RNA Secondary Structure as a First Step for Rational Design of the Oligonucleotides towards Inhibition of Influenza A Virus Replication

Influenza is an important research subject around the world because of its threat to humanity. Influenza A virus (IAV) causes seasonal epidemics and sporadic, but dangerous pandemics. A rapid antigen changes and recombination of the viral RNA genome contribute to the reduced effectiveness of vaccination and anti-influenza drugs. Hence, there is a necessity to develop new antiviral drugs and strategies to limit the influenza spread. IAV is a single-stranded negative sense RNA virus with a genome (viral RNA—vRNA) consisting of eight segments. Segments within influenza virion are assembled into viral ribonucleoprotein (vRNP) complexes that are independent transcription-replication units. Each step in the influenza life cycle is regulated by the RNA and is dependent on its interplay and dynamics. Therefore, viral RNA can be a proper target to design novel therapeutics. Here, we briefly described examples of anti-influenza strategies based on the antisense oligonucleotide (ASO), small interfering RNA (siRNA), microRNA (miRNA) and catalytic nucleic acids. In particular we focused on the vRNA structure-function relationship as well as presented the advantages of using secondary structure information in predicting therapeutic targets and the potential future of this field.

Download Full-text

A Host Susceptibility Gene, DR1, Facilitates Influenza A Virus Replication by Suppressing Host Innate Immunity and Enhancing Viral RNA Replication

Journal of Virology ◽

10.1128/jvi.03610-14 ◽

2015 ◽

Vol 89 (7) ◽

pp. 3671-3682 ◽

Cited By ~ 14

Author(s):

Shih-Feng Hsu ◽

Wen-Chi Su ◽

King-Song Jeng ◽

Michael M. C. Lai

Keyword(s):

Influenza A Virus ◽

Influenza A ◽

Susceptibility Gene ◽

Influenza Virus Infection ◽

Rna Replication ◽

Viral Rna ◽

Host Susceptibility ◽

Viral Rdrp ◽

Genome Wide ◽

A Genome

ABSTRACTInfluenza A virus (IAV) depends on cellular factors to complete its replication cycle; thus, investigation of the factors utilized by IAV may facilitate antiviral drug development. To this end, a cellular transcriptional repressor, DR1, was identified from a genome-wide RNA interference (RNAi) screen. Knockdown (KD) of DR1 resulted in reductions of viral RNA and protein production, demonstrating that DR1 acts as a positive host factor in IAV replication. Genome-wide transcriptomic analysis showed that there was a strong induction of interferon-stimulated gene (ISG) expression after prolonged DR1 KD. We found that beta interferon (IFN-β) was induced by DR1 KD, thereby activating the JAK-STAT pathway to turn on ISG expression, which led to a strong inhibition of IAV replication. This result suggests that DR1 in normal cells suppresses IFN induction, probably to prevent undesired cytokine production, but that this suppression may create a milieu that favors IAV replication once cells are infected. Furthermore, biochemical assays of viral RNA replication showed that DR1 KD suppressed viral RNA replication. We also showed that DR1 associated with all three subunits of the viral RNA-dependent RNA polymerase (RdRp) complex, indicating that DR1 may interact with individual components of the viral RdRp complex to enhance viral RNA replication. Thus, DR1 may be considered a novel host susceptibility gene for IAV replication via a dual mechanism, not only suppressing the host defense to indirectly favor IAV replication but also directly facilitating viral RNA replication.IMPORTANCEInvestigations of virus-host interactions involved in influenza A virus (IAV) replication are important for understanding viral pathogenesis and host defenses, which may manipulate influenza virus infection or prevent the emergence of drug resistance caused by a high error rate during viral RNA replication. For this purpose, a cellular transcriptional repressor, DR1, was identified from a genome-wide RNAi screen as a positive regulator in IAV replication. In the current studies, we showed that DR1 suppressed the gene expression of a large set of host innate immunity genes, which indirectly facilitated IAV replication in the event of IAV infection. Besides this scenario, DR1 also directly enhanced the viral RdRp activity, likely through associating with individual components of the viral RdRp complex. Thus, DR1 represents a novel host susceptibility gene for IAV replication via multiple functions, not only suppressing the host defense but also enhancing viral RNA replication. DR1 may be a potential target for drug development against influenza virus infection.

