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Gheibi-Hayat SM, Jamialahmadi K. Antisense Oligonucleotide (AS-ODN) Technology: Principle, Mechanism and Challenges. Biotechnol Appl Biochem 2020; 68:1086-1094. [PMID: 32964539 DOI: 10.1002/bab.2028] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/12/2020] [Indexed: 12/20/2022]
Abstract
Recently, there is a hopefully tremendous interest in antisense therapeutics for clinical purposes. Single-stranded synthetic antisense oligonucleotides (As-ODNs) with monomers of chemically modified 18-21 deoxynucleotides complement the mRNA sequence in target gene. The target gene expression can be blocked because of created cleavage or disability of the mRNA by binding the As-ODNs to cognate mRNA sequences via sequence-specific hybridization. The idea of antisense therapy has become particular concerning that any sequence longer than a minimal number of nucleotides (17 for DNA and 13 for RNA) can be observed only once within the human genome. The mRNA is omnipresent more probably to manipulate compared to DNA, which results in multiple in vitro and in vivo applications for As-ODNs in the field of regulatory mechanisms of biological processes, cancer, viral infections and hereditary impairments. Although, there are uncertain clinical outcomes on the ability of this approach in treatment procedures despite achieving promising findings based on previous investigations. Accordingly, the efficacy, off-target effects, delivery are issues that should be investigated to obtain satisfactory results. In this review, we will explain the mechanism of action of As-ODNs and various types of modifications and their therapeutic purposes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Khadijeh Jamialahmadi
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Markov AV, Kupryushkin MS, Goncharova EP, Amirkhanov RN, Vasilyeva SV, Pyshnyi DV, Zenkova MA, Logashenko EB. Antiviral Activity of a New Class of Chemically Modified Antisense Oligonucleotides against Influenza А Virus. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162019060268] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Anti-Niemann Pick C1 Single-Stranded Oligonucleotides with Locked Nucleic Acids Potently Reduce Ebola Virus Infection In Vitro. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 16:686-697. [PMID: 31125846 PMCID: PMC6529764 DOI: 10.1016/j.omtn.2019.04.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 02/12/2019] [Accepted: 04/10/2019] [Indexed: 12/12/2022]
Abstract
Ebola virus is the causative agent of Ebola virus disease, a severe, often fatal illness in humans. So far, there are no US Food and Drug Administration (FDA)-approved therapeutics directed against Ebola virus. Here, we selected the host factor Niemann-Pick C1 (NPC1), which has been shown to be essential for Ebola virus entry into host cytoplasm, as a therapeutic target for suppression by locked nucleic acid-modified antisense oligonucleotides. Screening of antisense oligonucleotides in human and murine cell lines led to identification of candidates with up to 94% knockdown efficiency and 50% inhibitory concentration (IC50) values in the submicromolar range. Selected candidate oligonucleotides led to efficient NPC1 protein knockdown in vitro without alteration of cell viability. Furthermore, they did not have immune stimulatory activity in cell-based assays. Treatment of Ebola-virus-infected HeLa cells with the most promising candidates resulted in significant (>99%) virus titer reduction, indicating that antisense oligonucleotides against NPC1 are a promising therapeutic approach for treatment of Ebola virus infection.
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Studzińska S. Review on investigations of antisense oligonucleotides with the use of mass spectrometry. Talanta 2017; 176:329-343. [PMID: 28917758 DOI: 10.1016/j.talanta.2017.08.025] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/03/2017] [Accepted: 08/07/2017] [Indexed: 11/17/2022]
Abstract
Antisense oligonucleotides have been investigated as potential drugs for years. They inhibit target gene or protein expression. The present review summarizes their modifications, modes of action, and applications of liquid chromatography coupled with mass spectrometry for qualitative and quantitative analysis of these compounds. The most recent reports on a given topic were given prominence, while some early studies were reviewed in order to provide a theoretical background. The present review covers the issues of using ion-exchange chromatography, ion-pair reversed-phase high performance liquid chromatography and hydrophilic interaction chromatography for the separation of antisense oligonucleotides. The application of mass spectrometry was described with regard to the ionization type used for the determination of these potential therapeutics. Moreover, the current approaches and applications of mass spectrometry for quantitative analysis of antisense oligonucleotides and their metabolites as well as their impurities during in vitro and in vivo studies were discussed. Finally, certain conclusions and perspectives on the determination of therapeutic oligonucleotides in various samples were briefly described.
