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Kang H, Ga YJ, Kim SH, Cho YH, Kim JW, Kim C, Yeh JY. Small interfering RNA (siRNA)-based therapeutic applications against viruses: principles, potential, and challenges. J Biomed Sci 2023; 30:88. [PMID: 37845731 PMCID: PMC10577957 DOI: 10.1186/s12929-023-00981-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/04/2023] [Indexed: 10/18/2023] Open
Abstract
RNA has emerged as a revolutionary and important tool in the battle against emerging infectious diseases, with roles extending beyond its applications in vaccines, in which it is used in the response to the COVID-19 pandemic. Since their development in the 1990s, RNA interference (RNAi) therapeutics have demonstrated potential in reducing the expression of disease-associated genes. Nucleic acid-based therapeutics, including RNAi therapies, that degrade viral genomes and rapidly adapt to viral mutations, have emerged as alternative treatments. RNAi is a robust technique frequently employed to selectively suppress gene expression in a sequence-specific manner. The swift adaptability of nucleic acid-based therapeutics such as RNAi therapies endows them with a significant advantage over other antiviral medications. For example, small interfering RNAs (siRNAs) are produced on the basis of sequence complementarity to target and degrade viral RNA, a novel approach to combat viral infections. The precision of siRNAs in targeting and degrading viral RNA has led to the development of siRNA-based treatments for diverse diseases. However, despite the promising therapeutic benefits of siRNAs, several problems, including impaired long-term protein expression, siRNA instability, off-target effects, immunological responses, and drug resistance, have been considerable obstacles to the use of siRNA-based antiviral therapies. This review provides an encompassing summary of the siRNA-based therapeutic approaches against viruses while also addressing the obstacles that need to be overcome for their effective application. Furthermore, we present potential solutions to mitigate major challenges.
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Affiliation(s)
- Hara Kang
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Yun Ji Ga
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Soo Hyun Kim
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Young Hoon Cho
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Jung Won Kim
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
- Convergence Research Center for Insect Vectors, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Chaeyeon Kim
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Jung-Yong Yeh
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea.
- Research Institute for New Drug Development, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea.
- Convergence Research Center for Insect Vectors, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea.
- KU Center for Animal Blood Medical Science, College of Veterinary Medicine, Konkuk University, 120 Neungdong-Ro, Gwangjin-Gu, Seoul, 05029, South Korea.
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Low ZY, Wong KH, Wen Yip AJ, Choo WS. The convergent evolution of influenza A virus: Implications, therapeutic strategies and what we need to know. Curr Res Microb Sci 2023; 5:100202. [PMID: 37700857 PMCID: PMC10493511 DOI: 10.1016/j.crmicr.2023.100202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023] Open
Abstract
Influenza virus infection, more commonly known as the 'cold flu', is an etiological agent that gives rise to recurrent annual flu and many pandemics. Dated back to the 1918- Spanish Flu, the influenza infection has caused the loss of many human lives and significantly impacted the economy and daily lives. Influenza virus can be classified into four different genera: influenza A-D, with the former two, influenza A and B, relevant to humans. The capacity of antigenic drift and shift in Influenza A has given rise to many novel variants, rendering vaccines and antiviral therapies useless. In light of the emergence of a novel betacoronavirus, the SARS-CoV-2, unravelling the underpinning mechanisms that support the recurrent influenza epidemics and pandemics is essential. Given the symptom similarities between influenza and covid infection, it is crucial to reiterate what we know about the influenza infection. This review aims to describe the origin and evolution of influenza infection. Apart from that, the risk factors entail the implication of co-infections, especially regarding the COVID-19 pandemic is further discussed. In addition, antiviral strategies, including the potential of drug repositioning, are discussed in this context. The diagnostic approach is also critically discussed in an effort to understand better and prepare for upcoming variants and potential influenza pandemics in the future. Lastly, this review encapsulates the challenges in curbing the influenza spread and provides insights for future directions in influenza management.
