1
|
Szabat M, Lorent D, Czapik T, Tomaszewska M, Kierzek E, Kierzek R. RNA Secondary Structure as a First Step for Rational Design of the Oligonucleotides towards Inhibition of Influenza A Virus Replication. Pathogens 2020; 9:pathogens9110925. [PMID: 33171815 PMCID: PMC7694947 DOI: 10.3390/pathogens9110925] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/05/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
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.
Collapse
|
2
|
Lenartowicz E, Nogales A, Kierzek E, Kierzek R, Martínez-Sobrido L, Turner DH. Antisense Oligonucleotides Targeting Influenza A Segment 8 Genomic RNA Inhibit Viral Replication. Nucleic Acid Ther 2016; 26:277-285. [PMID: 27463680 PMCID: PMC5067832 DOI: 10.1089/nat.2016.0619] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Influenza A virus (IAV) affects 5%–10% of the world's population every year. Through genome changes, many IAV strains develop resistance to currently available anti-influenza therapeutics. Therefore, there is an urgent need to find new targets for therapeutics against this important human respiratory pathogen. In this study, 2′-O-methyl and locked nucleic acid antisense oligonucleotides (ASOs) were designed to target internal regions of influenza A/California/04/2009 (H1N1) genomic viral RNA segment 8 (vRNA8) based on a base-pairing model of vRNA8. Ten of 14 tested ASOs showed inhibition of viral replication in Madin-Darby canine kidney cells. The best five ASOs were 11–15 nucleotides long and showed inhibition ranging from 5- to 25-fold. In a cell viability assay they showed no cytotoxicity. The same five ASOs also showed no inhibition of influenza B/Brisbane/60/2008 (Victoria lineage), indicating that they are sequence specific for IAV. Moreover, combinations of ASOs slightly improved anti-influenza activity. These studies establish the accessibility of IAV vRNA for ASOs in regions other than the panhandle formed between the 5′ and 3′ ends. Thus, these regions can provide targets for the development of novel IAV antiviral approaches.
Collapse
Affiliation(s)
| | - Aitor Nogales
- 2 Department of Microbiology and Immunology, University of Rochester , Rochester, New York
| | - Elzbieta Kierzek
- 3 Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan, Poland
| | - Ryszard Kierzek
- 3 Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan, Poland
| | - Luis Martínez-Sobrido
- 2 Department of Microbiology and Immunology, University of Rochester , Rochester, New York
| | - Douglas H Turner
- 1 Department of Chemistry, University of Rochester , Rochester, New York
| |
Collapse
|
3
|
A Conserved Secondary Structural Element in the Coding Region of the Influenza A Virus Nucleoprotein (NP) mRNA Is Important for the Regulation of Viral Proliferation. PLoS One 2015; 10:e0141132. [PMID: 26488402 PMCID: PMC4619443 DOI: 10.1371/journal.pone.0141132] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/05/2015] [Indexed: 11/22/2022] Open
Abstract
Influenza A virus is a threat to humans due to seasonal epidemics and infrequent, but dangerous, pandemics that lead to widespread infection and death. Eight segments of RNA constitute the genome of this virus and they encode greater than eight proteins via alternative splicing of coding (+)RNAs generated from the genomic (-)RNA template strand. RNA is essential in its life cycle. A bioinformatics analysis of segment 5, which encodes nucleoprotein, revealed a conserved structural motif in the (+)RNA. The secondary structure proposed by energy minimization and comparative analysis agrees with structure predicted based on experimental data using a 121 nucleotide in vitro RNA construct comprising an influenza A virus consensus sequence and also an entire segment 5 (+)RNA (strain A/VietNam/1203/2004 (H5N1)). The conserved motif consists of three hairpins with one being especially thermodynamically stable. The biological importance of this conserved secondary structure is supported in experiments using antisense oligonucleotides in cell line, which found that disruption of this motif led to inhibition of viral fitness. These results suggest that this conserved motif in the segment 5 (+)RNA might be a candidate for oligonucleotide-based antiviral therapy.
