1
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Jin Q, Yao Z, Liu F, Di Y, Gao J, Zhang X. The protective effect of a combination of human intracellular and extracellular antibodies against the highly pathogenic avian influenza H5N1 virus. Hum Vaccin Immunother 2022; 18:2035118. [PMID: 35240918 PMCID: PMC9009906 DOI: 10.1080/21645515.2022.2035118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background The highly pathogenic avian influenza H5N1 virus poses a serious threat to humans. Due to its antiviral activity, antibody-based therapy is one of the possible effective countermeasures. Here, a combination of intracellular and extracellular human antibodies was investigated and showed an improved protective effect. Methods The scFv4F5-based intracellular antibody vectors and IgG1 extracellular antibody were constructed and expressed, respectively, and the sensitivity, specificity, and affinity of these antibodies were determined in vitro. In vivo, the protective effect of IgG1 and the combination of antibodies were tested respectively. Furthermore, the dynamics of viral replication, the related cytokines and apoptosis-related proteins were detected. Results In vitro, the expressed intracellular antibody inhibited H5N1 virus propagation and the IgG1 exhibited high specificity, sensitivity, and affinity against the H5N1 virus. In vivo, the extracellular antibody could inhibit viral propagation in a dose-dependent manner. The protective effect of IgG1 was good in a mouse model, and the survival was 100% at a dose of 15 mg/kg under infection with 100 TCID50 virus. When the intracellular antibody was pre-transfected in combination with IgG1, it had a better protective effect. The survival was 16.67% under treatment with IgG1 alone and up to 83.33% under treatment with the combination of antibodies when challenge of 500 TCID 50 virus. Furthermore, the levels of cytokines IFN-γ, IL-6, IL-10 and some apoptosis-related proteins increased. Conclusions This antibody combination technique could be used as an appropriate and powerful alternative to antiviral therapy.
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Affiliation(s)
- Qiu Jin
- Key Laboratory of Antibody Technology, National Health Commission, Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Basic Medicine, Jiangsu College of Nursing, Huai`an, Jiangsu, China
| | - Zhangyu Yao
- Key Laboratory of Antibody Technology, National Health Commission, Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Head and Neck Surgery, Jiangsu Cancer Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu, China
| | - Fangzhou Liu
- Department of Head and Neck Surgery, Jiangsu Cancer Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yaxuan Di
- Key Laboratory of Antibody Technology, National Health Commission, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jun Gao
- Key Laboratory of Antibody Technology, National Health Commission, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiao Zhang
- Key Laboratory of Antibody Technology, National Health Commission, Nanjing Medical University, Nanjing, Jiangsu, China
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2
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Repkova M, Levina A, Ismagilov Z, Mazurkova N, Mazurkov O, Zarytova V. Effective Inhibition of Newly Emerged A/H7N9 Virus with Oligonucleotides Targeted to Conserved Regions of the Virus Genome. Nucleic Acid Ther 2021; 31:436-442. [PMID: 34665651 DOI: 10.1089/nat.2021.0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Newly emerged highly pathogenic A/H7N9 viruses with pandemic potential are effectively transmitted from birds to humans and require the development of novel antiviral drugs. For the first time, we studied the in vitro and in vivo antiviral activity against A/H7N9 of oligodeoxyribonucleotides (ODNs), which were delivered into the cells in the proposed TiO2-based nanocomposites (TiO2∼ODN). The highest inhibition of A/H7N9 in vitro (∼400-fold) and efficient, sequence-specific, and dose-dependent protection (up to 100%) of A/H7N9-infected mice was revealed when ODN was targeted to the conserved terminal 3'-noncoding region of viral (-)RNA. After the treatment with ODN, the virus titer values in the lungs of mice decreased by several orders of magnitude. The TiO2∼ODN nanocomposite did not show toxicity in mice under the treatment conditions. The proposed approach for effective inhibition of the A/H7N9 can be tested against other viruses, for example, new emerging influenza viruses and coronaviruses with pandemic potential.
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Affiliation(s)
- Marina Repkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Asya Levina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Zinfer Ismagilov
- Institute of Catalysis, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia Mazurkova
- FBRI State Research Center of Virology and Biotechnology "Vector", Novosibirsk, Russia
| | - Oleg Mazurkov
- FBRI State Research Center of Virology and Biotechnology "Vector", Novosibirsk, Russia
| | - Valentina Zarytova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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3
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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.
