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Falanga AP, D'Urso A, Travagliante G, Gangemi CMA, Marzano M, D'Errico S, Terracciano M, Greco F, De Stefano L, Dardano P, Rea I, Piccialli G, Oliviero G, Borbone N. Higher-order G-quadruplex structures and porphyrin ligands: Towards a non-ambiguous relationship. Int J Biol Macromol 2024; 268:131801. [PMID: 38670185 DOI: 10.1016/j.ijbiomac.2024.131801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/29/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024]
Abstract
Herein, we evaluated the interaction of the tetracationic porphyrin H2TCPPSpm4 with three distinct DNA G-quadruplex (G4) models, i.e., the tetramolecular G4 d(TGGGGT)4 (Q1), the 5'-5' stacked G4-dimer [d(CGGAGGT)4]2 (Q2), and a mixture of 5'-5' stacked G-wires [d(5'-CGGT-3'-3'-GGC-5')4]n (Qn). The combined data obtained from UV-Vis, CD, fluorescence, PAGE, RLS, AFM, NMR, and HPLC-SEC experiments allowed us to shed light on the binding mode of H2TCPPSpm4 with the three G4 models differing for the type and the number of available G4 ending faces, the length of the G4 units, and the number of stacked G4 building blocks. Specifically, we found that H2TCPPSpm4 interacted with the shortest Q1 as an end-stacking ligand, whereas the groove binding mode was ascertained in the case of the Q2 and Qn G4 models. In the case of the interaction with Q1 and Qn, we found that H2TCPPSpm4 induces the formation of supramolecular aggregates at porphyrin/G4 ratios higher than 2:1, whereas no significant aggregation was observed for the interaction with Q2 up to the 5:1 ratio. These results unambiguously demonstrated the suitability of porphyrins for the development of specific G4 ligands or G4-targeting diagnostic probes, being H2TCPPSpm4 capable to distinguish between different G4s.
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Affiliation(s)
- Andrea Patrizia Falanga
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Alessandro D'Urso
- Department of Chemical Sciences, University of Catania, viale Andrea Doria 6, 95125 Catania, Italy
| | - Gabriele Travagliante
- Department of Chemical Sciences, University of Catania, viale Andrea Doria 6, 95125 Catania, Italy
| | | | - Maria Marzano
- CESTEV, University of Naples Federico II, via Tommaso De Amicis 95, 80145 Naples, Italy
| | - Stefano D'Errico
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Monica Terracciano
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Francesca Greco
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Luca De Stefano
- Institute of Applied Sciences and Intelligent Systems, Unit of Naples, National Research Council, via Pietro Castellino 111, 80131 Naples, Italy
| | - Principia Dardano
- Institute of Applied Sciences and Intelligent Systems, Unit of Naples, National Research Council, via Pietro Castellino 111, 80131 Naples, Italy
| | - Ilaria Rea
- Institute of Applied Sciences and Intelligent Systems, Unit of Naples, National Research Council, via Pietro Castellino 111, 80131 Naples, Italy
| | - Gennaro Piccialli
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy.
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Liu X, Hu J, Ning Y, Xu H, Cai H, Yang A, Shi Z, Li Z. Aptamer Technology and Its Applications in Bone Diseases. Cell Transplant 2023; 32:9636897221144949. [PMID: 36591965 PMCID: PMC9811309 DOI: 10.1177/09636897221144949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Aptamers are single-stranded nucleic acids (DNA, short RNA, or other artificial molecules) produced by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology, which can be tightly and specifically combined with desired targets. As a comparable alternative to antibodies, aptamers have many advantages over traditional antibodies such as a strong chemical stability and rapid bulk production. In addition, aptamers can bind targets in various ways, and are not limited like the antigen-antibody combination. Studies have shown that aptamers have tremendous potential to diagnose and treat clinical diseases. However, only a few aptamer-based drugs have been used because of limitations of the aptamers and SELEX technology. To promote the development and applications of aptamers, we present a review of the methods optimizing the SELEX technology and modifying aptamers to boost the selection success rate and improve aptamer characteristics. In addition, we review the application of aptamers to treat bone diseases.