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Affiliation(s)
- Zheng Yao Low
- School of Science, Monash University Malaysia, 47500 Subang Jaya, Selangor, Malaysia
| | - Ka Heng Wong
- School of Science, Monash University Malaysia, 47500 Subang Jaya, Selangor, Malaysia
| | - Ashley Jia Wen Yip
- School of Science, Monash University Malaysia, 47500 Subang Jaya, Selangor, Malaysia
| | - Wee Sim Choo
- School of Science, Monash University Malaysia, 47500 Subang Jaya, Selangor, Malaysia
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Gencer D, Yesilyurt A, Ozsahin E, Muratoglu H, Acar Yazici Z, Demirbag Z, Nalcacioglu R. Identification of the potential matrix protein of invertebrate iridescent virus 6 (IIV6). J Invertebr Pathol 2023; 197:107885. [PMID: 36640993 DOI: 10.1016/j.jip.2023.107885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
Invertebrate iridescent virus 6 (IIV6) is a nucleocytoplasmic virus with a ∼212 kb linear dsDNA genome that encodes 215 putative open reading frames (ORFs). Proteomic analysis has revealed that the IIV6 virion consists of 54 virally encoded proteins. Interactions among the structural proteins were investigated using the yeast two-hybrid system, revealing that the protein of 415R ORF interacts reciprocally with the potential envelope protein 118L and the major capsid protein 274L. This result suggests that 415R might be a matrix protein that plays a role as a bridge between the capsid and the envelope proteins. To elucidate the function of 415R protein, we determined the localization of 415R in IIV6 structure and analyzed the properties of 415R-silenced IIV6. Specific antibodies produced against 415R protein were used to determine the location of the 415R protein in the virion structure. Both western blot hybridization and immunogold electron microscopy analyses showed that the 415R protein was found in virions treated with Triton X-100, which degrades the viral envelope. The 415R gene was silenced by the RNA interference (RNAi) technique. We used gene-specific dsRNA's to target 415R and showed that this treatment resulted in a significant drop in virus titer. Silencing 415R with dsRNA also reduced the transcription levels of other viral genes. These results provide important data on the role and location of IIV6 415R protein in the virion structure. Additionally, these results may also shed light on the identification of the homologs of 415R among the vertebrate iridoviruses.
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Affiliation(s)
- Donus Gencer
- Department of Property Protection and Security, Trabzon University, Trabzon, Turkey
| | - Aydın Yesilyurt
- Department of Medical Services and Techniques, Trabzon University, Trabzon, Turkey
| | - Emine Ozsahin
- Department of Molecular and Cellular Biology, University of Guelph, Ontario, Canada
| | - Hacer Muratoglu
- Department of Molecular Biology and Genetics, Karadeniz Technical University, Trabzon, Turkey
| | - Zihni Acar Yazici
- Clinical Microbiology Department, Recep Tayyip Erdogan University, Rize, Turkey
| | - Zihni Demirbag
- Department of Biology, Karadeniz Technical University, Trabzon, Turkey
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Abstract
Influenza A (IAV) is a major human respiratory pathogen that contributes to a significant threat to health security, worldwide. Despite vaccinations and previous immunisations through infections, humans can still be infected with influenza several times throughout their lives. This phenomenon is attributed to the antigenic changes of hemagglutinin (HA) and neuraminidase (NA) proteins in IAV via genetic mutation and reassortment, conferring antigenic drift and antigenic shift, respectively. Numerous findings indicate that slow antigenic drift and reassortment-derived antigenic shift exhibited by IAV are key processes that allow IAVs to overcome the previously acquired host immunity, which eventually leads to the annual re-emergence of seasonal influenza and even pandemic influenza, in rare occasions. As a result, current therapeutic options hit a brick wall quickly. As IAV remains a constant threat for new outbreaks worldwide, the underlying processes of genetic changes and alternative antiviral approaches for IAV should be further explored to improve disease management. In the light of the above, this review discusses the characteristics and mechanisms of mutations and reassortments that contribute to IAV's evolution. We also discuss several alternative RNA-targeting antiviral approaches, namely the CRISPR/Cas13 systems, RNA interference (RNAi), and antisense oligonucleotides (ASO) as potential antiviral approaches against IAV.
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Affiliation(s)
- Ka Heng Wong
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor DE, Malaysia
| | - Sunil K Lal
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor DE, Malaysia.
- Tropical Medicine & Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, 47500, Selangor, Malaysia.
