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Percze K, Tolnai ZJ, Eleveld M, Ou L, Du H, Olia AS, Kwong PD, de Jonge MI, Mészáros T. Tryptophan-like side chain holding aptamers inhibit respiratory syncytial virus infection of lung epithelial cells. Sci Rep 2023; 13:9403. [PMID: 37296186 PMCID: PMC10251311 DOI: 10.1038/s41598-023-36428-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023] Open
Abstract
Respiratory syncytial virus (RSV) is a leading cause of serious and even fatal acute lower respiratory tract infections in infants and in the elderly. Potent RSV neutralization has been achieved by antibodies that selectively bind the prefusion form of the viral fusion (F) protein. We hypothesised that similar potent neutralization could be achieved using F protein targeting aptamers. Aptamers have yet to reach their translational potential for therapeutics or diagnostics due to their short half-life and limited range of target-aptamer interactions; these shortcomings can, however, be ameliorated by application of amino acid-like side chain holding nucleotides. In this study, a stabilized version of the prefusion RSV F protein was targeted by aptamer selection using an oligonucleotide library holding a tryptophan-like side chain. This process resulted in aptamers that bound the F protein with high affinity and differentiated between its pre- and postfusion conformation. Identified aptamers inhibited viral infection of lung epithelial cells. Moreover, introduction of modified nucleotides extended aptamer half-lives. Our results suggest that targeting aptamers to the surface of viruses could yield effective drug candidates, which could keep pace with the continuously evolving pathogens.
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Affiliation(s)
- Krisztina Percze
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Zoltán János Tolnai
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Marc Eleveld
- Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Haijuan Du
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Marien I de Jonge
- Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tamás Mészáros
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary.
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Acquah C, Jeevanandam J, Tan KX, Danquah MK. Engineered Aptamers for Enhanced COVID-19 Theranostics. Cell Mol Bioeng 2021; 14:209-221. [PMID: 33488836 PMCID: PMC7810429 DOI: 10.1007/s12195-020-00664-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/08/2020] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION The 2019-novel coronavirus disease (COVID-19) is an intractable global health challenge resulting in an aberrant rate of morbidity and mortality worldwide. The mode of entry for SARS-CoV-2 into host cells occurs through clathrin-mediated endocytosis. As part of the efforts to mitigate COVID-19 infections, rapid and accurate detection methods, as well as smart vaccine and drug designs with SARS-CoV-2 targeting capabilities are critically needed. This systematic review aimed to present a good mapping between the structural and functional characteristics of aptamers and their potential applications in COVID-19 theranostics. METHODS In this study, extensive discussions into the potential development of aptameric systems as robust theranostics for rapid mitigation of the virulent SARS-CoV-2 was made. Information required for this study were extracted from a systematic review of literature in PubMed, SCOPUS, Web of Science (WOS), and other official related reports from reputable organisations. RESULTS The global burden of COVID-19 pandemic was discussed including the progress in rapid detection, repurposing of existing antiviral drugs, and development of prophylactic vaccines. Aptamers have highly specific and stable target binding characteristics which can be generated and engineered with less complexity for COVID-19 targeted theranostic applications. CONCLUSIONS There is an urgent need to develop safe innovative biomedical technologies to mitigate the dire impact of COVID-19 on public health worldwide. Research advances into aptameric systems bode well with the fact that they can be engineered for the development of effective and affordable diagnostics, therapeutics and prophylactic vaccines for SARS-CoV-2 and other infectious pathogens.