Collapse
|
4
|
Abstract
Global outbreaks of diseases caused by zoonotic viruses have steadily increased in recent years. Emerging zoonotic viruses are generally phylogenetically diverse, are unpredictable and are known to cause diseases with high case fatality rates in humans and are hard to protect against due to lack of approved antiviral drugs. The aim of this review is to discuss how advances in genomics, rational drug design and innate immune signaling can contribute to the design of nucleic acid-based drugs to combat these emerging threats. Specifically, the antiviral activity of siRNAs, antisense oligonucleotides is mediated by sequence-specific gene silencing, and broad-spectrum innate and antiviral immune responses can be elicited by toll-like receptor agonists. This review will summarize their current state of development, safety and efficacy, and provide perspectives on future development.
Collapse
|
5
|
Wang S, Zhang P, He F, Wang JG, Sun JZ, Li ZL, Yi B, Xi J, Mao YP, Hou Q, Yuan DL, Zhang ZD, Liu WQ. Combination of specific single chain antibody variable fragment and siRNA has a synergistic inhibitory effect on the propagation of avian influenza virus H5N1 in chicken cells. Virol J 2014; 11:208. [PMID: 25471220 PMCID: PMC4264339 DOI: 10.1186/s12985-014-0208-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 11/17/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The avian influenza virus (AIV) causes frequent disease with high morbidity and mortality. RNA interference (RNAi) has been shown to provide an effective antiviral defense in animals, and several studies have focused on harnessing small interfering RNAs (siRNAs) to inhibit viral infections. In addition, single chain variable fragments (scFvs) contain the complete antigen binding site, and specific scFvs can bind to and neutralize viruses. RESULTS Fourteen positive scFvs were selected by the yeast two-hybrid system. Using molecular docking technology, we selected the three highest affinity scFvs for further functional validation. Results of indirect ELISA and IFA showed that all three scFvs could bind to FJ13 strain and had neutralizing activity, decreasing the viral infectivity markedly. Chicken fibroblastic DF-1 cells were transfected with scFvs in combination with siRNA-NP604 (an siRNA of anti-AIV NP protein previously reported). Following infection with FJ13 virus, copy numbers of the virus were significantly reduced from 12 h to at least 60 h post-infection compared to that achieved in cells transfected with scFv or siRNA-NP604 separately. CONCLUSIONS A novel combination of antiviral siRNAs expressed in chicken cells and chicken antibody single-chain variable fragments (scFvs) secreted from the cells has a synergistic inhibitory effect on the avian influenza viral proliferation in vitro. Intracellular application of scFvs and anti-viral siRNA may provide a new approach to influenza prevention and treatment.
Collapse
Affiliation(s)
- Shuang Wang
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Peng Zhang
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Fei He
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Ji-Gui Wang
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Jia-Zeng Sun
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Zhi-Li Li
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Bao Yi
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Ji Xi
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Ya-Ping Mao
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Qiang Hou
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Dao-Li Yuan
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Zi-Ding Zhang
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Wei-Quan Liu
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
6
|
Krejcova L, Hynek D, Kopel P, Merlos Rodrigo MA, Adam V, Hubalek J, Babula P, Trnkova L, Kizek R. Development of a magnetic electrochemical bar code array for point mutation detection in the H5N1 neuraminidase gene. Viruses 2013; 5:1719-39. [PMID: 23860384 PMCID: PMC3738958 DOI: 10.3390/v5071719] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 06/10/2013] [Accepted: 07/01/2013] [Indexed: 12/29/2022] Open
Abstract
Since its first official detection in the Guangdong province of China in 1996, the highly pathogenic avian influenza virus of H5N1 subtype (HPAI H5N1) has reportedly been the cause of outbreaks in birds in more than 60 countries, 24 of which were European. The main issue is still to develop effective antiviral drugs. In this case, single point mutation in the neuraminidase gene, which causes resistance to antiviral drug and is, therefore, subjected to many studies including ours, was observed. In this study, we developed magnetic electrochemical bar code array for detection of single point mutations (mismatches in up to four nucleotides) in H5N1 neuraminidase gene. Paramagnetic particles Dynabeads® with covalently bound oligo (dT)25 were used as a tool for isolation of complementary H5N1 chains (H5N1 Zhejin, China and Aichi). For detection of H5N1 chains, oligonucleotide chains of lengths of 12 (+5 adenine) or 28 (+5 adenine) bp labeled with quantum dots (CdS, ZnS and/or PbS) were used. Individual probes hybridized to target molecules specifically with efficiency higher than 60%. The obtained signals identified mutations present in the sequence. Suggested experimental procedure allows obtaining further information from the redox signals of nucleic acids. Moreover, the used biosensor exhibits sequence specificity and low limits of detection of subnanogram quantities of target nucleic acids.