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Affiliation(s)
- Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100 Toruń, Poland.
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Studzińska S, Rola R, Buszewski B. The impact of ion-pairing reagents on the selectivity and sensitivity in the analysis of modified oligonucleotides in serum samples by liquid chromatography coupled with tandem mass spectrometry. J Pharm Biomed Anal 2017; 138:146-152. [PMID: 28208106 DOI: 10.1016/j.jpba.2017.02.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/04/2017] [Accepted: 02/06/2017] [Indexed: 11/28/2022]
Abstract
Present study highlights the usage of various ion-pairing agents and their impact on the process of separation and ionization of oligonucleotides in the fortified human serum samples. What is more, retention studies involved different stationary phases, including: octadecyl, phenyl, pentafluorophenyl groups and ligands with embedded polar groups. It was proved that retention of oligonucleotides strongly depends on the alkyl chain branching in the structure of ion pairing reagent. Furthermore ion-pairing agents build of straight alkyl chain are more easily adsorbed on the stationary phase modified with octadecyl groups, while branching of alkyl chain caused more effective adsorption of studied compounds at phenyl groups compared to octadecyl ones. The lowest limit of quantification values were obtained for 5mMN,N-dimethylbutylamine, while the highest values are characteristic for hexylamine. Moreover it was shown that a 2-fold increase of ion-pairing agent concentration results in higher LOQ. The greatest sensitivity was obtained for 2.5mMN,N-dimethylbutylamine/150mM hexafluoroisopropanol. On the other hand Hypersil GOLD aQ column was the most appropriate in terms of time and separation effectiveness. The developed method was successfully used for the determination of studied oligonucleotides and their metabolites in human serum samples. The compounds were separated in just 3.5min with high sensitivity (0.09-0.16ng).
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Affiliation(s)
- Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100 Toruń, Poland.
| | - Rafał Rola
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100 Toruń, Poland
| | - Bogusław Buszewski
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100 Toruń, Poland
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Application of hydrophilic interaction liquid chromatography coupled with mass spectrometry in the analysis of phosphorothioate oligonucleotides in serum. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1040:282-288. [PMID: 27825626 DOI: 10.1016/j.jchromb.2016.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 10/17/2016] [Accepted: 11/01/2016] [Indexed: 11/21/2022]
Abstract
Most of synthetic, modified oligonucleotides are candidates for therapeutics. Consequently, their quick, reliable and sensitive analysis has become a critical challenge for scientists. The main aim of the present study was an investigation of the influence of stationary phase type, mobile phase salt and its concentration on the separation and determination of the selected compounds by hydrophilic interaction liquid chromatography coupled with electrospray ionization tandem mass spectrometry. Three different columns, together with ammonium acetate and formate, were applied for this purpose. The separation of mixtures of phosphorothioate oligonucleotides and their synthetic metabolites was successfully performed. Moreover, an attempt to isolate these compounds from human serum samples was also made together with their separation, qualification and quantification by hydrophilic interaction liquid chromatography and tandem mass spectrometry. The method developed during the study appeared to be effective and sensitive, due to the limit of quantification which equaled 142-165ppb.
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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.
