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Berzal-Herranz A, Romero-López C. Aptamers' Potential to Fill Therapeutic and Diagnostic Gaps. Pharmaceuticals (Basel) 2024; 17:105. [PMID: 38256938 PMCID: PMC10818422 DOI: 10.3390/ph17010105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
More than 30 years ago, in 1990, three independent research groups published several papers demonstrating that genetics could be performed in vitro in the absence of living organisms or cells [...].
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Affiliation(s)
- Alfredo Berzal-Herranz
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas. PTS Granada, Av. del Conocimiento 17, 18016 Granada, Spain
| | - Cristina Romero-López
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas. PTS Granada, Av. del Conocimiento 17, 18016 Granada, Spain
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2
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Torres-Vázquez B, María de Lucas A, García-Crespo C, Antonio García-Martín J, Fragoso A, Fernández-Algar M, Perales C, Domingo E, Moreno M, Briones C. In vitro selection of high affinity DNA and RNA aptamers that detect hepatitis C virus core protein of genotypes 1 to 4 and inhibit virus production in cell culture. J Mol Biol 2022; 434:167501. [DOI: 10.1016/j.jmb.2022.167501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 02/07/2023]
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3
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Chen XF, Zhao X, Yang Z. Aptamer-Based Antibacterial and Antiviral Therapy against Infectious Diseases. J Med Chem 2021; 64:17601-17626. [PMID: 34854680 DOI: 10.1021/acs.jmedchem.1c01567] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA molecules selected in vitro that can bind to a broad range of targets with high affinity and specificity. As promising alternatives to conventional anti-infective agents, aptamers have gradually revealed their potential in the combat against infectious diseases. This article provides an overview on the state-of-art of aptamer-based antibacterial and antiviral therapeutic strategies. Diverse aptamers targeting pathogen-related components or whole pathogenic cells are summarized according to the species of microorganisms. These aptamers exhibited remarkable in vitro and/or in vivo inhibitory effect for pathogenic invasion, enzymatic activities, or viral replication, even for some highly drug-resistant strains and biofilms. Aptamer-mediated drug delivery and controlled drug release strategies are also included herein. Critical technical barriers of therapeutic aptamers are briefly discussed, followed by some future perspectives for their implementation into clinical utility.
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Affiliation(s)
- Xiao-Fei Chen
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou 510070, PR China
| | - Xin Zhao
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou 510070, PR China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, PR China.,Guangzhou Laboratory, Guangzhou 510320, PR China.,Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, Guangzhou 510005, PR China
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4
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Aptamers in Virology-A Consolidated Review of the Most Recent Advancements in Diagnosis and Therapy. Pharmaceutics 2021; 13:pharmaceutics13101646. [PMID: 34683938 PMCID: PMC8540715 DOI: 10.3390/pharmaceutics13101646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 01/05/2023] Open
Abstract
The use of short oligonucleotide or peptide molecules as target-specific aptamers has recently garnered substantial attention in the field of the detection and treatment of viral infections. Based on their high affinity and high specificity to desired targets, their use is on the rise to replace antibodies for the detection of viruses and viral antigens. Furthermore, aptamers inhibit intracellular viral transcription and translation, in addition to restricting viral entry into host cells. This has opened up a plethora of new targets for the research and development of novel vaccines against viruses. Here, we discuss the advances made in aptamer technology for viral diagnosis and therapy in the past decade.
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5
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Kim TH, Lee SW. Aptamers for Anti-Viral Therapeutics and Diagnostics. Int J Mol Sci 2021; 22:ijms22084168. [PMID: 33920628 PMCID: PMC8074132 DOI: 10.3390/ijms22084168] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/16/2022] Open
Abstract
Viral infections cause a host of fatal diseases and seriously affect every form of life from bacteria to humans. Although most viral infections can receive appropriate treatment thereby limiting damage to life and livelihood with modern medicine and early diagnosis, new types of viral infections are continuously emerging that need to be properly and timely treated. As time is the most important factor in the progress of many deadly viral diseases, early detection becomes of paramount importance for effective treatment. Aptamers are small oligonucleotide molecules made by the systematic evolution of ligands by exponential enrichment (SELEX). Aptamers are characterized by being able to specifically bind to a target, much like antibodies. However, unlike antibodies, aptamers are easily synthesized, modified, and are able to target a wider range of substances, including proteins and carbohydrates. With these advantages in mind, many studies on aptamer-based viral diagnosis and treatments are currently in progress. The use of aptamers for viral diagnosis requires a system that recognizes the binding of viral molecules to aptamers in samples of blood, serum, plasma, or in virus-infected cells. From a therapeutic perspective, aptamers target viral particles or host cell receptors to prevent the interaction between the virus and host cells or target intracellular viral proteins to interrupt the life cycle of the virus within infected cells. In this paper, we review recent attempts to use aptamers for the diagnosis and treatment of various viral infections.