Download Full-text

Faculty Opinions recommendation of Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.13918956.15376056 ◽

2012 ◽

Author(s):

Chandra Verma

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Influenza A Virus ◽

Influenza A ◽

Rational Design ◽

Dynamics Simulation ◽

Drug Resistant ◽

Resistant Mutants

Download Full-text

Viral RNA Polymerase: A Promising Antiviral Target for Influenza A Virus

Current Medicinal Chemistry ◽

10.2174/09298673113209990208 ◽

2013 ◽

Vol 20 (31) ◽

pp. 3923-3934 ◽

Cited By ~ 14

Author(s):

Fangyuan Shi ◽

Yuanchao Xie ◽

Lifang Shi ◽

Wenfang Xu

Keyword(s):

Rna Polymerase ◽

Influenza A Virus ◽

Influenza A ◽

Viral Rna

Download Full-text

Development of an HTS Assay for the Search of Anti-influenza Agents Targeting the Interaction of Viral RNA with the NS1 Protein

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057108318754 ◽

2008 ◽

Vol 13 (7) ◽

pp. 581-590 ◽

Cited By ~ 23

Author(s):

Marta Maroto ◽

Yolanda Fernandez ◽

Juan Ortin ◽

Fernando Pelaez ◽

M. Angerles Cabello

Keyword(s):

Influenza A Virus ◽

Influenza A ◽

Cytopathic Effect ◽

Nonstructural Protein ◽

Specific Interaction ◽

Chemical Compounds ◽

Viral Rna ◽

Ns1 Protein ◽

Rna Molecules ◽

Novel Target

The NS1 protein is a nonstructural protein encoded by the influenza A virus. It is responsible for many alterations produced in the cellular metabolism upon infection by the virus and for modulation of virus virulence. The NS1 protein is able to perform a large variety of functions due to its ability to bind various types of RNA molecules, from both viral and nonviral origin, and to interact with several cell factors. With the aim of exploring whether the binding of NS1 protein to viral RNA (vRNA) could constitute a novel target for the search of anti-influenza drugs, a filter-binding assay measuring the specific interaction between the recombinant His-NS1 protein from influenza A virus and a radiolabeled model vRNA ( 32P-vNSZ) was adapted to a format suitable for screening and easy automation. Flashplate® technology (PerkinElmer, Waltham, MA), either in 96- or 384-well plates, was used. The Flashplate® wells were precoated with the recombinant His-NS1 protein, and the binding of His-NS1 to a 35S-vNSZ probe was measured. A pilot screening of a collection of 27,520 mixtures of synthetic chemical compounds was run for inhibitors of NS1 binding to vRNA. We found 3 compounds in which the inhibition of NS1 binding to vRNA, observed at submicromolar concentrations, was correlated with a reduction of the cytopathic effect during the infection of cell cultures with influenza virus. These results support the hypothesis that the binding of NS1 to vRNA could be a novel target for the development of anti-influenza drugs. ( Journal of Biomolecular Screening 2008:581-590)

Download Full-text

Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency

PLoS Computational Biology ◽

10.1371/journal.pcbi.1005075 ◽

2016 ◽

Vol 12 (10) ◽

pp. e1005075 ◽

Cited By ~ 12

Author(s):

Max Schelker ◽

Caroline Maria Mair ◽

Fabian Jolmes ◽

Robert-William Welke ◽

Edda Klipp ◽

...

Keyword(s):

Virus Infection ◽

Influenza A Virus ◽

Influenza A ◽

Rna Degradation ◽

Viral Rna ◽

Infection Efficiency ◽

Influenza A Virus Infection ◽

And Diffusion

Download Full-text

The Fight against the Influenza A Virus H1N1: Synthesis, Molecular Modeling, and Biological Evaluation of Benzofurazan Derivatives as Viral RNA Polymerase Inhibitors

ChemMedChem ◽

10.1002/cmdc.201300378 ◽

2013 ◽

Vol 9 (1) ◽

pp. 129-150 ◽

Cited By ~ 16

Author(s):

Mafalda Pagano ◽

Daniele Castagnolo ◽

Martina Bernardini ◽

Anna Lucia Fallacara ◽

Ilaria Laurenzana ◽

...