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Affiliation(s)
- Xiangzhong Liu
- Department of Orthopaedics, Wuhan Third
Hospital, Tongren Hospital of Wuhan University, Wuhan, China
| | - Jing Hu
- Wuhan Children’s Hospital, Tongji
Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Yu Ning
- Department of Orthopaedics, Xiangyang
Hospital of Traditional Chinese Medicine Affiliated to Hubei University of Chinese
Medicine, Xiangyang, China
| | - Haijia Xu
- Department of Orthopaedics, Wuhan Third
Hospital, Tongren Hospital of Wuhan University, Wuhan, China
| | - Hantao Cai
- Department of Orthopaedics, Wenling
First People’s Hospital, Taizhou, China
| | - Aofei Yang
- Department of Orthopaedics, Hubei
Hospital of Traditional Chinese Medicine, Wuhan, China
| | - Zhengshuai Shi
- Department of Orthopaedics, Wuhan
Sports University, Wuhan, China
| | - Zhanghua Li
- Department of Orthopaedics, Wuhan Third
Hospital, Tongren Hospital of Wuhan University, Wuhan, China,Zhanghua Li, Department of Orthopaedics,
Wuhan Third Hospital, Tongren Hospital of Wuhan University, No. 216, Guanshan
Avenue, Hongshan District, Wuhan 430074, Hubei Province, China.
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Upasham S, Pali M, Jagannath B, Lin KC, Prasad S. Electrochemical Aptasensing for Lifestyle and Chronic Disease Management. Curr Med Chem 2023; 30:895-909. [PMID: 35619314 DOI: 10.2174/0929867329666220520111715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/21/2022] [Accepted: 03/10/2022] [Indexed: 11/22/2022]
Abstract
Over the past decade, researchers have investigated electrochemical sensing for the purpose of fabricating wearable point-of-use platforms. These wearable platforms have the ability to non-invasively track biomarkers that are clinically relevant and provide a comprehensive evaluation of the user's health. Due to many significant operational advantages, aptamer-based sensing is gaining traction.Aptamer-based sensors have properties like long-term stability, resistance to denaturation, and high sensitivity. Using electrochemical sensing with aptamer-based biorecognition is advantageous because it provides significant benefits like lower detection limits, a wider range of operations, and, most importantly, the ability to detect using a label-free approach. This paper provides an outlook into the current state of electrochemical aptasensing. This review looks into the significance of the detection of biomarkers like glucose, cortisol etc., for the purpose of lifestyle and chronic disease monitoring. Moreover, this review will also provide a comprehensive evaluation of the current challenges and prospects in this field.
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Affiliation(s)
- Sayali Upasham
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas-75080, USA
| | - Madhavi Pali
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas-75080, USA
| | - Badrinath Jagannath
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas-75080, USA
| | - Kai-Chun Lin
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas-75080, USA
| | - Shalini Prasad
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas-75080, USA
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4
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Designer DNA nanostructures for viral inhibition. Nat Protoc 2022; 17:282-326. [PMID: 35013618 DOI: 10.1038/s41596-021-00641-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 09/29/2021] [Indexed: 12/26/2022]
Abstract
Emerging viral diseases can substantially threaten national and global public health. Central to our ability to successfully tackle these diseases is the need to quickly detect the causative virus and neutralize it efficiently. Here we present the rational design of DNA nanostructures to inhibit dengue virus infection. The designer DNA nanostructure (DDN) can bind to complementary epitopes on antigens dispersed across the surface of a viral particle. Since these antigens are arranged in a defined geometric pattern that is unique to each virus, the structure of the DDN is designed to mirror the spatial arrangement of antigens on the viral particle, providing very high viral binding avidity. We describe how available structural data can be used to identify unique spatial patterns of antigens on the surface of a viral particle. We then present a procedure for synthesizing DDNs using a combination of in silico design principles, self-assembly, and characterization using gel electrophoresis, atomic force microscopy and surface plasmon resonance spectroscopy. Finally, we evaluate the efficacy of a DDN in inhibiting dengue virus infection via plaque-forming assays. We expect this protocol to take 2-3 d to complete virus antigen pattern identification from existing cryogenic electron microscopy data, ~2 weeks for DDN design, synthesis, and virus binding characterization, and ~2 weeks for DDN cytotoxicity and antiviral efficacy assays.