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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
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Application of a cholesterol stationary phase in the analysis of phosphorothioate oligonucleotides by means of ion pair chromatography coupled with tandem mass spectrometry. Talanta 2016; 154:270-7. [PMID: 27154674 DOI: 10.1016/j.talanta.2016.03.082] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/22/2016] [Accepted: 03/25/2016] [Indexed: 12/14/2022]
Abstract
The main aim of this study was the investigation of the influence of several ion pair reagents towards both the retention and the mass spectrometry sensitivity of phosphorothioate oligonucleotides. A cholesterol stationary phase was applied for the first time in the analysis of this group of compounds. The mobile phase composition was modified by changing the concentration and the type of amines and acetates or 1,1,1,3,3,3-hexafluoroisopropanol. It has been shown that the increase of amines concentration results in the retention factor increase for each oligonucleotide, on each adsorbent. The only exception was the mobile phase composed of triethylamine and 1,1,1,3,3,3-hexafluoroisopropanol. This is a consequence of interactions taking place between a cholesterol molecule and an alcohol. This effect was convenient when the mass spectrometry detection was applied, since it allowed an increase in the sensitivity. Moreover, optimization of the mobile phase composition and its impact on the efficiency of ionization process and on the sensitivity in mass spectrometry were also presented. The optimization of this new method, based on cholesterol stationary phase coupled with mass spectrometry detection, was finally applied for the determination of phosphorothioate oligonucleotides impurity in a real sample.
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Studzińska S, Rola R, Buszewski B. Development of a method based on ultra high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry for studying the in vitro metabolism of phosphorothioate oligonucleotides. Anal Bioanal Chem 2016; 408:1585-95. [PMID: 26758600 PMCID: PMC4737794 DOI: 10.1007/s00216-015-9266-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/15/2015] [Accepted: 12/10/2015] [Indexed: 11/29/2022]
Abstract
Ultra high performance liquid chromatography hyphenated with quadrupole time-of-flight mass spectrometry was used to determine the products of the in vitro metabolism of phosphorothioate oligonucleotides. These compounds may be used during antisense therapy as synthetic fragments of genes. For this reason, both a sample preparation method and a qualification method were developed during this study. Liquid–liquid extraction, protein or oligonucleotide precipitation, and solid-phase extraction were tested and compared in order to select the method that yielded the highest recoveries. Ion pair chromatography was used for separation while mass spectrometry was applied for metabolite identification. The influence of the type of ion pair reagent used on the resolution and sensitivity was investigated. Results indicated that a mixture of 1,1,1,3,3,3-hexafluoro-2-propanol, N,N-dimethylbutylamine, and methanol was the best mobile phase for maximizing both of these parameters. The developed method was applied to investigate the compounds that form during the incubation of phosphorothioate oligonucleotides with human liver microsomes. Metabolites with short sequences were created after 8 hours, while oligonucleotides constructed from a large number of nucleotide units were obtained after 12 hours of incubation. Moreover, regardless of the length of the polynucleotide chain, metabolites were produced by the same mechanism: enzymatic cleavage at the 3′ end of the sequence.
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Affiliation(s)
- Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100, Torun, Poland.
| | - Rafał Rola
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100, Torun, Poland
| | - Bogusław Buszewski
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100, Torun, Poland
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Small RNAs targeting the 5' end of the viral polymerase gene segments specifically interfere with influenza type A virus replication. J Biotechnol 2015; 210:85-90. [PMID: 26091771 DOI: 10.1016/j.jbiotec.2015.06.391] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/05/2015] [Accepted: 06/09/2015] [Indexed: 11/21/2022]
Abstract
Human and avian influenza A viruses, associated with seasonal epidemics and occasionally with pandemics, have a high impact on public health. The development of new antivirals to counteract the emergence of drug resistant influenza virus variants is a main concern. The aim of this study was to develop systems for the efficient and stable expression of small therapeutic RNAs into influenza virus infected cells in order to get further insights on the efficacy of nucleic acid-based antiviral strategies. To this end, lentiviral vectors expressing either microRNAs or antisense-RNAs targeting the 5' end of the PA, PB1 and PB2 influenza virus genomic sequences were generated. Derivative recombinant lentiviral particles were employed to transduce the influenza virus highly susceptible human alveolar basal epithelial A549 cells. The expression of both RNA molecules led to a reduction up to 3 logs of the viral titer when transduced A549 cells were challenged with different human and avian subtypes of influenza type A virus. Importantly, no inhibition of influenza type B virus was observed. Overall our data support the development of nucleic acid-based antiviral strategies to control human and avian influenza A virus infection.