Collapse
Affiliation(s)
- Ludmila Krejcova
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic; E-Mails: (L.K.); (D.H.); (P.K.); (M.A.M.R.); (V.A.); (L.T.)
| | - David Hynek
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic; E-Mails: (L.K.); (D.H.); (P.K.); (M.A.M.R.); (V.A.); (L.T.)
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic; E-Mails: (J.H.); (P.B.)
| | - Pavel Kopel
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic; E-Mails: (L.K.); (D.H.); (P.K.); (M.A.M.R.); (V.A.); (L.T.)
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic; E-Mails: (J.H.); (P.B.)
| | - Miguel Angel Merlos Rodrigo
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic; E-Mails: (L.K.); (D.H.); (P.K.); (M.A.M.R.); (V.A.); (L.T.)
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic; E-Mails: (J.H.); (P.B.)
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic; E-Mails: (L.K.); (D.H.); (P.K.); (M.A.M.R.); (V.A.); (L.T.)
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic; E-Mails: (J.H.); (P.B.)
| | - Jaromir Hubalek
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic; E-Mails: (J.H.); (P.B.)
- Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 10, Brno CZ-616 00, Czech Republic
| | - Petr Babula
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic; E-Mails: (J.H.); (P.B.)
- Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackeho 1-3, Brno CZ-612 42, Czech Republic
| | - Libuse Trnkova
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic; E-Mails: (L.K.); (D.H.); (P.K.); (M.A.M.R.); (V.A.); (L.T.)
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic; E-Mails: (J.H.); (P.B.)
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlarska 2, Brno CZ-611 37, Czech Republic
| | - Rene Kizek
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic; E-Mails: (L.K.); (D.H.); (P.K.); (M.A.M.R.); (V.A.); (L.T.)
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic; E-Mails: (J.H.); (P.B.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +420-545-133-350; Fax: +420-545-212-044
| |
Collapse
|
7
|
Hayden FG. Newer influenza antivirals, biotherapeutics and combinations. Influenza Other Respir Viruses 2013; 7 Suppl 1:63-75. [PMID: 23279899 PMCID: PMC5978626 DOI: 10.1111/irv.12045] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
This summary provides an overview of investigational antiviral agents for influenza and of future directions for development of influenza therapeutics. While progress in developing clinically useful antiviral agents for influenza has been generally slow, especially with respect to seriously ill and high-risk patients, important clinical studies of intravenous neuraminidase inhibitors, antibodies and drug combinations are currently in progress. The current decade offers the promise of developing small molecular weight inhibitors with novel mechanisms of action, including host-directed therapies, new biotherapeutics and drug combinations, that should provide more effective antiviral therapies and help mitigate the problem of antiviral resistance. Immunomodulatory interventions also offer promise but need to be based on better understanding of influenza pathogenesis, particularly in seriously ill patients. The development of combination interventions, immunomodulators and host-directed therapies presents unique clinical trial design and regulatory hurdles that remain to be addressed.