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Serumula W, Fernandez G, Gonzalez VM, Parboosing R. Anti-HIV Aptamers: Challenges and Prospects. Curr HIV Res 2022; 20:7-19. [PMID: 34503417 DOI: 10.2174/1570162x19666210908114825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
Human Immunodeficiency Virus (HIV) infection continues to be a significant health burden in many countries around the world. Current HIV treatment through a combination of different antiretroviral drugs (cART) effectively suppresses viral replication, but drug resistance and crossresistance are significant challenges. This has prompted the search for novel targets and agents, such as nucleic acid aptamers. Nucleic acid aptamers are oligonucleotides that attach to the target sites with high affinity and specificity. This review provides a target-by-target account of research into anti-HIV aptamers and summarises the challenges and prospects of this therapeutic strategy, specifically in the unique context of HIV infection.
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Affiliation(s)
- William Serumula
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, c/o Inkosi Albert Luthuli Central Hospital, 5th Floor Laboratory Building, 800 Bellair Road, Mayville, Durban 4091, South Africa
| | - Geronimo Fernandez
- Departamento de Bioquímica-Investigación, Aptus Biotech SL, Avda. Cardenal Herrera Oria, 298-28035 Madrid. Spain
| | - Victor M Gonzalez
- Departamento de Bioquímica-Investigación, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)-Hospital Ramón y Cajal, 28034 Madrid, Spain
| | - Raveen Parboosing
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, c/o Inkosi Albert Luthuli Central Hospital, 5th Floor Laboratory Building, 800 Bellair Road, Mayville, Durban 4091, South Africa
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6
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Sheet SK, Rabha M, Sen B, Patra SK, Aguan K, Khatua S. Ruthenium(II) Complex-Based G-quadruplex DNA Selective Luminescent 'Light-up' Probe for RNase H Activity Detection. Chembiochem 2021; 22:2880-2887. [PMID: 34314094 DOI: 10.1002/cbic.202100229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/03/2021] [Indexed: 12/14/2022]
Abstract
A bis-heteroleptic ruthenium(II) complex, 1[PF6 ]2 of benzothiazole amide substituted 2,2'-bipyridine ligand (bmbbipy) has been synthesized for the selective detection of G-quadruplex (GQ) DNA and luminescence-assay-based RNase H activity monitoring. Compound 1[PF6 ]2 exhibited aggregation-caused quenching (ACQ) in water. Aggregate formation was supported by DLS, UV-vis, and 1 H NMR spectroscopy results, and the morphology of aggregated particles was witnessed by SEM and TEM. 1[PF6 ]2 acted as an efficient GQ DNA-selective luminescent light-up probe over single-stranded and double-stranded DNA. The competency of 1[PF6 ]2 for selective GQ structure detection was established by PL and CD spectroscopy. For 1[PF6 ]2 , the PL light-up is exclusively due to the rigidification of the benzothiazole amide side arm in the presence of GQ-DNA. The interaction between the probe and GQ-DNA was analyzed by molecular docking analysis. The GQ structure detection capability of 1[PF6 ]2 was further applied in the luminescent 'off-on' RNase H activity detection. The assay utilized an RNA:DNA hybrid, obtained from 22AG2-RNA and 22AG2-DNA sequences. RNase H solely hydrolyzed the RNA of the RNA:DNA duplex and released G-rich 22AG2-DNA, which was detected via the PL enhancement of 1[PF6 ]2 . The selectivity of RNase H activity detection over various other restriction enzymes was also demonstrated.
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Affiliation(s)
- Sanjoy Kumar Sheet
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| | - Monosh Rabha
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| | - Bhaskar Sen
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| | - Sumit Kumar Patra
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| | - Kripamoy Aguan
- Department of Biotechnology and Bioinformatics, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| | - Snehadrinarayan Khatua
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
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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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8
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Could gene therapy cure HIV? Life Sci 2021; 277:119451. [PMID: 33811896 DOI: 10.1016/j.lfs.2021.119451] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/12/2021] [Accepted: 03/27/2021] [Indexed: 02/05/2023]
Abstract
The Human Immunodeficiency Virus (HIV)/Acquired Immune Deficiency Syndrome (AIDS) continues to be a major global public health issue, having claimed almost 33 million lives so far. According to the recent report of the World Health Organization (WHO) in 2019, about 38 million people are living with AIDS. Hence, finding a solution to overcome this life-threatening virus can save millions of lives. Scientists and medical doctors have prescribed HIV patients with specific drugs for many years. Methods such antiretroviral therapy (ART) or latency-reversing agents (LRAs) have been used for a while to treat HIV patients, however they have some side effects and drawbacks causing their application to be not quite successful. Instead, the application of gene therapy which refers to the utilization of the therapeutic delivery of nucleic acids into a patient's cells as a drug to treat disease has shown promising results to control HIV infection. Therefore, in this review, we will summarize recent advances in gene therapy approach against HIV.