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Abstract
INTRODUCTION Both vaccines and antiviral drugs represent the mainstay for preventing and treating influenza. However, approved M2 ion channel inhibitors, neuraminidase inhibitors, polymerase inhibitors, and various vaccines cannot meet therapeutic needs because of viral resistance. Thus, the discovery of new targets for the virus or host and the development of more effective inhibitors are essential to protect humans from the influenza virus. AREAS COVERED This review summarizes the latest progress in vaccines and antiviral drug research to prevent and treat influenza, providing the foothold for developing novel antiviral inhibitors. EXPERT OPINION Vaccines embody the most effective approach to preventing influenza virus infection, and recombinant protein vaccines show promising prospects in developing next-generation vaccines. Compounds targeting the viral components of RNA polymerase, hemagglutinin and nucleoprotein, and the modification of trusted neuraminidase inhibitors are future research directions for anti-influenza virus drugs. In addition, some host factors affect the replication of virus in vivo, which can be used to develop antiviral drugs.
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Affiliation(s)
- Jinshen Wang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou Guangdong China
| | - Yihang Sun
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou Guangdong China
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou Guangdong China.,State Key Laboratory of Organ Failure Research, Guangdong Provincial Institute of Nephrology, Southern Medical University, Nanfang Hospital, Guangzhou Guangdong China
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Ayyagari VS. Design of siRNA molecules for silencing of membrane glycoprotein, nucleocapsid phosphoprotein, and surface glycoprotein genes of SARS-CoV2. J Genet Eng Biotechnol 2022; 20:65. [PMID: 35482116 DOI: 10.1186/s43141-022-00346-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 04/18/2022] [Indexed: 12/24/2022]
Abstract
The global COVID-19 pandemic caused by SARS-CoV2 infected millions of people and resulted in more than 4 million deaths worldwide. Apart from vaccines and drugs, RNA silencing is a novel approach for treating COVID-19. In the present study, siRNAs were designed for the conserved regions targeting three structural genes, M, N, and S, from forty whole-genome sequences of SARS-CoV2 using four different software, RNAxs, siDirect, i-Score Designer, and OligoWalk. Only siRNAs which were predicted in common by all the four servers were considered for further shortlisting. A multistep filtering approach has been adopted in the present study for the final selection of siRNAs by the usage of different online tools, viz., siRNA scales, MaxExpect, DuplexFold, and SMEpred. All these web-based tools consider several important parameters for designing functional siRNAs, e.g., target-site accessibility, duplex stability, position-specific nucleotide preference, inhibitory score, thermodynamic parameters, GC content, and efficacy in cleaving the target. In addition, a few parameters like GC content and dG value of the entire siRNA were also considered for shortlisting of the siRNAs. Antisense strands were subjected to check for any off-target similarities using BLAST. Molecular docking was carried out to study the interactions of guide strands with AGO2 protein. A total of six functional siRNAs (two for each gene) have been finally selected for targeting M, N, and S genes of SARS-CoV2. The siRNAs have not shown any off-target effects, interacted with the domain(s) of AGO2 protein, and were efficacious in cleaving the target mRNA. However, the siRNAs designed in the present study need to be tested in vitro and in vivo in the future.
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Rodriguez-Salazar CA, Recalde-Reyes DP, Bedoya JP, Padilla-Sanabria L, Castaño-Osorio JC, Giraldo MI. In Vitro Inhibition of Replication of Dengue Virus Serotypes 1-4 by siRNAs Bound to Non-Toxic Liposomes. Viruses 2022; 14:339. [PMID: 35215929 PMCID: PMC8875542 DOI: 10.3390/v14020339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/29/2022] [Accepted: 02/05/2022] [Indexed: 12/04/2022] Open
Abstract
Dengue virus is a ssRNA+ flavivirus, which produces the dengue disease in humans. Currently, no specific treatment exists. siRNAs regulate gene expression and have been used systematically to silence viral genomes; however, they require controlled release. Liposomes show favorable results encapsulating siRNA for gene silencing. The objective herein was to design and evaluate in vitro siRNAs bound to liposomes that inhibit DENV replication. siRNAs were designed against DENV1-4 from conserved regions using siDirect2.0 and Web-BLOCK-iT™ RNAiDesigner; the initial in vitro evaluation was carried out through transfection into HepG2 cells. siRNA with silencing capacity was encapsulated in liposomes composed of D-Lin-MC3-DMA, DSPC, Chol. Cytotoxicity, hemolysis, pro-inflammatory cytokine release and antiviral activity were evaluated using plaque assay and RT-qPCR. A working concentration of siRNA was established at 40 nM. siRNA1, siRNA2, siRNA3.1, and siRNA4 were encapsulated in liposomes, and their siRNA delivery through liposomes led to a statistically significant decrease in viral titers, yielded no cytotoxicity or hemolysis and did not stimulate release of pro-inflammatory cytokines. Finally, liposomes were designed with siRNA against DENV, which proved to be safe in vitro.