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Affiliation(s)
- Tae-Hyeong Kim
- Department of Molecular Biology, Dankook University, Cheonan 31116, Korea;
| | - Seong-Wook Lee
- Department of Life Convergence, Research Institute of Advanced Omics, Dankook University, Yongin 16890, Korea
- R&D Center, Rznomics Inc., Seongnam 13486, Korea
- Correspondence:
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6
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Two Examples of RNA Aptamers with Antiviral Activity. Are Aptamers the Wished Antiviral Drugs? Pharmaceuticals (Basel) 2020; 13:ph13080157. [PMID: 32707768 PMCID: PMC7463695 DOI: 10.3390/ph13080157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/03/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023] Open
Abstract
The current Covid-19 pandemic has pointed out some major deficiencies of the even most advanced societies to fight against viral RNA infections. Once more, it has been demonstrated that there is a lack of efficient drugs to control RNA viruses. Aptamers are efficient ligands of a great variety of molecules including proteins and nucleic acids. Their specificity and mechanism of action make them very promising molecules for interfering with the function encoded in viral RNA genomes. RNA viruses store essential information in conserved structural genomic RNA elements that promote important steps for the consecution of the infective cycle. This work describes two well documented examples of RNA aptamers with antiviral activity against highly conserved structural domains of the HIV-1 and HCV RNA genome, respectively, performed in our laboratory. They are two good examples that illustrate the potential of the aptamers to fill the therapeutic gaps in the fight against RNA viruses.
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7
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Berzal-Herranz A, Romero-López C, Berzal-Herranz B, Ramos-Lorente S. Potential of the Other Genetic Information Coded by the Viral RNA Genomes as Antiviral Target. Pharmaceuticals (Basel) 2019; 12:ph12010038. [PMID: 30871174 PMCID: PMC6469156 DOI: 10.3390/ph12010038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/07/2019] [Accepted: 03/10/2019] [Indexed: 02/05/2023] Open
Abstract
In addition to the protein coding information, viral RNA genomes code functional information in structurally conserved units termed functional RNA domains. These RNA domains play essential roles in the viral cycle (e.g., replication and translation). Understanding the molecular mechanisms behind their function is essential to understanding the viral infective cycle. Further, interfering with the function of the genomic RNA domains offers a potential means of developing antiviral strategies. Aptamers are good candidates for targeting structural RNA domains. Besides its potential as therapeutics, aptamers also provide an excellent tool for investigating the functionality of RNA domains in viral genomes. This review briefly summarizes the work carried out in our laboratory aimed at the structural and functional characterization of the hepatitis C virus (HCV) genomic RNA domains. It also describes the efforts we carried out for the development of antiviral aptamers targeting specific genomic domains of the HCV and the human immunodeficiency virus type-1 (HIV-1).
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Affiliation(s)
- Alfredo Berzal-Herranz
- Instituto de Parasitología y Biomedicina López-Neyra, (IPBLN-CSIC); Av. del Conocimiento 17, PTS Granada, Armilla, 18016 Granada, Spain.
| | - Cristina Romero-López
- Instituto de Parasitología y Biomedicina López-Neyra, (IPBLN-CSIC); Av. del Conocimiento 17, PTS Granada, Armilla, 18016 Granada, Spain.
| | - Beatriz Berzal-Herranz
- Instituto de Parasitología y Biomedicina López-Neyra, (IPBLN-CSIC); Av. del Conocimiento 17, PTS Granada, Armilla, 18016 Granada, Spain.
| | - Sara Ramos-Lorente
- Instituto de Parasitología y Biomedicina López-Neyra, (IPBLN-CSIC); Av. del Conocimiento 17, PTS Granada, Armilla, 18016 Granada, Spain.