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9
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Emerging Technologies for the Treatment of COVID-19. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1321:81-96. [PMID: 33656715 DOI: 10.1007/978-3-030-59261-5_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The new coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), turned into a pandemic affecting more than 200 countries. Due to the high rate of transmission and mortality, finding specific and effective treatment options for this infection is currently of urgent importance. Emerging technologies have created a promising platform for developing novel treatment options for various viral diseases such as the SARS-CoV-2 virus. Here, we have described potential novel therapeutic options based on the structure and pathophysiological mechanism of the SARS-CoV-2 virus, as well as the results of previous studies on similar viruses such as SARS and MERS. Many of these approaches can be used for controlling viral infection by reducing the viral damage or by increasing the potency of the host response. Owing to their high sensitivity, specificity, and reproducibility, siRNAs, aptamers, nanobodies, neutralizing antibodies, and different types of peptides can be used for interference with viral replication or for blocking internalization. Receptor agonists and interferon-inducing agents are also potential options to balance and enhance the innate immune response against SARS-CoV-2. Solid evidence on the efficacy and safety of such novel technologies is yet to be established although many well-designed clinical trials are underway to address these issues.
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10
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Chen C, Hu X, Wang C, Lan W, Wu X, Cao C. Structure- and Mechanism-Based Research Progress of Anti-acquired Immune Deficiency Syndrome Drugs. CHINESE J ORG CHEM 2021. [DOI: 10.6023/cjoc202012036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Moranguinho I, Valente ST. Block-And-Lock: New Horizons for a Cure for HIV-1. Viruses 2020; 12:v12121443. [PMID: 33334019 PMCID: PMC7765451 DOI: 10.3390/v12121443] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/01/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
HIV-1/AIDS remains a global public health problem. The world health organization (WHO) reported at the end of 2019 that 38 million people were living with HIV-1 worldwide, of which only 67% were accessing antiretroviral therapy (ART). Despite great success in the clinical management of HIV-1 infection, ART does not eliminate the virus from the host genome. Instead, HIV-1 remains latent as a viral reservoir in any tissue containing resting memory CD4+ T cells. The elimination of these residual proviruses that can reseed full-blown infection upon treatment interruption remains the major barrier towards curing HIV-1. Novel approaches have recently been developed to excise or disrupt the virus from the host cells (e.g., gene editing with the CRISPR-Cas system) to permanently shut off transcription of the virus (block-and-lock and RNA interference strategies), or to reactivate the virus from cell reservoirs so that it can be eliminated by the immune system or cytopathic effects (shock-and-kill strategy). Here, we will review each of these approaches, with the major focus placed on the block-and-lock strategy.
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12
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Han J, Gao L, Wang J, Wang J. Application and development of aptamer in cancer: from clinical diagnosis to cancer therapy. J Cancer 2020; 11:6902-6915. [PMID: 33123281 PMCID: PMC7592013 DOI: 10.7150/jca.49532] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/20/2020] [Indexed: 01/04/2023] Open
Abstract
Traditional anticancer therapies can cause serious side effects in clinical treatment due to their nonspecific of tumor cells. Aptamers, also termed as 'chemical antibodies', are short DNA or RNA oligonucleotides selected from the synthetic large random single-strand oligonucleotide library by systematic evolution of ligands by exponential enrichment (SELEX) to bind to lots of different targets, such as proteins or nucleic acid structures. Aptamers have good affinities and high specificity with target molecules, thus may be able to act as drugs themselves to directly inhibit the proliferation of tumor cells, or own great potentialities in the targeted drug delivery systems which can be used in tumor diagnosis and target specific tumor cells, thereby minimizing the toxicity to normal cells. Here we review the unique properties of aptamer represents a great opportunity when applied to the rapidly developing fields of biotechnology and discuss the recent developments in the use of aptamers as powerful tools for analytic, diagnostic and therapeutic applications for cancer.