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4
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Guo J, Gao X, Liu B, Li Y, Liu W, Lu J, Liu C, Xue R, Li X. Mouse adaptation of the H9N2 avian influenza virus causes the downregulation of genes related to innate immune responses and ubiquitin-mediated proteolysis in mice. Med Microbiol Immunol 2020; 209:151-161. [PMID: 31982962 PMCID: PMC7087327 DOI: 10.1007/s00430-020-00656-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/06/2020] [Indexed: 11/25/2022]
Abstract
H9N2 avian influenza viruses sporadically infect humans worldwide. These viruses have also contributed internal genes to H5N1, H5N6, H7N9, and H10N8 viruses, which have been isolated from humans with infections and are a substantial public health threat. To investigate the potential pathogenic mechanism of the H9N2 virus, we performed serial lung-to-lung passage of an avirulent H9N2 avian influenza virus (A/Chicken/Shandong/416/2016 [SD/416]) in mice to increase the pathogenicity of this virus. We generated a mouse-adapted (MA) virus that exhibited increased viral titers in the lungs, caused severe lung damage in mice, and induced body weight loss in mice; however, the avirulent parental virus did not cause any clinical symptoms in infected mice. Global gene expression analysis was performed and indicated that the transcriptional responses of these viruses were distinct. The lungs of mice infected with the MA virus exhibited the downregulation of genes related to innate immunity and ubiquitin-mediated proteolysis, which was not seen in infections with the avirulent parental virus. These data indicated that the MA virus might evade immune surveillance and changed its replication capacity to increase the viral replication level and pathogenicity. Our study demonstrates that host factors play an important role in the adaptive evolution of influenza virus in new hosts.
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Affiliation(s)
- Jing Guo
- College of Agricultural, Liaocheng University, No. 1 Hunan Road, Shandong, Liaocheng, 252000, People's Republic of China. .,State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China.
| | - Xinxin Gao
- College of Agricultural, Liaocheng University, No. 1 Hunan Road, Shandong, Liaocheng, 252000, People's Republic of China
| | - Baotao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, People's Republic of China
| | - Yubao Li
- College of Agricultural, Liaocheng University, No. 1 Hunan Road, Shandong, Liaocheng, 252000, People's Republic of China
| | - Wenqiang Liu
- College of Agricultural, Liaocheng University, No. 1 Hunan Road, Shandong, Liaocheng, 252000, People's Republic of China
| | - Jianbiao Lu
- College of Agricultural, Liaocheng University, No. 1 Hunan Road, Shandong, Liaocheng, 252000, People's Republic of China
| | - Cheng Liu
- College of Agricultural, Liaocheng University, No. 1 Hunan Road, Shandong, Liaocheng, 252000, People's Republic of China
| | - Rui Xue
- College of Agricultural, Liaocheng University, No. 1 Hunan Road, Shandong, Liaocheng, 252000, People's Republic of China
| | - Xuyong Li
- College of Agricultural, Liaocheng University, No. 1 Hunan Road, Shandong, Liaocheng, 252000, People's Republic of China.
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5
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Role of cytosine-phosphate-guanosine-Oligodeoxynucleotides (CpG ODNs) as adjuvant in poultry vaccines. WORLD POULTRY SCI J 2019. [DOI: 10.1017/s0043933918000508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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6
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Michalak P, Soszynska-Jozwiak M, Biala E, Moss WN, Kesy J, Szutkowska B, Lenartowicz E, Kierzek R, Kierzek E. Secondary structure of the segment 5 genomic RNA of influenza A virus and its application for designing antisense oligonucleotides. Sci Rep 2019; 9:3801. [PMID: 30846846 PMCID: PMC6406010 DOI: 10.1038/s41598-019-40443-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/12/2019] [Indexed: 12/20/2022] Open
Abstract
Influenza virus causes seasonal epidemics and dangerous pandemic outbreaks. It is a single stranded (-)RNA virus with a segmented genome. Eight segments of genomic viral RNA (vRNA) form the virion, which are then transcribed and replicated in host cells. The secondary structure of vRNA is an important regulator of virus biology and can be a target for finding new therapeutics. In this paper, the secondary structure of segment 5 vRNA is determined based on chemical mapping data, free energy minimization and structure-sequence conservation analysis for type A influenza. The revealed secondary structure has circular folding with a previously reported panhandle motif and distinct novel domains. Conservations of base pairs is 87% on average with many structural motifs that are highly conserved. Isoenergetic microarray mapping was used to additionally validate secondary structure and to discover regions that easy bind short oligonucleotides. Antisense oligonucleotides, which were designed based on modeled secondary structure and microarray mapping, inhibit influenza A virus proliferation in MDCK cells. The most potent oligonucleotides lowered virus titer by ~90%. These results define universal for type A structured regions that could be important for virus function, as well as new targets for antisense therapeutics.