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Affiliation(s)
- Caleb Acquah
- Faculty of Health Sciences, University of Ottawa, Ottawa, ON K1H 8M5 Canada
| | - Jaison Jeevanandam
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
| | - Kei Xian Tan
- School of Materials Science & Engineering, Nanyang Technological University, Singapore, 639798 Singapore
| | - Michael K. Danquah
- Department of Chemical Engineering, University of Tennessee, Chattanooga, TN 37403 USA
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Scott TP, Nel LH. Rabies Prophylactic and Treatment Options: An In Vitro Study of siRNA- and Aptamer-Based Therapeutics. Viruses 2021; 13:881. [PMID: 34064911 PMCID: PMC8150346 DOI: 10.3390/v13050881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/28/2021] [Accepted: 05/06/2021] [Indexed: 10/26/2022] Open
Abstract
If the goal of eliminating dog-mediated human rabies by 2030 is to be achieved, effective mass dog vaccination needs to be complemented by effective prophylaxis for individuals exposed to rabies. Aptamers and short-interfering RNAs (siRNAs) have been successful in therapeutics, but few studies have investigated their potential as rabies therapeutics. In this study, siRNAs and aptamers-using a novel selection method-were developed and tested against rabies virus (RABV) in a post-infection (p.i.) scenario. Multiple means of delivery were tested for siRNAs, including the use of Lipofectamine and conjugation with the developed aptamers. One siRNA (N53) resulted in an 80.13% reduction in viral RNA, while aptamer UPRET 2.03 demonstrated a 61.3% reduction when used alone at 2 h p.i. At 24 h p.i., chimera UPRET 2.03-N8 (aptamer-siRNA) resulted in a 36.5% inhibition of viral replication. To our knowledge, this is the first study using siRNAs or aptamers that (1) demonstrated significant inhibition of RABV using an aptamer, (2) tested Lipofectamine RNAi-Max as a means for delivery, and (3) produced significant RABV inhibition at 24 h p.i. This study serves as a proof-of-concept to potentially use aptamers and siRNAs as rabies immunoglobulin (RIG) replacements or therapeutic options for RABV and provides strong evidence towards their further investigation.
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Affiliation(s)
| | - Louis Hendrik Nel
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa;
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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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Chong C, Low C. Synthetic antibody: Prospects in aquaculture biosecurity. FISH & SHELLFISH IMMUNOLOGY 2019; 86:361-367. [PMID: 30502461 DOI: 10.1016/j.fsi.2018.11.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/12/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
The emerging technology of aptamers that is also known as synthetic antibodies is rivalling antibodies research in the recent years. The unique yet important features of aptamers are advancing antibodies in diverse applications, which include disease diagnosis, prophylactic and therapeutic. The versatility of aptamer has further extended its application to function as gene expression modulator, known as synthetic riboswitches. This report reviewed and discussed the applications of aptamers technology in the biosecurity of aquaculture, the promising developments in biosensor detection for disease diagnosis as well as prophylactic and therapeutic measurements. The application of aptamers technology in immunophenotyping study of aquatic animal is highlighted. Lastly, the future perspective of aptamers in the management of aquatic animal health is discussed, special emphasis on the potential application of aptamers as synthetic riboswitches to enhance host immunity, as well as the growth performance.
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Affiliation(s)
- ChouMin Chong
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - ChenFei Low
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia.
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Therapeutic aptamers in discovery, preclinical and clinical stages. Adv Drug Deliv Rev 2018; 134:51-64. [PMID: 30125605 DOI: 10.1016/j.addr.2018.08.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/11/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023]
Abstract
The aptamer field witnessed steady growth during the past 28 years as evident from the exponentially increasing number of related publications. The field is "coming of age", but like other biomedical research areas facing a global push towards translational research to carry ideas from bench- to bedside, there is pressure to show impact for aptamers at the clinical end. Being easy-to-make, non-immunogenic, stable and high-affinity nano-ligands, aptamers are perfectly poised to move in this direction. They can specifically bind targets ranging from small molecules to complex multimeric structures, making them potentially useful in a limitless variety of therapeutic approaches. This review will summarize efforts made to accomplish the therapeutic promise of aptamers, with a focus on aptamers directly acting as therapeutic molecules, rather than those used in targeted delivery of other drugs. The review will showcase representative examples at various stages of development, covering different disease categories.
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8
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Pan Q, Luo F, Liu M, Zhang XL. Oligonucleotide aptamers: promising and powerful diagnostic and therapeutic tools for infectious diseases. J Infect 2018; 77:83-98. [PMID: 29746951 PMCID: PMC7112547 DOI: 10.1016/j.jinf.2018.04.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 01/02/2018] [Accepted: 04/08/2018] [Indexed: 12/21/2022]
Abstract
The entire human population is at risk of infectious diseases worldwide. Thus far, the diagnosis and treatment of human infectious diseases at the molecular and nanoscale levels have been extremely challenging tasks because of the lack of effective probes to identify and recognize biomarkers of pathogens. Oligonucleotide aptamers are a class of small nucleic acid ligands that are composed of single-stranded DNA (ssDNA) or RNA and act as affinity probes or molecular recognition elements for a variety of targets. These aptamers have an exciting potential for diagnose and/or treatment of specific diseases. In this review, we highlight areas where aptamers have been developed as diagnostic and therapeutic agents for both bacterial and viral infectious diseases as well as aptamer-based detection.