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Affiliation(s)
- Jing Han
- Department of Reproductive Medicine, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, 046000 China
| | - Liang Gao
- Department of Dermatology, Heji Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, 046000 China
| | - Jinsheng Wang
- Department of Pathology, Changzhi Medical College, Changzhi, Shanxi, 046000 China
| | - Jia Wang
- Department of Immunology, Changzhi Medical College, Changzhi, Shanxi, 046000 China
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Mohammadinezhad R, Jalali SAH, Farahmand H. Evaluation of different direct and indirect SELEX monitoring methods and implementation of melt-curve analysis for rapid discrimination of variant aptamer sequences. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3823-3835. [PMID: 32676627 DOI: 10.1039/d0ay00491j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Systematic Evolution of Ligands by Exponential enrichment (SELEX) is an iterative method for in vitro selection of aptamers from a random synthetic oligonucleotide library. Successful retrieving of aptamers by SELEX relies on optimization of various steps including target immobilization, aptamer partitioning, amplification, and ssDNA generation, which all require spending considerable effort and cost. Furthermore, due to the random nature of the initial library, SELEX may redirect toward the selection of low-affinity aptamers that are over-represented in the ssDNA population due to PCR bias. Thus, precise monitoring of the SELEX process is crucial to ensure the selection of target-specific aptamers. In the present study, we investigated the reliability and simplicity of different direct and indirect monitoring methods including UV-Vis spectroscopy, real-time PCR quantification and melt-curve analysis, electrophoretic mobility shift assay (EMSA) and enzyme-linked oligonucleotide assay (ELONA) for selection of DNA aptamers for a protein target. All the examined methods were capable of illustrating the gradual evolution of specific aptamers by the progression of SELEX and showed almost similar results regarding the identification of the enriched round of selection. Moreover, we describe the use of melt-curve analysis in the colony real-time PCR method as a simple, robust, and repeatable tool for pre-sequencing separation of distinct aptamer clones.
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Affiliation(s)
- Rezvan Mohammadinezhad
- Research Institute for Biotechnology and Bioengineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
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14
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Liu Y, Jiang W, Yang S, Hu J, Lu H, Han W, Wen J, Zeng Z, Qi J, Xu L, Zhou H, Sun H, Zu Y. Rapid Detection of Mycoplasma-Infected Cells by an ssDNA Aptamer Probe. ACS Sens 2019; 4:2028-2038. [PMID: 31403764 DOI: 10.1021/acssensors.9b00582] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mycoplasmas are unique cell wall-free bacteria. Because they lack a cell wall and have resistance to β-lactam antibiotics, mycoplasma is the major pathogen that infects cultured cells in research laboratories. For rapid detection of mycoplasma-infected cells, we developed an ssDNA aptamer sequence composed of 40 nucleotides. Flow cytometry analysis showed that the synthetic aptamer probe selectively targeted mycoplasma-infected culture cells with high specificity identical to commercially available PCR-based assays. Additionally, fluorescent microscopy studies revealed that the aptamer probe rapidly stained mycoplasma-infected cells with higher sensitivity compared to Hoechst dye-mediated cellular DNA content stains. Moreover, confocal microscopy studies of trypsin-treated cells validated that the aptamer probes selectively targeted mycoplasma components on the surface of infected cells. Finally, preclinical studies of peripheral blood cells demonstrated that the aptamer probe was able to detect in vitro mycoplasma infection of primary lymphocytes. Taken together, these findings indicate that the aptamer probe will not only allow rapid detection of mycoplasma-infected culture cells for research purposes but also provide a simple method to monitor mycoplasma infection in primary cell products for clinical use.