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Studzińska S, Mounicou S, Szpunar J, Łobiński R, Buszewski B. New approach to the determination phosphorothioate oligonucleotides by ultra high performance liquid chromatography coupled with inductively coupled plasma mass spectrometry. Anal Chim Acta 2014; 855:13-20. [PMID: 25542085 DOI: 10.1016/j.aca.2014.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 12/03/2014] [Accepted: 12/04/2014] [Indexed: 01/27/2023]
Abstract
This text presents a novel method for the separation and detection of phosphorothioate oligonucleotides with the use of ion pair ultra high performance liquid chromatography coupled with inductively coupled plasma mass spectrometry The research showed that hexafluoroisopropanol/triethylamine based mobile phases may be successfully used when liquid chromatography is coupled with such elemental detection. However, the concentration of both HFIP and TEA influences the final result. The lower concentration of HFIP, the lower the background in ICP-MS and the greater the sensitivity. The method applied for the analysis of serum samples was based on high resolution inductively coupled plasma mass spectrometry. Utilization of this method allows determination of fifty times lower quantity of phosphorothioate oligonucleotides than in the case of quadrupole mass analyzer. Monitoring of (31)P may be used to quantify these compounds at the level of 80 μg L(-1), while simultaneous determination of sulfur is very useful for qualitative analysis. Moreover, the results presented in this paper demonstrate the practical applicability of coupling LC with ICP-MS in determining phosphorothioate oligonucleotides and their metabolites in serum within 7 min with a very good sensitivity. The method was linear in the concentration range between 0.2 and 3 mg L(-1). The limit of detection was in the range of 0.07 and 0.13 mg L(-1). Accuracy varied with concentration, but was in the range of 3%.
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Affiliation(s)
- Sylwia Studzińska
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100 Torun, Poland.
| | - Sandra Mounicou
- CNRS/UPPA, Laboratoire de Chimie Analytique Bio-inorganique et Environnement, UMR 5254, Hélioparc, 2 av. Pr. Angot, F-64053 Pau, France
| | - Joanna Szpunar
- CNRS/UPPA, Laboratoire de Chimie Analytique Bio-inorganique et Environnement, UMR 5254, Hélioparc, 2 av. Pr. Angot, F-64053 Pau, France
| | - Ryszard Łobiński
- CNRS/UPPA, Laboratoire de Chimie Analytique Bio-inorganique et Environnement, UMR 5254, Hélioparc, 2 av. Pr. Angot, F-64053 Pau, France
| | - Bogusław Buszewski
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100 Torun, Poland
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Zhang T, Wang TC, Zhao PS, Liang M, Gao YW, Yang ST, Qin C, Wang CY, Xia XZ. Antisense oligonucleotides targeting the RNA binding region of the NP gene inhibit replication of highly pathogenic avian influenza virus H5N1. Int Immunopharmacol 2011; 11:2057-61. [PMID: 21933722 DOI: 10.1016/j.intimp.2011.08.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2010] [Revised: 08/24/2011] [Accepted: 08/26/2011] [Indexed: 01/21/2023]
Abstract
The H5N1 avian influenza virus (AIV) causes widespread infections in bird and human respiratory tracts, and vaccines and drug therapy are limited in their effectiveness. Recent studies of AIV structures have been published and provide new targets for designing antiviral drugs such as antisense oligonucleotides (AS ODNs), which effectively inhibit gene replication. In this study, we designed and synthesized three AS ODNs (NP267, NP628, NP749) that were specific for the RNA binding region of nucleoprotein (NP) based on AIV structure. Results showed that all three AS ODNs could inhibit viral replication in MDCK cells. The NP628 showed the best antiviral effect of all through viral titers, quantitative RT-PCR and indirect immunofluorescence (IFA) assays. In addition, the liposome mediated NP628 could partially protect the mice from a lethal H5N1 influenza virus challenge. Moreover, the NP628 group had a lower viral titer and lung index in the infected mice when compared with the viral control. Our results showed that AS ODN targeting of the AIV NP gene could potently inhibit AIV H5N1 reproduction, thus, formulating a candidate for an emergent therapeutic drug for the pathogenic H5N1 influenza virus infection.