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Affiliation(s)
- Qin Pan
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Fengling Luo
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Min Liu
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China.
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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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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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Kadioglu O, Malczyk AH, Greten HJ, Efferth T. Aptamers as a novel tool for diagnostics and therapy. Invest New Drugs 2015; 33:513-20. [PMID: 25637166 DOI: 10.1007/s10637-015-0213-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/21/2015] [Indexed: 11/27/2022]
Abstract
Aptamers are short single-stranded DNA or RNA oligonucleotides that are capable of binding small molecules, proteins, or nucleotides with high specificity. They show a stable conformation and high binding affinity for their target molecules. There are numerous applications for aptamers in biotechnology, molecular diagnostics and targeted therapy of diseases. Their production is cheap, and they generally display lower immunogenicity than monoclonal antibodies. In the present review, we give an introduction to the preparation of aptamers and provide examples for their use in biotechnology, diagnostics and therapy of diseases.
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Affiliation(s)
- Onat Kadioglu
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Staudinger Weg 5, 55128, Mainz, Germany
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Lee CH, Lee YJ, Kim JH, Lim JH, Kim JH, Han W, Lee SH, Noh GJ, Lee SW. Inhibition of hepatitis C virus (HCV) replication by specific RNA aptamers against HCV NS5B RNA replicase. J Virol 2013; 87:7064-74. [PMID: 23596299 PMCID: PMC3676086 DOI: 10.1128/jvi.00405-13] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 04/09/2013] [Indexed: 12/15/2022] Open
Abstract
This study identified specific and avid RNA aptamers consisting of 2'-hydroxyl- or 2'-fluoropyrimidines against hepatitis C virus (HCV) NS5B replicase, an enzyme that is essential for HCV replication. These aptamers acted as potent decoys to competitively impede replicase-catalyzed RNA synthesis activity. Cytoplasmic expression of the 2'-hydroxyl aptamer efficiently inhibited HCV replicon replication in human liver cells through specific interaction with, and sequestration of, the target protein without either off-target effects or escape mutant generation. A selected 2'-fluoro aptamer could be truncated to a chemically manufacturable length of 29 nucleotides (nt), with increase in the affinity to HCV NS5B. Noticeably, transfection of the truncated aptamer efficiently suppressed HCV replication in cells without escape mutant appearance. The aptamer was further modified through conjugation of a cholesterol or galactose-polyethylene glycol ligand for in vivo availability and liver-specific delivery. The conjugated aptamer efficiently entered cells and inhibited genotype 1b subgenomic and genotype 2a full-length HCV JFH-1 RNA replication without toxicity and innate immunity induction. Importantly, a therapeutically feasible amount of the conjugated aptamer was delivered in vivo to liver tissue in mice. Therefore, cytoplasmic expression of 2'-hydroxyl aptamer or direct administration of chemically synthesized and ligand-conjugated 2'-fluoro aptamer against HCV NS5B could be a potent anti-HCV approach.
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Affiliation(s)
- Chang Ho Lee
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, Dankook University, Yongin, Republic of Korea
| | - Young Ju Lee
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, Dankook University, Yongin, Republic of Korea
| | - Ji Hyun Kim
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, Dankook University, Yongin, Republic of Korea
| | - Jong Hoon Lim
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, Dankook University, Yongin, Republic of Korea
| | - Jung-Hye Kim
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, Dankook University, Yongin, Republic of Korea
| | | | - Soo-Han Lee
- Departments of Clinical Pharmacology and Therapeutics
| | - Gyu-Jeong Noh
- Departments of Clinical Pharmacology and Therapeutics
- Anesthesiology and Pain Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seong-Wook Lee
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, Dankook University, Yongin, Republic of Korea
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Binning JM, Leung DW, Amarasinghe GK. Aptamers in virology: recent advances and challenges. Front Microbiol 2012; 3:29. [PMID: 22347221 PMCID: PMC3274758 DOI: 10.3389/fmicb.2012.00029] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 01/17/2012] [Indexed: 01/23/2023] Open
Abstract
Aptamers generated from randomized libraries of nucleic acids have found utility in a wide variety of fields and in the clinic. Aptamers can be used to target both intracellular and extracellular components, including small molecules, proteins, cells, and viruses. With recent technological developments in stringent selection and rapid isolation strategies, it is likely that aptamers will continue to make an impact as useful tools and reagents. Although many recently developed aptamers are intended for use as therapeutic and diagnostic agents, use of aptamers for basic research, including target validation, remains an active area with high potential to impact our understanding of molecular mechanisms and for drug discovery. In this brief review, we will discuss recent aptamer discoveries, their potential role in structural virology, as well as challenges and future prospects.