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Affiliation(s)
- Paula Michalak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Marta Soszynska-Jozwiak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Ewa Biala
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Julita Kesy
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Barbara Szutkowska
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Elzbieta Lenartowicz
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland.
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7
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Kesy J, Patil KM, Kumar SR, Shu Z, Yong HY, Zimmermann L, Ong AAL, Toh DFK, Krishna MS, Yang L, Decout JL, Luo D, Prabakaran M, Chen G, Kierzek E. A Short Chemically Modified dsRNA-Binding PNA (dbPNA) Inhibits Influenza Viral Replication by Targeting Viral RNA Panhandle Structure. Bioconjug Chem 2019; 30:931-943. [PMID: 30721034 DOI: 10.1021/acs.bioconjchem.9b00039] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNAs play critical roles in diverse catalytic and regulatory biological processes and are emerging as important disease biomarkers and therapeutic targets. Thus, developing chemical compounds for targeting any desired RNA structures has great potential in biomedical applications. The viral and cellular RNA sequence and structure databases lay the groundwork for developing RNA-binding chemical ligands through the recognition of both RNA sequence and RNA structure. Influenza A virion consists of eight segments of negative-strand viral RNA (vRNA), all of which contain a highly conserved panhandle duplex structure formed between the first 13 nucleotides at the 5' end and the last 12 nucleotides at the 3' end. Here, we report our binding and cell culture anti-influenza assays of a short 10-mer chemically modified double-stranded RNA (dsRNA)-binding peptide nucleic acid (PNA) designed to bind to the panhandle duplex structure through novel major-groove PNA·RNA2 triplex formation. We demonstrated that incorporation of chemically modified PNA residues thio-pseudoisocytosine (L) and guanidine-modified 5-methyl cytosine (Q) previously developed by us facilitates the sequence-specific recognition of Watson-Crick G-C and C-G pairs, respectively, at physiologically relevant conditions. Significantly, the chemically modified dsRNA-binding PNA (dbPNA) shows selective binding to the dsRNA region in panhandle structure over a single-stranded RNA (ssRNA) and a dsDNA containing the same sequence. The panhandle structure is not accessible to traditional antisense DNA or RNA with a similar length. Conjugation of the dbPNA with an aminosugar neamine enhances the cellular uptake. We observed that 2-5 μM dbPNA-neamine conjugate results in a significant reduction of viral replication. In addition, the 10-mer dbPNA inhibits innate immune receptor RIG-I binding to panhandle structure and thus RIG-I ATPase activity. These findings would provide the foundation for developing novel dbPNAs for the detection of influenza viral RNAs and therapeutics with optimal antiviral and immunomodulatory activities.
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Affiliation(s)
- Julita Kesy
- Institute of Bioorganic Chemistry, Polish Academy of Sciences , Noskowskiego 12/14 , 61-704 Poznan , Poland
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | | | - Zhiyu Shu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Hui Yee Yong
- Lee Kong Chian School of Medicine , Nanyang Technological University , EMB 03-07, 59 Nanyang Drive , 636921 , Singapore.,NTU Institute of Structural Biology , Nanyang Technological University , EMB 06-01, 59 Nanyang Drive , 636921 , Singapore.,School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , 636921 , Singapore
| | - Louis Zimmermann
- Département de Pharmacochimie Moléculaire , University Grenoble Alpes, CNRS, ICMG FR 2607, UMR 5063 , 470 Rue de la Chimie , F-38041 Grenoble , France
| | - Alan Ann Lerk Ong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Lixia Yang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Jean-Luc Decout
- Département de Pharmacochimie Moléculaire , University Grenoble Alpes, CNRS, ICMG FR 2607, UMR 5063 , 470 Rue de la Chimie , F-38041 Grenoble , France
| | - Dahai Luo
- Lee Kong Chian School of Medicine , Nanyang Technological University , EMB 03-07, 59 Nanyang Drive , 636921 , Singapore.,NTU Institute of Structural Biology , Nanyang Technological University , EMB 06-01, 59 Nanyang Drive , 636921 , Singapore
| | - Mookkan Prabakaran
- Temasek Life Science Laboratory, 1 Research Link , National University of Singapore , 117604 , Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences , Noskowskiego 12/14 , 61-704 Poznan , Poland
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8