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Affiliation(s)
- Tao Zhang
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China.
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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.
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Affiliation(s)
- Simone Giannecchini
- Virology Unit, Department of Public Health, University of Florence, Florence, Italy.
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Oligonucleotides derived from the packaging signal at the 5' end of the viral PB2 segment specifically inhibit influenza virus in vitro. Arch Virol 2009; 154:821-32. [PMID: 19370391 DOI: 10.1007/s00705-009-0380-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Accepted: 04/02/2009] [Indexed: 10/20/2022]
Abstract
The development of new antiviral molecules to fight the possible emergence of influenza viruses with pandemic potential is needed. In this study, phosphorothioate oligonucleotides (S-ONs) derived from the packaging signals in the 3' and 5' ends of the viral PB2 RNA were associated with liposomes and tested against influenza virus in vitro. A 15-mer S-ON derived from the 5' end of the viral PB2 RNA, complementary to the 3' end of its coding region (nucleotides 2279-2293) and designated 5-15b, proved markedly inhibitory. The antiviral activity of 5-15b was dose- and time-dependent but was independent of the cell substrate and multiplicity of infection used. Importantly, inhibition of influenza A and B viruses required S-ONs reproducing the respective packaging signals. Furthermore, 5-15b and its antisense derivative S-ON activity did not affect intracellular accumulation of viral RNA. Confocal microscopy showed that 5-15b is clearly nucleophilic. These findings indicate that the packaging signal at the 5' end of the PB2 RNA is an interesting target for the design of new anti-influenza-virus compounds.
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Gabriel G, Nordmann A, Stein DA, Iversen PL, Klenk HD. Morpholino oligomers targeting the PB1 and NP genes enhance the survival of mice infected with highly pathogenic influenza A H7N7 virus. J Gen Virol 2008; 89:939-948. [PMID: 18343835 DOI: 10.1099/vir.0.83449-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Peptide-conjugated phosphorodiamidate morpholino oligomers (PPMO) are single-stranded nucleic acid-analogue antisense agents that enter cells readily and can reduce gene expression by steric blocking of complementary RNA (cRNA) sequences. Here, we tested a panel of PPMO designed to target conserved sequences in the RNA genome segments encoding polymerase subunits of a highly pathogenic mouse-adapted influenza A virus (SC35M; H7N7). Three PPMO, targeting the translation start site region of PB1 or NP mRNA or the 3'-terminal region of NP viral RNA (vRNA), potently inhibited virus replication in MDCK cells. Primer extension assays showed that treatment with any of the effective PPMO led to markedly reduced levels of mRNA, cRNA and vRNA. Initially, the potential toxicity of a range of intranasally administered PPMO doses was evaluated, by measuring their effect on body weight of uninfected mice. Subsequently, a non-toxic dosing regimen was used to investigate the effect of various PPMO on SC35M infection in a mouse model. Mice administered intranasal treatment of PPMO targeting the PB1-AUG region or NP vRNA, at 3 mug per dose, given once 3 h before and once 2 days after intranasal infection with 10xLD(50) of SC35M, showed a 2 log(10) reduction of viral titre in the lungs and 50 % survival for the 16 day duration of the experiment, whereas the NP-AUG-targeted PPMO treatment resulted in 30 % survival of an otherwise lethal infection. These data suggest that PPMO provide a useful reagent to investigate influenza virus molecular biology and may constitute a therapeutic strategy against highly pathogenic influenza viruses.