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Affiliation(s)
- Jennifer M Binning
- Department of Pathology and Immunology, Washington University School of Medicine St. Louis, MO, USA
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Zhu C, Wen Y, Li D, Wang L, Song S, Fan C, Willner I. Inhibition of the in vitro replication of DNA by an aptamer-protein complex in an autonomous DNA machine. Chemistry 2010; 15:11898-903. [PMID: 19777511 DOI: 10.1002/chem.200901275] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
DNA replication plays a central role in living organisms. Unregulated or uncontrollable DNA replication is well known to result in many pathological states, such as cancer, autoimmune diseases, and viral/bacterial infections. We report that an aptamer-protein complex could indirectly inhibit in vitro replication of DNA. An isothermal DNA machine based on the strand-displacement amplification is employed to support our assumption. An antithrombin aptamer sequence is rationally encoded into the DNA replication template. Once thrombin binds to the template, the as-formed aptamer-protein complexes can, in turn, become a barrier to the polymerase and inhibit the DNA replication activities in both static and dynamic modes. The inhibition is successfully confirmed by both fluorescence and gel-electrophoresis experiments. Considering the availability of a broad library of aptamers and the existence of various DNA/protein interactions, our results imply the possibility for the rational regulation of DNA replication in vivo.
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Affiliation(s)
- Changfeng Zhu
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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Yadav R, Dwivedi S, Kumar S, Chaudhury A. Trends and Perspectives of Biosensors for Food and Environmental Virology. FOOD AND ENVIRONMENTAL VIROLOGY 2010; 2. [PMCID: PMC7090531 DOI: 10.1007/s12560-010-9034-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Food and environmental virology has become a very important and interesting area of research because of food safety and public health concerns. During the last few decades, increasing foodborne diseases and environmental generated illnesses are considered to be highly challenging issues. Biosensor technology holds great promise for the healthcare market, and the security sector. Similar to clinical diagnostic tools, biosensors are being developed for the rapid, reliable, yet inexpensive identification and enumeration of pathogenic viruses which are adulterating environment, food and feed commodities. In this modern era, bio-and nano-technologies play a pivotal role in virological diagnostics of food industry, environmental and veterinary samples. This review covers the recent advances and future prospects of nanotechnology-based bioanalytical microsystems for food and environmental virology.
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Affiliation(s)
- Rakesh Yadav
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, 125001 Haryana India
| | - Sadhana Dwivedi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, 125001 Haryana India
| | - Sandeep Kumar
- Division of Biochemistry, Directorate of Rapeseed-Mustard Research, ICAR, Sewar, Bharatpur, 321303 Rajasthan India
| | - Ashok Chaudhury
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, 125001 Haryana India
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Abstract
The current standard of care for the treatment of hepatitis C virus infection, pegylated interferon-alpha and ribavirin, is costly, associated with significant side effects, and effective in only 50% of patients. There is therefore a need for the development of novel antiviral therapies. One such approach involves the application of gene silencing technologies, including antisense oligonucleotides, ribozymes, RNA interference, and aptamers. However, despite great scientific advances over the past decade, and promising in vitro data, several significant challenges continue to limit the translation of this technology to the clinical setting. This review provides a concise update of the current literature.
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Affiliation(s)
- Alexander J V Thompson
- Division of Gastroenterology/Hepatology, Duke Clinical Research Institute, Duke University, Durham, NC 27715, USA
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Kanamori H, Yuhashi K, Uchiyama Y, Kodama T, Ohnishi S. In vitro selection of RNA aptamers that bind the RNA-dependent RNA polymerase of hepatitis C virus: a possible role of GC-rich RNA motifs in NS5B binding. Virology 2009; 388:91-102. [PMID: 19328515 DOI: 10.1016/j.virol.2009.02.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 12/16/2008] [Accepted: 02/23/2009] [Indexed: 11/24/2022]
Abstract
We employed SELEX (systematic evolution of ligands by exponential enrichment) and identified high affinity RNA aptamers to the hepatitis C virus NS5B RNA-dependent RNA polymerase (RdRp). GC-rich stretches were identified in many of the aptamers. Deletion of the 5'-end single-stranded GC-stretch (CGGG) of the highest binding RNA impaired the binding and the inhibitory activity of the RNA to NS5B RdRp. The majority of the mutants with a single base substitution on the CGGG motif exhibited weaker binding to NS5B. Interestingly, the CGGG motif is present on the stem structure of the NS5B coding RNA (5BSL3.2), which is considered to be an important cis-acting replication element. The 5BSL3.2 RNA showed substantial binding to NS5B, while a point mutation on the CGGG motif reduced the binding of RNA to NS5B. These results suggest a GC-stretch to be the RNA element recognized by NS5B.