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8
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Fernández-Sanlés A, Ríos-Marco P, Romero-López C, Berzal-Herranz A. Functional Information Stored in the Conserved Structural RNA Domains of Flavivirus Genomes. Front Microbiol 2017; 8:546. [PMID: 28421048 PMCID: PMC5376627 DOI: 10.3389/fmicb.2017.00546] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/15/2017] [Indexed: 02/05/2023] Open
Abstract
The genus Flavivirus comprises a large number of small, positive-sense single-stranded, RNA viruses able to replicate in the cytoplasm of certain arthropod and/or vertebrate host cells. The genus, which has some 70 member species, includes a number of emerging and re-emerging pathogens responsible for outbreaks of human disease around the world, such as the West Nile, dengue, Zika, yellow fever, Japanese encephalitis, St. Louis encephalitis, and tick-borne encephalitis viruses. Like other RNA viruses, flaviviruses have a compact RNA genome that efficiently stores all the information required for the completion of the infectious cycle. The efficiency of this storage system is attributable to supracoding elements, i.e., discrete, structural units with essential functions. This information storage system overlaps and complements the protein coding sequence and is highly conserved across the genus. It therefore offers interesting potential targets for novel therapeutic strategies. This review summarizes our knowledge of the features of flavivirus genome functional RNA domains. It also provides a brief overview of the main achievements reported in the design of antiviral nucleic acid-based drugs targeting functional genomic RNA elements.
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Affiliation(s)
- Alba Fernández-Sanlés
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas (IPBLN-CSIC)Granada, Spain
| | - Pablo Ríos-Marco
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas (IPBLN-CSIC)Granada, Spain
| | - Cristina Romero-López
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas (IPBLN-CSIC)Granada, Spain
| | - Alfredo Berzal-Herranz
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas (IPBLN-CSIC)Granada, Spain
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9
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González VM, Martín ME, Fernández G, García-Sacristán A. Use of Aptamers as Diagnostics Tools and Antiviral Agents for Human Viruses. Pharmaceuticals (Basel) 2016; 9:ph9040078. [PMID: 27999271 PMCID: PMC5198053 DOI: 10.3390/ph9040078] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/12/2016] [Accepted: 12/13/2016] [Indexed: 02/05/2023] Open
Abstract
Appropriate diagnosis is the key factor for treatment of viral diseases. Time is the most important factor in rapidly developing and epidemiologically dangerous diseases, such as influenza, Ebola and SARS. Chronic viral diseases such as HIV-1 or HCV are asymptomatic or oligosymptomatic and the therapeutic success mainly depends on early detection of the infective agent. Over the last years, aptamer technology has been used in a wide range of diagnostic and therapeutic applications and, concretely, several strategies are currently being explored using aptamers against virus proteins. From a diagnostics point of view, aptamers are being designed as a bio-recognition element in diagnostic systems to detect viral proteins either in the blood (serum or plasma) or into infected cells. Another potential use of aptamers is for therapeutics of viral infections, interfering in the interaction between the virus and the host using aptamers targeting host-cell matrix receptors, or attacking the virus intracellularly, targeting proteins implicated in the viral replication cycle. In this paper, we review how aptamers working against viral proteins are discovered, with a focus on recent advances that improve the aptamers' properties as a real tool for viral infection detection and treatment.
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Affiliation(s)
- Víctor M González
- Departamento de Bioquímica-Investigación, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)-Hospital Ramón y Cajal, 28034 Madrid, Spain.
| | - M Elena Martín
- Departamento de Bioquímica-Investigación, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)-Hospital Ramón y Cajal, 28034 Madrid, Spain.
| | - Gerónimo Fernández
- Aptus Biotech SL, c/Faraday, 7, Parque Científico de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Ana García-Sacristán
- Aptus Biotech SL, c/Faraday, 7, Parque Científico de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain.