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Affiliation(s)
- Carlos Andrés Rodriguez-Salazar
- Center of Biomedical Research, Faculty of Health Sciences, Universidad del Quindío, Armenia 630003, Colombia; (D.P.R.-R.); (J.P.B.); (L.P.-S.); (J.C.C.-O.)
- Molecular Biology and Virology Laboratory, Faculty of Medicine and Health Sciences, Corporación Universitaria Empresarial Alexander Von Humboldt, Armenia 630003, Colombia
| | - Delia Piedad Recalde-Reyes
- Center of Biomedical Research, Faculty of Health Sciences, Universidad del Quindío, Armenia 630003, Colombia; (D.P.R.-R.); (J.P.B.); (L.P.-S.); (J.C.C.-O.)
- Molecular Biology and Virology Laboratory, Faculty of Medicine and Health Sciences, Corporación Universitaria Empresarial Alexander Von Humboldt, Armenia 630003, Colombia
| | - Juan Pablo Bedoya
- Center of Biomedical Research, Faculty of Health Sciences, Universidad del Quindío, Armenia 630003, Colombia; (D.P.R.-R.); (J.P.B.); (L.P.-S.); (J.C.C.-O.)
| | - Leonardo Padilla-Sanabria
- Center of Biomedical Research, Faculty of Health Sciences, Universidad del Quindío, Armenia 630003, Colombia; (D.P.R.-R.); (J.P.B.); (L.P.-S.); (J.C.C.-O.)
| | - Jhon Carlos Castaño-Osorio
- Center of Biomedical Research, Faculty of Health Sciences, Universidad del Quindío, Armenia 630003, Colombia; (D.P.R.-R.); (J.P.B.); (L.P.-S.); (J.C.C.-O.)
| | - Maria Isabel Giraldo
- Department of Microbiology, Immunology University of Texas Medical Branch, Galveston, TX 77555, USA
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Zhang G, Ng F, Chen M. Short-hairpin RNAs delivered by recombinant adeno-associated virus inhibited the replication of influenza A viruses in vitro. Virology 2021; 564:46-52. [PMID: 34653774 DOI: 10.1016/j.virol.2021.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 11/18/2022]
Abstract
Antiviral short-hairpin RNAs (shRNAs) delivered by recombinant adeno-associated virus (rAAV) were investigated for their potential prophylactic and therapeutic applications related to the influenza A virus (IAV). To express shRNAs efficiently, an H1 promoter was inserted into the commercial rAAV2 system. The modified rAAV2 system could express shRNAs, and the purified rAAV was obtained at levels over 1013 viral genomes/ml and 1010 viral infection units/ml. The shNP-1496-n and shM2-925 delivered by rAAV could inhibit the replication of the H1N1 and H5N1 virus by targeting the conserved regions of the IAV nucleoprotein and matrix 2 genes in MDCK cells. The shNP-1496-n and shM2-925 expressed by rAAV could provide potent and long-term anti-H5N1 virus effects in rAAV-shRNA-enriched MDCK cells. Our findings provide a rational basis for developing RNA interference for the prevention and therapy of IAV infection.