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Affiliation(s)
- Hiroshi Kanamori
- Department of Gastroenterology, University of Tokyo, Tokyo, Japan.
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18
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Abstract
For almost three decades, researchers have studied the possibility to use nucleic acids as antiviral therapeutics. In theory, compounds such as antisense oligonucleotides, ribozymes, DNAzymes, and aptamers can be designed to trigger the sequence-specific inhibition of particular mRNA transcripts, including viral genomes. However, difficulties with their efficiency, off-target effects, toxicity, delivery, and stability halted the development of nucleic acid-based therapeutics that can be used in the clinic. So far, only a single antisense drug, Vitravene for the treatment of CMV-induced retinitis in AIDS patients, has made it to the clinic. Since the discovery of RNA interference (RNAi), there is a renewed interest in the development of nucleic acid-based therapeutics. Antiviral RNAi approaches are highly effective in vitro and in animal models and are currently being tested in clinical trials. Here we give an overview of antiviral nucleic acid-based therapeutics. We focus on antisense and RNAi-based compounds that have been shown to be effective in animal model systems.
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Affiliation(s)
- Hans-Georg Kräusslich
- Hygiene Institute Department of Virology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, Heidelberg, 69120 Germany
| | - Ralf Bartenschlager
- Hygiene Institute Department of Virology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, Heidelberg, 69120 Germany
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19
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20
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Levy-Nissenbaum E, Radovic-Moreno AF, Wang AZ, Langer R, Farokhzad OC. Nanotechnology and aptamers: applications in drug delivery. Trends Biotechnol 2008; 26:442-9. [PMID: 18571753 DOI: 10.1016/j.tibtech.2008.04.006] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Revised: 04/03/2008] [Accepted: 04/18/2008] [Indexed: 12/17/2022]
Abstract
Nucleic acid ligands, also known as aptamers, are a class of macromolecules that are being used in several novel nanobiomedical applications. Aptamers are characterized by high affinity and specificity for their target, a versatile selection process, ease of chemical synthesis and a small physical size, which collectively make them attractive molecules for targeting diseases or as therapeutics. These properties will enable aptamers to facilitate innovative new nanotechnologies with applications in medicine. In this review, we will highlight recent developments in using aptamers in nanotechnology solutions for treating and diagnosing disease.
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Affiliation(s)
- Etgar Levy-Nissenbaum
- Laboratory of Nanomedicine and Biomaterials, Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis St, Boston, MA 02115, USA
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21
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Abstract
Systematic evolution of ligand by exponential enrichment (SELEX) is a new combinational chemical methodology for in vitro selection of specific aptamers. Aptamers are artificial oligonucleotide ligands with high affinity binding to target molecules. They are isolated from combinational libraries of synthetic oligonucleotide by an iterative process of affinity selection, recovery and amplification. Several properties of aptamers such as convenient affinity selection and high affinity and specificify make them widely used. Their affinity and specificity for a given protein are superior to antibodies and make it possible to isolate a matching ligand and adjust its bioactivity. This article reviews the development and potentially clinical application of aptamers targeting at hepatitis C virus.