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10
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The cis-acting replication element of the Hepatitis C virus genome recruits host factors that influence viral replication and translation. Sci Rep 2016; 6:25729. [PMID: 27165399 PMCID: PMC4863150 DOI: 10.1038/srep25729] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/21/2016] [Indexed: 02/08/2023] Open
Abstract
The cis-acting replication element (CRE) of the hepatitis C virus (HCV) RNA genome is a region of conserved sequence and structure at the 3′ end of the open reading frame. It participates in a complex and dynamic RNA-RNA interaction network involving, among others, essential functional domains of the 3′ untranslated region and the internal ribosome entry site located at the 5′ terminus of the viral genome. A proper balance between all these contacts is critical for the control of viral replication and translation, and is likely dependent on host factors. Proteomic analyses identified a collection of proteins from a hepatoma cell line as CRE-interacting candidates. A large fraction of these were RNA-binding proteins sharing highly conserved RNA recognition motifs. The vast majority of these proteins were validated by bioinformatics tools that consider RNA-protein secondary structure. Further characterization of representative proteins indicated that hnRNPA1 and HMGB1 exerted negative effects on viral replication in a subgenomic HCV replication system. Furthermore DDX5 and PARP1 knockdown reduced the HCV IRES activity, suggesting an involvement of these proteins in HCV translation. The identification of all these host factors provides new clues regarding the function of the CRE during viral cycle progression.
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Marton S, Cleto F, Krieger MA, Cardoso J. Isolation of an Aptamer that Binds Specifically to E. coli. PLoS One 2016; 11:e0153637. [PMID: 27104834 PMCID: PMC4841571 DOI: 10.1371/journal.pone.0153637] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/01/2016] [Indexed: 01/24/2023] Open
Abstract
Escherichia coli is a bacterial species found ubiquitously in the intestinal flora of animals, although pathogenic variants cause major public health problems. Aptamers are short oligonucleotides that bind to targets with high affinity and specificity, and have great potential for use in diagnostics and therapy. We used cell-based Systematic Evolution of Ligands by EXponential enrichment (cell-SELEX) to isolate four single stranded DNA (ssDNA) aptamers that bind strongly to E. coli cells (ATCC generic strain 25922), with Kd values in the nanomolar range. Fluorescently labeled aptamers label the surface of E. coli cells, as viewed by fluorescent microscopy. Specificity tests with twelve different bacterial species showed that one of the aptamers–called P12-31—is highly specific for E. coli. Importantly, this aptamer binds to Meningitis/sepsis associated E. coli (MNEC) clinical isolates, and is the first aptamer described with potential for use in the diagnosis of MNEC-borne pathologies.
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Affiliation(s)
- Soledad Marton
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
| | - Fernanda Cleto
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
| | - Marco Aurélio Krieger
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil.,Instituto Carlos Chagas, Laboratório de Genomica Functional, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
| | - Josiane Cardoso
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
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Lee CH, Lee SH, Kim JH, Noh YH, Noh GJ, Lee SW. Pharmacokinetics of a Cholesterol-conjugated Aptamer Against the Hepatitis C Virus (HCV) NS5B Protein. MOLECULAR THERAPY. NUCLEIC ACIDS 2015; 4:e254. [PMID: 26440598 PMCID: PMC4881758 DOI: 10.1038/mtna.2015.30] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/25/2015] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) is the major cause of progressive liver disease such as chronic hepatitis, cirrhosis, and hepatocellular carcinoma. Previously, we reported that a 29 nucleotide-long 2'-F pyrimidine modified RNA aptamer against the HCV nonstructural protein 5B efficiently inhibited HCV replication and suppressed HCV infectious virus particle formation in a cell culture system. In this study, we modified this aptamer through conjugation of cholesterol for in vivo availability. This cholesterol-conjugated aptamer (chol-aptamer) efficiently entered the cell and inhibited HCV RNA replication, without any alteration in gene expression profiling including innate immune response-related genes. Moreover, systemic administration of the chol-aptamer was well tolerated without any abnormalities in mice. To evaluate the pharmacokinetics of the chol-aptamer in vivo, dose proportionality, bioavailability, and pharmacokinetic parameters were evaluated by noncompartmental analyses in normal BALB/c mice. Population analysis was performed using nonlinear mixed effects modeling. Moreover, the pharmacokinetics of two different routes (intravenous, IV, versus intraperitoneal, IP) were compared. Cholesterol conjugation showed dose proportionality, extended the time that the aptamer was in the plasma, and enhanced aptamer exposure to the body. Noticeably, the IV route was more suitable than the IP route due to the chol-aptamer remaining in the plasma for a longer period of time.