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Soszynska-Jozwiak M, Michalak P, Moss WN, Kierzek R, Kesy J, Kierzek E. Influenza virus segment 5 (+)RNA - secondary structure and new targets for antiviral strategies. Sci Rep 2017; 7:15041. [PMID: 29118447 PMCID: PMC5678188 DOI: 10.1038/s41598-017-15317-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/24/2017] [Indexed: 01/05/2023] Open
Abstract
Influenza A virus is a threat for humans due to seasonal epidemics and occasional pandemics. This virus can generate new strains that are dangerous through nucleotide/amino acid changes or through segmental recombination of the viral RNA genome. It is important to gain wider knowledge about influenza virus RNA to create new strategies for drugs that will inhibit its spread. Here, we present the experimentally determined secondary structure of the influenza segment 5 (+)RNA. Two RNAs were studied: the full-length segment 5 (+)RNA and a shorter construct containing only the coding region. Chemical mapping data combined with thermodynamic energy minimization were used in secondary structure prediction. Sequence/structure analysis showed that the determined secondary structure of segment 5 (+)RNA is mostly conserved between influenza virus type A strains. Microarray mapping and RNase H cleavage identified accessible sites for oligonucleotides in the revealed secondary structure of segment 5 (+)RNA. Antisense oligonucleotides were designed based on the secondary structure model and tested against influenza virus in cell culture. Inhibition of influenza virus proliferation was noticed, identifying good targets for antisense strategies. Effective target sites fall within two domains, which are conserved in sequence/structure indicating their importance to the virus.
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Affiliation(s)
- Marta Soszynska-Jozwiak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Paula Michalak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, United States of America
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Julita Kesy
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland.
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9
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Lin J, Lee JHJ, Paramasivam K, Pathak E, Wang Z, Pramono ZAD, Lim B, Wee KB, Surana U. Induced-Decay of Glycine Decarboxylase Transcripts as an Anticancer Therapeutic Strategy for Non-Small-Cell Lung Carcinoma. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 9:263-273. [PMID: 29246305 PMCID: PMC5675722 DOI: 10.1016/j.omtn.2017.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 10/03/2017] [Accepted: 10/03/2017] [Indexed: 01/04/2023]
Abstract
Self-renewing tumor-initiating cells (TICs) are thought to be responsible for tumor recurrence and chemo-resistance. Glycine decarboxylase, encoded by the GLDC gene, is reported to be overexpressed in TIC-enriched primary non-small-cell lung carcinoma (NSCLC). GLDC is a component of the mitochondrial glycine cleavage system, and its high expression is required for growth and tumorigenic capacity. Currently, there are no therapeutic agents against GLDC. As a therapeutic strategy, we have designed and tested splicing-modulating steric hindrance antisense oligonucleotides (shAONs) that efficiently induce exon skipping (half maximal inhibitory concentration [IC50] at 3.5–7 nM), disrupt the open reading frame (ORF) of GLDC transcript (predisposing it for nonsense-mediated decay), halt cell proliferation, and prevent colony formation in both A549 cells and TIC-enriched NSCLC tumor sphere cells (TS32). One candidate shAON causes 60% inhibition of tumor growth in mice transplanted with TS32. Thus, our shAONs candidates can effectively inhibit the expression of NSCLC-associated metabolic enzyme GLDC and may have promising therapeutic implications.
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Affiliation(s)
- Jing Lin
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Singapore 138671, Singapore; Institute of High Performance Computing, A*STAR, 1 Fusionopolis Way, Singapore 138632, Singapore
| | - Jia Hui Jane Lee
- Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore 138672, Singapore
| | - Kathirvel Paramasivam
- Department of Pharmacology, National University of Singapore, 16 Medical Drive, Singapore 117660, Singapore
| | - Elina Pathak
- Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore 138672, Singapore
| | - Zhenxun Wang
- Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore 138672, Singapore
| | | | - Bing Lim
- Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore 138672, Singapore
| | - Keng Boon Wee
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Singapore 138671, Singapore; Institute of High Performance Computing, A*STAR, 1 Fusionopolis Way, Singapore 138632, Singapore.
| | - Uttam Surana
- Department of Pharmacology, National University of Singapore, 16 Medical Drive, Singapore 117660, Singapore; Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, Singapore 138668, Singapore; Institute of Molecular and Cellular Biology, A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore.