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Affiliation(s)
- Gui Zhang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China.
| | - Fai Ng
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Min Chen
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
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Shah S, Chougule MB, Kotha AK, Kashikar R, Godugu C, Raghuvanshi RS, Singh SB, Srivastava S. Nanomedicine based approaches for combating viral infections. J Control Release 2021; 338:80-104. [PMID: 34375690 PMCID: PMC8526416 DOI: 10.1016/j.jconrel.2021.08.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 12/12/2022]
Abstract
Millions of people die each year from viral infections across the globe. There is an urgent need to overcome the existing gap and pitfalls of the current antiviral therapy which include increased dose and dosing frequency, bioavailability challenges, non-specificity, incidences of resistance and so on. These stumbling blocks could be effectively managed by the advent of nanomedicine. Current review emphasizes over an enhanced understanding of how different lipid, polymer and elemental based nanoformulations could be potentially and precisely used to bridle the said drawbacks in antiviral therapy. The dawn of nanotechnology meeting vaccine delivery, role of RNAi therapeutics in antiviral treatment regimen, various regulatory concerns towards clinical translation of nanomedicine along with current trends and implications including unexplored research avenues for advancing the current drug delivery have been discussed in detail.
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Affiliation(s)
- Saurabh Shah
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Mahavir Bhupal Chougule
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, University of Mississippi, MS, USA; Department Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA
| | - Arun K Kotha
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, University of Mississippi, MS, USA; Department Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA
| | - Rama Kashikar
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, University of Mississippi, MS, USA; Department Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA
| | - Chandraiah Godugu
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Rajeev Singh Raghuvanshi
- Indian Pharmacopoeia Commission, Ministry of Health & Family Welfare, Government of India, India
| | - Shashi Bala Singh
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Saurabh Srivastava
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
Zinc finger proteins are one of the most abundant families of proteins and present a wide range of structures and functions. The structural zinc ion provides the correct conformation to specifically recognize DNA, RNA and protein sequences. Zinc fingers have essential functions in transcription, protein degradation, DNA repair, cell migration, and others. Recently, reports on the extensive participation of zinc fingers in disease have been published. On the other hand, much information remains to be unravelled as many genomes and proteomes are being reported. A variety of zinc fingers have been identified; however, their functions are still under investigation. Because zinc fingers have identified functions in several diseases, they are being increasingly recognized as drug targets. The replacement of Zn(ii) by another metal ion in zinc fingers is one of the most prominent methods of inhibition. From one side, zinc fingers play roles in the toxicity mechanisms of Ni(ii), Hg(ii), Cd(ii) and others. From the other side, gold, platinum, cobalt, and selenium complexes are amongst the compounds being developed as zinc finger inhibitors for therapy. The main challenge in the design of therapeutic zinc finger inhibitors is to achieve selectivity. Recently, the design of novel compounds and elucidation of the mechanisms of zinc substitution have renewed the possibilities of selective zinc finger inhibition by metal complexes. This review aims to update the status of novel strategies to selectively target zinc finger domains by metal complexes.
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Affiliation(s)
- C Abbehausen
- Institute of Chemistry, University of Campinas - UNICAMP, P.O. Box 6154, CEP 13083-970, Campinas, São Paulo, Brazil.
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Teng D, Obika S, Ueda K, Honda T. A Small Interfering RNA Cocktail Targeting the Nucleoprotein and Large Protein Genes Suppresses Borna Disease Virus Infection. Front Microbiol 2019; 10:2781. [PMID: 31849913 PMCID: PMC6895540 DOI: 10.3389/fmicb.2019.02781] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/14/2019] [Indexed: 12/18/2022] Open
Abstract
Recently, Borna disease virus (BoDV-1)-related fatal encephalitis human cases have been reported, which highlights the potential of BoDV-1 to cause fatal human diseases. To protect the infected brain from lethal damage, it is critical to control BoDV-1 as quickly as possible. At present, antivirals against BoDV-1 are limited, and therefore, novel types of antivirals are needed. Here, we developed a novel treatment using small interfering RNAs (siRNAs) against BoDV-1. We screened several siRNAs targeting the viral N, M, and L genes for BoDV-1-reducing activity. Among the screened candidates, we chose two siRNAs that efficiently decreased the BoDV-1 load in persistently BoDV-1-infected cells to prepare a siRNA cocktail (TD-Borna) for BoDV-1 treatment. TD-Borna successfully reduced the BoDV-1 load without enhancing the risk of emergence of escape mutants. The combination of TD-Borna and T-705, a previously reported antiviral agent against bornaviruses, decreased the BoDV-1 load more efficiently than TD-Borna or T-705 alone. Furthermore, TD-Borna efficiently decreased the BoDV-1 load in BoDV-1-infected neuron-derived cells, in which T-705 did not decrease the viral load. Overall, we developed a novel antiviral candidate against BoDV-1, TD-Borna, that can be used in combination with T-705 and is effective against BoDV-1 in neuron-derived cells, in which T-705 is less effective. Considering that BoDV-1 is highly neurotropic, TD-Borna can offer a promising option to improve the outcome of BoDV-1 infection.