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Affiliation(s)
- Chang Ho Lee
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, and Research Institute of Advanced Omics, Dankook University, Yongin, Korea
| | - Soo-Han Lee
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Konkuk University, Seoul, Korea
| | - Ji Hyun Kim
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, and Research Institute of Advanced Omics, Dankook University, Yongin, Korea
| | - Yook-Hwan Noh
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California, San Francisco, California, USA
| | - Gyu-Jeong Noh
- Department of Anesthesiology and Pain Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Clinical Pharmacology and Therapeutics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seong-Wook Lee
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, and Research Institute of Advanced Omics, Dankook University, Yongin, Korea
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RNA Aptamers as Molecular Tools to Study the Functionality of the Hepatitis C Virus CRE Region. Molecules 2015; 20:16030-47. [PMID: 26364632 PMCID: PMC6331917 DOI: 10.3390/molecules200916030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 08/25/2015] [Accepted: 08/29/2015] [Indexed: 02/05/2023] Open
Abstract
Background: Hepatitis C virus (HCV) contains a (+) ssRNA genome with highly conserved structural, functional RNA domains, many of them with unknown roles for the consecution of the viral cycle. Such genomic domains are candidate therapeutic targets. This study reports the functional characterization of a set of aptamers targeting the cis-acting replication element (CRE) of the HCV genome, an essential partner for viral replication and also involved in the regulation of protein synthesis. Methods: Forty-four aptamers were tested for their ability to interfere with viral RNA synthesis in a subgenomic replicon system. Some of the most efficient inhibitors were further evaluated for their potential to affect the recruitment of the HCV RNA-dependent RNA polymerase (NS5B) and the viral translation in cell culture. Results: Four aptamers emerged as potent inhibitors of HCV replication by direct interaction with functional RNA domains of the CRE, yielding a decrease in the HCV RNA levels higher than 90%. Concomitantly, one of them also induced a significant increase in viral translation (>50%). The three remaining aptamers efficiently competed with the binding of the NS5B protein to the CRE. Conclusions: Present findings confirm the potential of the CRE as an anti-HCV target and support the use of aptamers as molecular tools for investigating the functionality of RNA domains in viral genomes.
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Tuplin A, Struthers M, Cook J, Bentley K, Evans DJ. Inhibition of HCV translation by disrupting the structure and interactions of the viral CRE and 3' X-tail. Nucleic Acids Res 2015; 43:2914-26. [PMID: 25712095 PMCID: PMC4357731 DOI: 10.1093/nar/gkv142] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A phylogenetically conserved RNA structure within the NS5B coding region of hepatitis C virus functions as a cis-replicating element (CRE). Integrity of this CRE, designated SL9266 (alternatively 5BSL3.2), is critical for genome replication. SL9266 forms the core of an extended pseudoknot, designated SL9266/PK, involving long distance RNA–RNA interactions between unpaired loops of SL9266 and distal regions of the genome. Previous studies demonstrated that SL9266/PK is dynamic, with ‘open’ and ‘closed’ conformations predicted to have distinct functions during virus replication. Using a combination of site-directed mutagenesis and locked nucleic acids (LNA) complementary to defined domains of SL9266 and its interacting regions, we have explored the influence of this structure on genome translation and replication. We demonstrate that LNAs which block formation of the closed conformation inhibit genome translation. Inhibition was at least partly independent of the initiation mechanism, whether driven by homologous or heterologous internal ribosome entry sites or from a capped message. Provision of SL9266/PK in trans relieved translational inhibition, and mutational analysis implied a mechanism in which the closed conformation recruits a cellular factor that would otherwise suppresses translation. We propose that SL9266/PK functions as a temporal switch, modulating the mutually incompatible processes of translation and replication.