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22
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Inhibition of hepatitis C virus (HCV) RNA polymerase by DNA aptamers: mechanism of inhibition of in vitro RNA synthesis and effect on HCV-infected cells. Antimicrob Agents Chemother 2008; 52:2097-110. [PMID: 18347106 DOI: 10.1128/aac.01227-07] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We describe here the further characterization of two DNA aptamers that specifically bind to hepatitis C virus (HCV) RNA polymerase (NS5B) and inhibit its polymerase activity in vitro. Although they were obtained from the same selection procedure and contain an 11-nucleotide consensus sequence, our results indicate that aptamers 27v and 127v use different mechanisms to inhibit HCV polymerase. While aptamer 27v was able to compete with the RNA template for binding to the enzyme and blocked both the initiation and the elongation of RNA synthesis, aptamer 127v competed poorly and exclusively inhibited initiation and postinitiation events. These results illustrate the power of the selective evolution of ligands by exponential enrichment in vitro selection procedure approach to select specific short DNA aptamers able to inhibit HCV NS5B by different mechanisms. We also determined that, in addition to an in vitro inhibitory effect on RNA synthesis, aptamer 27v was able to interfere with the multiplication of HCV JFH1 in Huh7 cells. The efficient cellular entry of these short DNAs and the inhibitory effect observed on human cells infected with HCV indicate that aptamers are useful tools for the study of HCV RNA synthesis, and their use should become a very attractive and alternative approach to therapy for HCV infection.
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23
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Warsinke A. Electrochemical biochips for protein analysis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 109:155-93. [PMID: 17928973 DOI: 10.1007/10_2007_079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Proteins bear important functions for most life processes. It is estimated that the human proteome comprises more than 250,000 proteins. Over the last years, highly sophisticated and powerful instruments have been developed that allow their detection and characterization with great precision and sensitivity. However, these instruments need well-equipped laboratories and a well-trained staff. For the determination of proteins in a hospital, in a doctor's office, or at home, low-budget protein analysis methods are needed that are easy to perform. In addition, for a proteomic approach, highly parallel measurements with small sample sizes are required. Biochips are considered as promising tools for such applications. The following chapter describes electrochemical biochips for protein analysis that use antibodies or aptamers as recognition elements.
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Affiliation(s)
- Axel Warsinke
- University of Potsdam, Institute of Biochemistry and Biology, iPOC Research Group, Karl-Liebknecht-Strasse 24-25, D-14476 Golm, Germany.
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24
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Abstract
Aptamers are rare nucleic acid ligands, which can be concocted in the laboratory from the randomized pool of molecules by affinity and amplification processes. Aptamers have several properties as they can be applied complementarily to antibodies and have several advantages over antibodies. In the past, several aptamers have been selected with a view to develop antiviral agents for therapeutic applications. This review summarizes potent antiviral aptamers and their strategies to prevent the viral replication.
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Affiliation(s)
- S C B Gopinath
- Functional Nucleic Acids Group, Institute for Biological Resources and Functions and Center for Applied Near Field Optics Research, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
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25
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Wochner A, Menger M, Rimmele M. Characterisation of aptamers for therapeutic studies. Expert Opin Drug Discov 2007; 2:1205-24. [DOI: 10.1517/17460441.2.9.1205] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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26
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Abstract
Aptamers are artificial nucleic acid ligands that can be generated in vitro against a wide range of molecules, including the gene products of viruses. Aptamers are isolated from complex libraries of synthetic nucleic acids by an iterative, cell-free process that involves repetitively reducing the complexity of the library by partitioning on the basis of selective binding to the target molecule, followed by reamplification. For virologists, aptamers have potential uses as tools to help to analyse the molecular biology of virus replication, as a complement to the more familiar monoclonal antibodies. They also have potential applications as diagnostic biosensors and in the development of antiviral agents. In recent years, these two promising avenues have been explored increasingly by virologists; here, the progress that has been made is reviewed.
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Affiliation(s)
- William James
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX2 3RE, UK
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27
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Warsinke A, Nagel B. Towards Separation‐Free Electrochemical Affinity Sensors by Using Antibodies, Aptamers, and Molecularly Imprinted Polymers—A Review. ANAL LETT 2006. [DOI: 10.1080/00032710600853903] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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28
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Abstract
Nucleic-acid aptamers have the molecular recognition properties of antibodies, and can be isolated robotically for high-throughput applications in diagnostics, research and therapeutics. Unlike antibodies, however, they can be chemically derivatized easily to extend their lifetimes in biological fluids and their bioavailability in animals. The first aptamer-based clinical drugs have recently entered service. Meanwhile, active research programmes have identified a wide range of anti-viral aptamers that could form the basis for future therapeutics.