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Affiliation(s)
- Da Teng
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Shunsuke Obika
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Keiji Ueda
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Tomoyuki Honda
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
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Brodskaia AV, Timin AS, Gorshkov AN, Muslimov AR, Bondarenko AB, Tarakanchikova YV, Zabrodskaya YA, Baranovskaya IL, Il'inskaja EV, Sakhenberg EI, Sukhorukov GB, Vasin AV. Inhibition of influenza A virus by mixed siRNAs, targeting the PA, NP, and NS genes, delivered by hybrid microcarriers. Antiviral Res 2018; 158:147-160. [PMID: 30092251 DOI: 10.1016/j.antiviral.2018.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 07/02/2018] [Accepted: 08/03/2018] [Indexed: 12/28/2022]
Abstract
In the present study, a highly effective carrier system has been developed for the delivery of antiviral siRNA mixtures. The developed hybrid microcarriers, made of biodegradable polymers and SiO2 nanostructures, more efficiently mediate cellular uptake of siRNA than commercially available liposome-based reagents and polyethyleneimine (PEI); they also demonstrate low in vitro toxicity and protection of siRNA from RNase degradation. A series of siRNA designs (targeting the most conserved regions of three influenza A virus (IAV) genes: NP, NS, and PA) were screened in vitro using RT-qPCR, ELISA analysis, and hemagglutination assay. Based on the results of screening, the three most effective siRNAs (PA-1630, NP-717, and NS-777) were selected for in situ encapsulation into hybrid microcarriers. It was revealed that pre-treatment of cells with a mixture of PA-1630, NP-717, and NS-777 siRNAs, delivered by hybrid microcarriers, provided stronger inhibition of viral M1 mRNA expression and control of NP protein level, after viral infection, than single pre-treatment by any of three encapsulated siRNAs used in the study. Moreover, the effective inhibition of replication in several IAV subtypes (H1N1, H1N1pdm, H5N2, and H7N9) using a cocktail of the three selected siRNAs, delivered by our hybrid capsules to the cells, was achieved. In conclusion, we have developed a proof-of-principle which shows that our hybrid microcarrier technology (utilizing a therapeutic siRNA cocktail) may represent a promising approach in anti-influenza therapy.
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Affiliation(s)
- Aleksandra V Brodskaia
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251, St. Petersburg, Russian Federation.
| | - Alexander S Timin
- RASA Center, National Research Tomsk Polytechnic University, Lenin Avenue, 30, 634050, Tomsk, Russian Federation; First I. P. Pavlov State Medical University of St. Petersburg, Lev Tolstoy str., 6/8, 197022, St. Petersburg, Russian Federation.
| | - Andrey N Gorshkov
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; Institute of Cytology, Russian Academy of Sciences, Tikhoretsky ave. 4, 194064, St. Petersburg, Russian Federation
| | - Albert R Muslimov
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; First I. P. Pavlov State Medical University of St. Petersburg, Lev Tolstoy str., 6/8, 197022, St. Petersburg, Russian Federation
| | - Andrei B Bondarenko
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; St. Petersburg State University, Vasilyevsky Island, Liniya 16-ya, 29, 199178, St. Petersburg, Russian Federation
| | - Yana V Tarakanchikova
- Saratov State University, Astrakhanskaya Street 83, 410012, Saratov, Russian Federation
| | - Yana A Zabrodskaya
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; Petersburg Nuclear Physics Institute in Honor of B. P. Konstantinov, National Research Center "Kurchatov Institute", 188300, Gatchina, Russian Federation
| | - Irina L Baranovskaya
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251, St. Petersburg, Russian Federation
| | - Eugenia V Il'inskaja
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation
| | - Elena I Sakhenberg
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; Institute of Cytology, Russian Academy of Sciences, Tikhoretsky ave. 4, 194064, St. Petersburg, Russian Federation
| | - Gleb B Sukhorukov
- Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251, St. Petersburg, Russian Federation; School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Andrey V Vasin
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popova str., 15/17, 197376, St. Petersburg, Russian Federation; Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251, St. Petersburg, Russian Federation; St. Petersburg State Chemical Pharmaceutical Academy, Prof. Popova str., 14 A, 197376, St. Petersburg, Russian Federation.