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10
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Lenartowicz E, Kesy J, Ruszkowska A, Soszynska-Jozwiak M, Michalak P, Moss WN, Turner DH, Kierzek R, Kierzek E. Self-Folding of Naked Segment 8 Genomic RNA of Influenza A Virus. PLoS One 2016; 11:e0148281. [PMID: 26848969 PMCID: PMC4743857 DOI: 10.1371/journal.pone.0148281] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/15/2016] [Indexed: 01/10/2023] Open
Abstract
Influenza A is a negative sense RNA virus that kills hundreds of thousands of humans each year. Base pairing in RNA is very favorable, but possibilities for RNA secondary structure of the influenza genomic RNA have not been investigated. This work presents the first experimentally-derived exploration of potential secondary structure in an influenza A naked (protein-free) genomic segment. Favorable folding regions are revealed by in vitro chemical structure mapping, thermodynamics, bioinformatics, and binding to isoenergetic microarrays of an entire natural sequence of the 875 nt segment 8 vRNA and of a smaller fragment. Segment 8 has thermodynamically stable and evolutionarily conserved RNA structure and encodes essential viral proteins NEP and NS1. This suggests that vRNA self-folding may generate helixes and loops that are important at one or more stages of the influenza life cycle.
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Affiliation(s)
- Elzbieta Lenartowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Julita Kesy
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Agnieszka Ruszkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Marta Soszynska-Jozwiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Paula Michalak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Walter N. Moss
- Department of Chemistry, University of Rochester, Rochester, New York, 14627, United States of America
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, Rochester, New York, 14627, United States of America
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
- * E-mail:
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11
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Discovery of Influenza A Virus Sequence Pairs and Their Combinations for Simultaneous Heterosubtypic Targeting that Hedge against Antiviral Resistance. PLoS Comput Biol 2016; 12:e1004663. [PMID: 26771381 PMCID: PMC4714944 DOI: 10.1371/journal.pcbi.1004663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 11/17/2015] [Indexed: 12/27/2022] Open
Abstract
The multiple circulating human influenza A virus subtypes coupled with the perpetual genomic mutations and segment reassortment events challenge the development of effective therapeutics. The capacity to drug most RNAs motivates the investigation on viral RNA targets. 123,060 segment sequences from 35,938 strains of the most prevalent subtypes also infecting humans-H1N1, 2009 pandemic H1N1, H3N2, H5N1 and H7N9, were used to identify 1,183 conserved RNA target sequences (≥15-mer) in the internal segments. 100% theoretical coverage in simultaneous heterosubtypic targeting is achieved by pairing specific sequences from the same segment ("Duals") or from two segments ("Doubles"); 1,662 Duals and 28,463 Doubles identified. By combining specific Duals and/or Doubles to form a target graph wherein an edge connecting two vertices (target sequences) represents a Dual or Double, it is possible to hedge against antiviral resistance besides maintaining 100% heterosubtypic coverage. To evaluate the hedging potential, we define the hedge-factor as the minimum number of resistant target sequences that will render the graph to become resistant i.e. eliminate all the edges therein; a target sequence or a graph is considered resistant when it cannot achieve 100% heterosubtypic coverage. In an n-vertices graph (n ≥ 3), the hedge-factor is maximal (= n- 1) when it is a complete graph i.e. every distinct pair in a graph is either a Dual or Double. Computational analyses uncover an extensive number of complete graphs of different sizes. Monte Carlo simulations show that the mutation counts and time elapsed for a target graph to become resistant increase with the hedge-factor. Incidentally, target sequences which were reported to reduce virus titre in experiments are included in our target graphs. The identity of target sequence pairs for heterosubtypic targeting and their combinations for hedging antiviral resistance are useful toolkits to construct target graphs for different therapeutic objectives.