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Affiliation(s)
- Gülsah Gabriel
- Institute of Virology, Philipps University Marburg, Germany
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Lupfer C, Stein DA, Mourich DV, Tepper SE, Iversen PL, Pastey M. Inhibition of influenza A H3N8 virus infections in mice by morpholino oligomers. Arch Virol 2008; 153:929-37. [PMID: 18369525 DOI: 10.1007/s00705-008-0067-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Accepted: 02/09/2008] [Indexed: 11/27/2022]
Abstract
New methods to combat influenza A virus (FLUAV) in humans and animals are needed. The H3N8 subtype virus was the cause of the pandemic of 1890 and has recently undergone cross-species transmission from horses to dogs in the USA. In 2007 H3N8 spread to Australia, a continent previously devoid of equine influenza. Here, we show that antisense-peptide-conjugated phosphorodiamidate morpholino oligomers (PPMOs), delivered by intranasal administration, are able to inhibit the replication of FLUAV A/Eq/Miami/1/63 (H3N8) in mice by over 95% compared to controls. Monitoring of body weight and immune cell infiltrates in the lungs of noninfected mice indicated that PPMO treatment was not toxic at a concentration shown to be effectively antiviral in vivo. In addition, we detected a naturally occurring mutation within the PPMO target site of a viral gene that may be the cause of resistance to one of the two antisense PPMO sequences tested. These data indicate that PPMOs targeting highly conserved regions of FLUAV are promising novel therapeutic candidates.
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Affiliation(s)
- Christopher Lupfer
- Genetics Program, College of Agricultural Science, Oregon State University, Corvallis, OR 97331, USA
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Wu Y, Zhang G, Li Y, Jin Y, Dale R, Sun LQ, Wang M. Inhibition of highly pathogenic avian H5N1 influenza virus replication by RNA oligonucleotides targeting NS1 gene. Biochem Biophys Res Commun 2007; 365:369-74. [PMID: 17996729 DOI: 10.1016/j.bbrc.2007.10.196] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Accepted: 10/31/2007] [Indexed: 10/22/2022]
Abstract
H5N1 avian influenza virus (AIV) has caused widespread infections in poultry and wild birds, and has the potential to emerge as a pandemic threat to human. In order to explore novel approaches to inhibiting highly pathogenic H5N1 influenza virus infection, we have developed short RNA oligonucleotides, specific for conserved regions of the non-structural protein gene (NS1) of AIV. In vitro the hemagglutination (HA) titers in RNA oligonucleotide-treated cells were at least 5-fold lower than that of the control. In vivo, the treatment with three doses of RNA oligonucleotides protected the infected chickens from H5N1 virus-induced death at a rate of up to 87.5%. Plaque assay and real-time PCR analysis showed a significant reduction of the PFU and viral RNA level in the lung tissues of the infected animals treated with the mixed RNA oligonucleotides targeting the NS1 gene. Together, our findings revealed that the RNA oligonucleotides targeting at the AIV NS1 gene could potently inhibit avian H5N1 influenza virus reproduction and present a rationale for the further development of the RNA oligonucleotides as prophylaxis and therapy for highly pathogenic H5N1 influenza virus infection in humans.
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Affiliation(s)
- Yanhua Wu
- College of Veterinary Medicine, China Agriculture University, Beijing 100094, PR China
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Li YC, Kong LH, Cheng BZ, Li KS. Construction of influenza virus siRNA expression vectors and their inhibitory effects on multiplication of influenza virus. Avian Dis 2005; 49:562-73. [PMID: 16405000 DOI: 10.1637/7365-041205r2.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Three plasmid constructs were prepared that express small interfering RNAs (siRNAs) targeted to sequences encoding the ribonucleoprotein member, nucleoprotein (NP) and/or PA, of influenza virus genome. The antiviral properties of siRNAs against the H5N1 strain of influenza virus were studied by evaluating their capacity to silence expression of target genes as well as their effect on influenza virus-induced apoptosis in Madin-Darby canine kidney cells, chicken embryo fibroblast cells, and embryonated chicken eggs in a transient replication model. The results demonstrated that all three siRNAs expressing plasmids efficiently transcribed the short hairpin RNAs and inhibited expression of the NP or PA proteins measured by northern blot and western blot analyses, respectively, in the transfected cells. We also found that the integrated siRNA expression plasmid pEGFP/NP+PA, which we constructed for the first time to synchronously target NP and PA segments of the influenza virus genome, could more efficiently inhibit synthesis of influenza virus detected by cytopathogenic effects, hemagglutinin, and plaque-forming unit assays in the transfected cells. Furthermore, the integrated siRNA expression plasmid pEGFP/NP+PA could remarkably interrupt the cellular apoptotic course caused by influenza virus, which protected infected cells from apoptotic damage. In contrast, a control siRNA expression plasmid, pEGFP/HK, could neither inhibit the protein expression and production of influenza virus nor interrupt the cell apoptotic course mediated by influenza virus. These results demonstrate that RNA interference (RNAi) can be used to inhibit protein expression and replication of influenza virus and that RNAi treatment holds potential as a new approach to prevent avian influenza.