Keyword(s):

Molecular Modeling ◽

Rna Polymerase ◽

Influenza A Virus ◽

Influenza A ◽

Biological Evaluation ◽

Viral Rna ◽

Virus H1n1 ◽

Polymerase Inhibitors

Download Full-text

Deep learning predicts short non-coding RNA functions from only raw sequence data

PLoS Computational Biology ◽

10.1371/journal.pcbi.1008415 ◽

2020 ◽

Vol 16 (11) ◽

pp. e1008415

Author(s):

Teresa Maria Rosaria Noviello ◽

Francesco Ceccarelli ◽

Michele Ceccarelli ◽

Luigi Cerulo

Keyword(s):

Secondary Structure ◽

Sequence Data ◽

Computational Cost ◽

Large Data ◽

Sequence Information ◽

Structure Information ◽

Non Coding Rna ◽

A Genome ◽

Data Volume ◽

Biological Functionality

Small non-coding RNAs (ncRNAs) are short non-coding sequences involved in gene regulation in many biological processes and diseases. The lack of a complete comprehension of their biological functionality, especially in a genome-wide scenario, has demanded new computational approaches to annotate their roles. It is widely known that secondary structure is determinant to know RNA function and machine learning based approaches have been successfully proven to predict RNA function from secondary structure information. Here we show that RNA function can be predicted with good accuracy from a lightweight representation of sequence information without the necessity of computing secondary structure features which is computationally expensive. This finding appears to go against the dogma of secondary structure being a key determinant of function in RNA. Compared to recent secondary structure based methods, the proposed solution is more robust to sequence boundary noise and reduces drastically the computational cost allowing for large data volume annotations. Scripts and datasets to reproduce the results of experiments proposed in this study are available at: https://github.com/bioinformatics-sannio/ncrna-deep.

Download Full-text

Small Interfering RNA Targeting M2 Gene Induces Effective and Long Term Inhibition of Influenza A Virus Replication

PLoS ONE ◽

10.1371/journal.pone.0005671 ◽

2009 ◽

Vol 4 (5) ◽

pp. e5671 ◽

Cited By ~ 43

Author(s):

Hong-Yan Sui ◽

Guang-Yu Zhao ◽

Jian-Dong Huang ◽

Dong-Yan Jin ◽

Kwok-Yung Yuen ◽

...

Keyword(s):

Influenza A Virus ◽

Virus Replication ◽

Small Interfering Rna ◽

Influenza A ◽

Rna Targeting ◽

Interfering Rna

Download Full-text

Highly Conserved Regions of Influenza A Virus Polymerase Gene Segments Are Critical for Efficient Viral RNA Packaging

Journal of Virology ◽

10.1128/jvi.02267-07 ◽

2007 ◽

Vol 82 (5) ◽

pp. 2295-2304 ◽

Cited By ~ 111

Author(s):

Glenn A. Marsh ◽

Raúl Rabadán ◽

Arnold J. Levine ◽

Peter Palese

Keyword(s):

Influenza A Virus ◽

Influenza A ◽

Large Scale ◽

Viral Rna ◽

Polymerase Gene ◽

Viral Rnas ◽

Synonymous Mutations ◽

Conserved Regions ◽

Selective Incorporation ◽

Incorporation Model

ABSTRACT The genome of the influenza A virus is composed of eight different segments of negative-sense RNA. These eight segments are incorporated into budding virions in an equimolar ratio through a mechanism that is not fully understood. Two different models have been proposed for packaging the viral ribonucleoproteins into newly assembling virus particles: the random-incorporation model and the selective-incorporation model. In the last few years, increasing evidence from many different laboratories that supports the selective-incorporation model has been accumulated. In particular, different groups have shown that some large viral RNA regions within the coding sequences at both the 5′ and 3′ ends of almost every segment are sufficient for packaging foreign RNA sequences. If the packaging regions are crucial for the viability of the virus, we would expect them to be conserved. Using large-scale analysis of influenza A virus sequences, we developed a method of identifying conserved RNA regions whose conservation cannot be explained by population structure or amino acid conservation. Interestingly, the conserved sequences are located within the regions identified as important for efficient packaging. By utilizing influenza virus reverse genetics, we have rescued mutant viruses containing synonymous mutations within these highly conserved regions. Packaging of viral RNAs in these viruses was analyzed by reverse transcription using a universal primer and quantitative PCR for individual segments. Employing this approach, we have identified regions in the polymerase gene segments that, if mutated, result in reductions of more than 90% in the packaging of that particular polymerase viral RNA. Reductions in the level of packaging of a polymerase viral RNA frequently resulted in reductions of other viral RNAs as well, and the results form a pattern of hierarchy of segment interactions. This work provides further evidence for a selective packaging mechanism for influenza A viruses, demonstrating that these highly conserved regions are important for efficient packaging.

Download Full-text