Collapse
Affiliation(s)
- Frederick G Hayden
- Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.
| |
Collapse
|
8
|
Levina AS, Repkova MN, Ismagilov ZR, Shikina NV, Malygin EG, Mazurkova NA, Zinov'ev VV, Evdokimov AA, Baiborodin SI, Zarytova VF. High-performance method for specific effect on nucleic acids in cells using TiO2~DNA nanocomposites. Sci Rep 2012; 2:756. [PMID: 23091696 PMCID: PMC3477653 DOI: 10.1038/srep00756] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 09/27/2012] [Indexed: 11/11/2022] Open
Abstract
Nanoparticles are used to solve the current drug delivery problem. We present a high-performance method for efficient and selective action on nucleic acid target in cells using unique TiO2·PL-DNA nanocomposites (polylysine-containing DNA fragments noncovalently immobilized onto TiO2 nanoparticles capable of transferring DNA). These nanocomposites were used for inhibition of human influenza A (H3N2) virus replication in infected MDCK cells. They showed a low toxicity (TC50 ≈ 1800 μg/ml) and a high antiviral activity (>99.9% inhibition of the virus replication). The specificity factor (antisense effect) appeared to depend on the delivery system of DNA fragments. This factor for nanocomposites is ten-times higher than for DNA in the presence of lipofectamine. IC50 for nanocomposites was estimated to be 1.5 μg/ml (30 nM for DNA), so its selectivity index was calculated as ~1200. Thus, the proposed nanocomposites are prospective for therapeutic application.
Collapse
Affiliation(s)
- Asya S Levina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Giannecchini S, Wise HM, Digard P, Clausi V, Del Poggetto E, Vesco L, Puzelli S, Donatelli I, Azzi A. Packaging signals in the 5'-ends of influenza virus PA, PB1, and PB2 genes as potential targets to develop nucleic-acid based antiviral molecules. Antiviral Res 2011; 92:64-72. [PMID: 21741410 DOI: 10.1016/j.antiviral.2011.06.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 06/10/2011] [Accepted: 06/21/2011] [Indexed: 11/16/2022]
Abstract
In a previous study a 15-mer phosphorothioate oligonucleotide (S-ON) derived from the packaging signal in the 5' end of segment 1 (PB2) of influenza A virus (designated 5-15b) proved markedly inhibitory to virus replication. Here we investigated whether analogous inhibitory S-ONs targeting the 5' end of segments 2 (PB1) and 3 (PA) could be identified and whether viral resistance to S-ONs can be developed. Similar to our earlier result, 20-mer S-ONs reproducing the 5' ends of segments 2 or 3 (complementary to the 3'-coding regions of PB1 and PA, respectively) exerted a powerful antiviral activity against a variety of influenza A virus subtypes in MDCK cells. Serial passage of the A/Taiwan/1/86 H1N1 strain in the presence of S-ON 5-15b or its antisense as5-15b analogue showed that mutant viruses with reduced susceptibility to the S-ON could indeed be generated, although the resistant viruses displayed reduced replicative fitness. Sequencing the resistant viruses identified mutations in the PB1, PB2, PA and M1 genes. Introduction of these changes into the A/PR/8/34 H1N1 strain by reverse genetics, suggested that alterations to RNA function in the packaging regions of segments 2 and 3 were important in developing resistance to S-ON inhibition. However, many of the other sequence changes induced by S-ON treatment were markedly deleterious to virus fitness. We conclude that packaging signals in the influenza A virus polymerase segments provide feasible targets for nucleic acid-based antivirals that may be difficult for the virus to evade through resistance mutations.
Collapse
Affiliation(s)
- Simone Giannecchini
- Virology Unit, Department of Public Health, University of Florence, Florence, Italy.
| | | | | | | | | | | | | | | | | |
Collapse
|