis Small RNA following Infection of Cultured Macrophages

Strong Binding and Off–On Signaling Functions of Deep‐Red Fluorescent TO‐PRO‐3 for Influenza A Virus RNA Promoter Region

Small molecules targeting viral RNA

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