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Levina AS, Repkova MN, Bessudnova EV, Filippova EI, Mazurkova NA, Zarytova VF. High antiviral effect of TiO 2·PL-DNA nanocomposites targeted to conservative regions of (-)RNA and (+)RNA of influenza A virus in cell culture. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:1166-1173. [PMID: 27826491 PMCID: PMC5082348 DOI: 10.3762/bjnano.7.108] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/20/2016] [Indexed: 05/22/2023]
Abstract
Background: The development of new antiviral drugs based on nucleic acids is under scrutiny. An important problem in this aspect is to find the most vulnerable conservative regions in the viral genome as targets for the action of these agents. Another challenge is the development of an efficient system for their delivery into cells. To solve this problem, we proposed a TiO2·PL-DNA nanocomposite consisting of titanium dioxide nanoparticles and polylysine (PL)-containing oligonucleotides. Results: The TiO2·PL-DNA nanocomposites bearing the DNA fragments targeted to different conservative regions of (-)RNA and (+)RNA of segment 5 of influenza A virus (IAV) were studied for their antiviral activity in MDCK cells infected with the H1N1, H5N1, and H3N2 virus subtypes. Within the negative strand of each of the studied strains, the efficiency of DNA fragments increased in the direction of its 3'-end. Thus, the DNA fragment aimed at the 3'-noncoding region of (-)RNA was the most efficient and inhibited the reproduction of different IAV subtypes by 3-4 orders of magnitude. Although to a lesser extent, the DNA fragments targeted at the AUG region of (+)RNA and the corresponding region of (-)RNA were also active. For all studied viral subtypes, the nanocomposites bearing the DNA fragments targeted to (-)RNA appeared to be more efficient than those containing fragments aimed at the corresponding (+)RNA regions. Conclusion: The proposed TiO2·PL-DNA nanocomposites can be successfully used for highly efficient and site-specific inhibition of influenza A virus of different subtypes. Some patterns of localization of the most vulnerable regions in IAV segment 5 for the action of DNA-based drugs were found. The (-)RNA strand of IAV segment 5 appeared to be more sensitive as compared to (+)RNA.
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Affiliation(s)
- Asya S Levina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent’eva 8, Novosibirsk, 630090, Russia
| | - Marina N Repkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent’eva 8, Novosibirsk, 630090, Russia
| | - Elena V Bessudnova
- Institute of Catalysis, Siberian Branch of Russian Academy of Sciences, pr. Lavrent’eva 5, Novosibirsk, 630090, Russia
| | - Ekaterina I Filippova
- FBRI State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk region, 630559, Russia
| | - Natalia A Mazurkova
- FBRI State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk region, 630559, Russia
| | - Valentina F Zarytova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent’eva 8, Novosibirsk, 630090, Russia
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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.
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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.
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Levina AS, Repkova MN, Mazurkova NA, Makarevich EV, Ismagilov ZR, Zarytova VF. Knockdown of different influenza A virus subtypes in cell culture by a single antisense oligodeoxyribonucleotide. Int J Antimicrob Agents 2015; 46:125-8. [PMID: 25963340 DOI: 10.1016/j.ijantimicag.2015.03.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 02/04/2015] [Accepted: 03/06/2015] [Indexed: 11/17/2022]
Abstract
Influenza is a heavy socially significant viral infection that affects humans, birds, and wild and domestic animals. The threat of existing and new highly pathogenic subtypes of influenza A virus (IAV) makes it necessary to develop an effective drug that may affect different IAV strains. For this purpose, oligodeoxynucleotides (DNA fragments) attached to titanium dioxide (TiO2) nanoparticles through a polylysine linker, forming TiO2·PL-DNA nanocomposites, that penetrated into cells without transfection agents were used. For the first time, efficient (≥99.9%) suppression of the reproduction of different subtypes of IAV, including highly pathogenic H5N1 and H1N1, was achieved. These results were obtained using the TiO2·PL-DNA nanocomposite bearing a single antisense oligodeoxynucleotide (0.1μM) targeted to the conserved 3'-noncoding region of RNA segment 5, which is common to all tested strains. Very efficient suppression of the reproduction of different subtypes of IAV was probably achieved due to the use of the proposed delivery system for oligonucleotides in the form of the TiO2·PL-DNA nanocomposites. These results indicate the possibility of creating an efficient drug to affect existing and newly emerging pathogenic IAV strains.
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Affiliation(s)
- Asya S Levina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent'eva 8, Novosibirsk 630090, Russia
| | - Marina N Repkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent'eva 8, Novosibirsk 630090, Russia
| | - Natalia A Mazurkova
- FBRI State Research Center of Virology and Biotechnology, 'Vector', Koltsovo, Novosibirsk 630559, Russia
| | - Elena V Makarevich
- FBRI State Research Center of Virology and Biotechnology, 'Vector', Koltsovo, Novosibirsk 630559, Russia
| | - Zinfer R Ismagilov
- Institute of Catalysis, Siberian Branch of Russian Academy of Sciences, pr. Lavrent'eva 5, Novosibirsk 630090, Russia
| | - Valentina F Zarytova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent'eva 8, Novosibirsk 630090, Russia.
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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.
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Affiliation(s)
- Frederick G Hayden
- Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.
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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.
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Affiliation(s)
- Asya S Levina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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