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Affiliation(s)
- David H J Bunka
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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Trepanier JB, Tanner JE, Alfieri C. Oligonucleotide-Based Therapeutic Options against Hepatitis C Virus Infection. Antivir Ther 2006. [DOI: 10.1177/135965350601100315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The hepatitis C virus (HCV) is the cause of a silent pandemic that, due to the chronic nature of the disease and the absence of curative therapy, continues to claim an ever-increasing number of lives. Current antiviral regimens have proven largely unsatisfactory for patients with HCV drug-resistant genotypes. It is therefore important to explore alternative therapeutic stratagems whose mode of action allows them to bypass viral resistance. Antisense oligonucleotides, ribozymes, small interfering RNAs, aptamers and deoxyribozymes constitute classes of oligonucleotide-based compounds designed to target highly conserved or functionally crucial regions contained within the HCV genome. The therapeutic expectation for such compounds is the elimination of HCV from infected individuals. Progress in oligonucleotide-based HCV antivirals towards clinical application depends on development of nucleotide designs that bolster efficacy while minimizing toxicity, improvement in liver-targeting delivery systems, and refinement of small-animal models for preclinical testing.
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Affiliation(s)
- Janie B Trepanier
- Sainte-Justine Hospital Research Centre, and the Department of Microbiology and Immunology, Université de Montréal, Montréal, Québec, Canada
| | | | - Caroline Alfieri
- Sainte-Justine Hospital Research Centre, and the Department of Microbiology and Immunology, Université de Montréal, Montréal, Québec, Canada
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Jones LA, Clancy LE, Rawlinson WD, White PA. Recent advances in discovery and development of promising therapeutics against hepatitis C virus NS5B RNA-dependent RNA polymerase. Mini Rev Med Chem 2006; 50:3019-27. [PMID: 16940097 PMCID: PMC1563542 DOI: 10.1128/aac.01603-05] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lack of highly effective and safe therapeutics for hepatitis C virus (HCV) infection provides an opportunity as well as a challenge to discover novel and potent anti-HCV drugs. HCV NS5B RNA-dependent RNA polymerase (RdRp) is responsible for viral genome replication and thus constitutes a valid target for therapeutic intervention. To date, numerous HCV NS5B RdRp inhibitors have been discovered. This review focuses on the recent advances in discovery, mechanism of action studies and biological characterization of several distinct classes of potent inhibitors for NS5B RdRp. The clinical efficacy and developmental status of several promising compounds are also outlined.
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Affiliation(s)
- Louisa A Jones
- Department of Microbiology, Prince Wales Hospital, Randwick, Sydney, NSW 2031, Australia
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Métifiot M, Leon O, Tarrago-Litvak L, Litvak S, Andréola ML. Targeting HIV-1 integrase with aptamers selected against the purified RNase H domain of HIV-1 RT. Biochimie 2005; 87:911-9. [PMID: 16164998 DOI: 10.1016/j.biochi.2005.03.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2004] [Revised: 02/10/2005] [Accepted: 03/18/2005] [Indexed: 11/17/2022]
Abstract
Several in vitro strategies have been developed to selectively screen for nucleic acid sequences that bind to specific proteins. We previously used the SELEX procedure to search for aptamers against HIV-1 RNase H activity associated with reverse transcriptase (RT) and human RNase H1. Aptamers containing G-rich sequences were selected in both cases. To investigate whether the interaction with G-rich oligonucleotides (ODNs) was a characteristic of these enzymes, a second in vitro selection was performed with an isolated RNase H domain of HIV-1 RT (p15) as a target and a new DNA library. In this work we found that the second SELEX led again to the isolation of G-rich aptamers. But in contrast to the first selection, these latter ODNs were not able to inhibit the RNase H activity of either the p15 domain or the RNase H embedded in the complete RT. On the other hand, the aptamers from the first SELEX that were inhibitors of the RT-associated RNase H did not inhibit the activity of the isolated p15 domain. This suggests that the active conformation of both RNase H domains is different according to the presence or absence of the DNA polymerase domain. HIV-1 RNase H and integrase both belong to the phosphotransferase family and share structural similarities. An interesting result was obtained when the DNA aptamers initially raised against p15 RNase H were assayed against HIV-1 integrase. In contrast to RNase H, the HIV-1 integrase was inhibited by these aptamers. Our results point out that prototype structures can be exploited to develop inhibitors of two related enzymes.
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Affiliation(s)
- Mathieu Métifiot
- UMR 5097 CNRS, Université Victor Segalen Bordeaux 2, 146, rue Léo Saignat, 33076 Bordeaux cedex, France
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32
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Warsinke A, Stöcklein W, Leupold E, Micheel E, Scheller FW. Electrochemical Immunosensors on the Route to Proteomic Chips. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s1871-0069(05)01014-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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