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Affiliation(s)
- Andrew Tuplin
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Madeleine Struthers
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Jonathan Cook
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Kirsten Bentley
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - David J Evans
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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15
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Lee CH, Kim JH, Lee SW. Prospects for nucleic acid-based therapeutics against hepatitis C virus. World J Gastroenterol 2013; 19:8949-8962. [PMID: 24379620 PMCID: PMC3870548 DOI: 10.3748/wjg.v19.i47.8949] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 11/10/2013] [Accepted: 11/30/2013] [Indexed: 02/06/2023] Open
Abstract
In this review, we discuss recent advances in nucleic acid-based therapeutic technologies that target hepatitis C virus (HCV) infection. Because the HCV genome is present exclusively in RNA form during replication, various nucleic acid-based therapeutic approaches targeting the HCV genome, such as ribozymes, aptamers, siRNAs, and antisense oligonucleotides, have been suggested as potential tools against HCV. Nucleic acids are potentially immunogenic and typically require a delivery tool to be utilized as therapeutics. These limitations have hampered the clinical development of nucleic acid-based therapeutics. However, despite these limitations, nucleic acid-based therapeutics has clinical value due to their great specificity, easy and large-scale synthesis with chemical methods, and pharmaceutical flexibility. Moreover, nucleic acid therapeutics are expected to broaden the range of targetable molecules essential for the HCV replication cycle, and therefore they may prove to be more effective than existing therapeutics, such as interferon-α and ribavirin combination therapy. This review focuses on the current status and future prospects of ribozymes, aptamers, siRNAs, and antisense oligonucleotides as therapeutic reagents against HCV.
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Aptamer-based therapeutics: new approaches to combat human viral diseases. Pharmaceuticals (Basel) 2013; 6:1507-42. [PMID: 24287493 PMCID: PMC3873675 DOI: 10.3390/ph6121507] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 11/12/2013] [Accepted: 11/15/2013] [Indexed: 12/18/2022] Open
Abstract
Viruses replicate inside the cells of an organism and continuously evolve to contend with an ever-changing environment. Many life-threatening diseases, such as AIDS, SARS, hepatitis and some cancers, are caused by viruses. Because viruses have small genome sizes and high mutability, there is currently a lack of and an urgent need for effective treatment for many viral pathogens. One approach that has recently received much attention is aptamer-based therapeutics. Aptamer technology has high target specificity and versatility, i.e., any viral proteins could potentially be targeted. Consequently, new aptamer-based therapeutics have the potential to lead a revolution in the development of anti-infective drugs. Additionally, aptamers can potentially bind any targets and any pathogen that is theoretically amenable to rapid targeting, making aptamers invaluable tools for treating a wide range of diseases. This review will provide a broad, comprehensive overview of viral therapies that use aptamers. The aptamer selection process will be described, followed by an explanation of the potential for treating virus infection by aptamers. Recent progress and prospective use of aptamers against a large variety of human viruses, such as HIV-1, HCV, HBV, SCoV, Rabies virus, HPV, HSV and influenza virus, with particular focus on clinical development of aptamers will also be described. Finally, we will discuss the challenges of advancing antiviral aptamer therapeutics and prospects for future success.
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Romero-López C, Berzal-Herranz A. Unmasking the information encoded as structural motifs of viral RNA genomes: a potential antiviral target. Rev Med Virol 2013; 23:340-54. [PMID: 23983005 PMCID: PMC7169113 DOI: 10.1002/rmv.1756] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 07/23/2013] [Accepted: 07/24/2013] [Indexed: 02/05/2023]
Abstract
RNA viruses show enormous capacity to evolve and adapt to new cellular and molecular contexts, a consequence of mutations arising from errors made by viral RNA-dependent RNA polymerase during replication. Sequence variation must occur, however, without compromising functions essential for the completion of the viral cycle. RNA viruses are safeguarded in this respect by their genome carrying conserved information that does not code only for proteins but also for the formation of structurally conserved RNA domains that directly perform these critical functions. Functional RNA domains can interact with other regions of the viral genome and/or proteins to direct viral translation, replication and encapsidation. They are therefore potential targets for novel therapeutic strategies. This review summarises our knowledge of the functional RNA domains of human RNA viruses and examines the achievements made in the design of antiviral compounds that interfere with their folding and therefore their function.
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Affiliation(s)
- Cristina Romero-López
- Instituto de Parasitología y Biomedicina 'López-Neyra', IPBLN-CSIC, PTS Granada, Armilla, Granada, Spain
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