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Affiliation(s)
- Yao-Chen Li
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou Guangdong 515031, China
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Willems AV, Deforce DL, Van Peteghem CH, Van Bocxlaer JF. Development of a quality control method for the characterization of oligonucleotides by capillary zone electrophoresis-electrospray ionization-quadrupole time of flight-mass spectrometry. Electrophoresis 2005; 26:1412-23. [PMID: 15765471 DOI: 10.1002/elps.200406201] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A capillary zone electrophoresis-negative electrospray ionization-quadrupole time of flight-mass spectrometric method was developed for the characterization of oligonucleotides after synthesis, using model compounds. The major difficulty is the adduction of metal cations to the polyanionic backbone of the oligonucleotide sample, resulting in complex spectra and decreased sensitivity. Several approaches were investigated to circumvent this problem. Separation was performed in an ammonium carbonate buffer. During separation, the interfering metal ions were exchanged for ammonium ions, which are less tightly bound to the oligonucleotide when ionized. The influence of the addition of piperidine and imidazole or trans-1,2-diaminocyclohexane-N,N,N',N'-tetraacetic acid (CDTA) to the running buffer for further reduction of cation adduction was investigated. Addition of CDTA to the buffer system resulted in a deconvoluted spectrum with very little adducts. On-line sample stacking proved vital to preconcentrate the samples. The pH and the concentration of the ammonium carbonate buffer as well as the electrophoresis voltage were optimized to achieve the best signal response for the oligonucleotides and a maximum reduction of the cation adducts as well as a short analysis time. Finally, the sheath liquid composition was examined for further improvement of the signal. The developed method was used to analyze different oligonucleotides (5000-9200 Da) in light of its use as a final quality control method for oligonucleotides in terms of purity and sequence homogeneity of the synthesized products. In all cases, very little adducts were observed in the deconvoluted spectra, and the relative errors of the measured molecular masses ranged from 3 to 35 ppm.
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Affiliation(s)
- An V Willems
- Laboratory of Medical Biochemistry & Clinical Analysis, Ghent University, Belgium
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Arnedo A, Espuelas S, Irache JM. Albumin nanoparticles as carriers for a phosphodiester oligonucleotide. Int J Pharm 2002; 244:59-72. [PMID: 12204565 DOI: 10.1016/s0378-5173(02)00300-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The goal of this study was the evaluation of albumin nanoparticles as drug delivery systems for antisense oligonucleotides. Bovine serum albumin (BSA) nanoparticles were prepared by a coacervation process. A phosphodiester oligonucleotide was either incorporated into the matrix of the particles by incubation with the albumin prior the coacervation process or adsorbed onto the pre-formed nanoparticles. Incorporated and/or adsorbed oligonucleotide was estimated by capillary electrophoresis and fluorescence spectroscopy. The adsorbed amount of oligonucleotide was dramatically dependent on the pH of the medium. Desorption of the oligonucleotide was also affected by the pH and ionic strength of the medium. This indicated that electrostatic forces play a major role in the interaction between the oligonucleotide and the nanoparticles. When the oligonucleotide was incubated with the albumin prior to nanoparticle formation, the profile of release confirmed that a fraction was incorporated into the matrix and its release was controlled by the albumin degradation. The hybridisation capability of the oligonucleotide in both nanoparticle formulations was retained. However, only the oligonucleotide incorporated into the nanoparticle matrix was protected against enzymatic degradation.
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Affiliation(s)
- A Arnedo
- Departamento de Farmacia y Tecnología Farmacéutica, Centro Galénico, Universidad de Navarra, 31008 Pamplona, Spain
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