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Han L. Research progress of siRNA in anti-influenza viral infection. Infection International 2018; 7:50-5. [DOI: 10.2478/ii-2018-0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AbstractThe harms of seasonal flu and global pandemic influenza have generally attracted attention. However, the currently administered influenza drugs and flu vaccines have certain limitations. Since the discovery of the small interfering RNA (siRNA) and its mediated RNA interference process, this molecule has been widely used in the study of anti-influenza viral infections because of its high specificity and strong selectivity. The results provided new concepts for the prevention and treatment of influenza virus. However, the siRNA still faces an enormous challenge despite extensive studies on this molecule. The research progress of siRNA in anti-influenza viral infection was reviewed in this study.
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Huang DTN, Lu CY, Shao PL, Chang LY, Wang JY, Chang YH, Lai MJ, Chi YH, Huang LM. In vivo inhibition of influenza A virus replication by RNA interference targeting the PB2 subunit via intratracheal delivery. PLoS One 2017; 12:e0174523. [PMID: 28380007 PMCID: PMC5381882 DOI: 10.1371/journal.pone.0174523] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/10/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Influenza virus infection is a major threat to human health. Small interfering RNA (siRNA) is a promising approach for the prevention and treatment of viral infections. In this study, we constructed a series of DNA vector-based short hairpin RNAs (shRNAs) that target various genes of the influenza A virus using the polymerase III U6-RNA promoter to prevent influenza virus infection in vitro and in a mouse model. RESULTS Three sets of DNA vector-based shRNA, two targeting genes encoding the polymerase acidic protein (PA) and one targeting polymerase basic protein 2 (PB2), efficiently inhibited the replication of influenza virus A/WSN/33(H1N1) in vitro. We also successfully prevented influenza virus A/WSN/33(H1N1) infection in a C57BL/6 mouse model by intratracheal delivery of anti-PB2 shRNA. CONCLUSIONS Our findings suggest that the PB2-targeting shRNA plasmid showed potential for use as an RNAi-based therapeutic for influenza virus infection.
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Affiliation(s)
- Daniel Tsung-Ning Huang
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- * E-mail: (LMH); (DTH)
| | - Chun-Yi Lu
- Department of Pediatrics, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pei-Lan Shao
- Department of Pediatrics, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Luan-Yin Chang
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jin-Yuan Wang
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | - Yi-Hsuan Chang
- Department of Pediatrics, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Mei-Ju Lai
- Department of Pediatrics, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ya-Hui Chi
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Li-Min Huang
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
- * E-mail: (LMH); (DTH)
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Han Y, Liu Y, Zhang H, He F, Shu C, Dong L. Utilizing Selected Di- and Trinucleotides of siRNA to Predict RNAi Activity. Comput Math Methods Med 2017; 2017:5043984. [PMID: 28243313 DOI: 10.1155/2017/5043984] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/15/2016] [Indexed: 02/04/2023]
Abstract
Small interfering RNAs (siRNAs) induce posttranscriptional gene silencing in various organisms. siRNAs targeted to different positions of the same gene show different effectiveness; hence, predicting siRNA activity is a crucial step. In this paper, we developed and evaluated a powerful tool named “siRNApred” with a new mixed feature set to predict siRNA activity. To improve the prediction accuracy, we proposed 2-3NTs as our new features. A Random Forest siRNA activity prediction model was constructed using the feature set selected by our proposed Binary Search Feature Selection (BSFS) algorithm. Experimental data demonstrated that the binding site of the Argonaute protein correlates with siRNA activity. “siRNApred” is effective for selecting active siRNAs, and the prediction results demonstrate that our method can outperform other current siRNA activity prediction methods in terms of prediction accuracy.
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