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Affiliation(s)
- Yanting Liu
- Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Wenqi Jiang
- Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Shuanghui Yang
- Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Jianzhong Hu
- Xiangya Hospital, Central South University, Changsha 410008, China
| | - Hongbin Lu
- Xiangya Hospital, Central South University, Changsha 410008, China
| | - Wei Han
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Jianguo Wen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Zihua Zeng
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Jianjun Qi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Ling Xu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Haijun Zhou
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Hongguang Sun
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
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Xu J, Cai Y, Jiang B, Li X, Jin H, Liu W, Kong Z, Hong J, Sealy JE, Iqbal M, Li Y. An optimized aptamer-binding viral tegument protein VP8 inhibits the production of Bovine Herpesvirus-1 through blocking nucleocytoplasmic shuttling. Int J Biol Macromol 2019; 140:1226-1238. [PMID: 31445153 DOI: 10.1016/j.ijbiomac.2019.08.165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/18/2019] [Accepted: 08/19/2019] [Indexed: 10/26/2022]
Abstract
Bovine herpesvirus 1 (BoHV-1) is a major pathogen of infectious bovine rhinotracheitis in bovine. Previously, we generated the aptamer IBRV A4 using systemic evolution of ligands by exponential enrichment. This aptamer inhibited infectivity of BoHV-1 by blocking viral particle absorption onto cell membranes. In this study, we found that the major tegument protein VP8 of BoHV-1 was involved in inhibition of infectious virus production by IBRV A4. We improved the affinity of IBRV A4 for VP8 by optimizing aptamer's structure and repeat conformation. An optimized aptamer, IBRV A4.7, was constructed with quadruple binding sites and a new stem-loop structure, which had a stronger binding affinity for VP8 or BoHV-1 than raw aptamer IBRV A4. IBRV A4.7 bound to VP8 with a dissociation constant (Kd) value of 0.2054 ± 0.03948 nM and bound to BoHV-1 with a Kd value of 0.3637 ± 0.05452 nM. Crucially, IBRV A4.7 had improved antiviral activity compared to IBRV A4, with a half-maximal inhibitory concentration of 1.16 ± 0.042 μM. Our results also revealed IBRV A4.7 inhibited BoHV-1 production in MDBK cells through blocking nucleocytoplasmic shuttling of viral VP8 in BoHV-1-infected MDBK cells. In conclusion, the aptamer IBRV A4.7 may have potency in preventing outbreaks in herds due to reactivation of latency.
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Affiliation(s)
- Jian Xu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Research Center for Infectious Disease in Livestock and Poultry, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Sino-UK Joint Laboratory for Prevention & Control of Infectious Diseases in Livestock and Poultry, Beijing 100097, PR China
| | - Yunhong Cai
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Research Center for Infectious Disease in Livestock and Poultry, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Sino-UK Joint Laboratory for Prevention & Control of Infectious Diseases in Livestock and Poultry, Beijing 100097, PR China
| | - Bo Jiang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Research Center for Infectious Disease in Livestock and Poultry, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Sino-UK Joint Laboratory for Prevention & Control of Infectious Diseases in Livestock and Poultry, Beijing 100097, PR China
| | - Xiaoyang Li
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Research Center for Infectious Disease in Livestock and Poultry, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Sino-UK Joint Laboratory for Prevention & Control of Infectious Diseases in Livestock and Poultry, Beijing 100097, PR China
| | - Huan Jin
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Research Center for Infectious Disease in Livestock and Poultry, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Sino-UK Joint Laboratory for Prevention & Control of Infectious Diseases in Livestock and Poultry, Beijing 100097, PR China
| | - Wenxiao Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Research Center for Infectious Disease in Livestock and Poultry, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Sino-UK Joint Laboratory for Prevention & Control of Infectious Diseases in Livestock and Poultry, Beijing 100097, PR China
| | - Zimeng Kong
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Research Center for Infectious Disease in Livestock and Poultry, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, PR China
| | - Jiabing Hong
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Research Center for Infectious Disease in Livestock and Poultry, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, PR China
| | - Joshua E Sealy
- Sino-UK Joint Laboratory for Prevention & Control of Infectious Diseases in Livestock and Poultry, Beijing 100097, PR China; The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, United Kingdom
| | - Munir Iqbal
- Sino-UK Joint Laboratory for Prevention & Control of Infectious Diseases in Livestock and Poultry, Beijing 100097, PR China; The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, United Kingdom
| | - Yongqing Li
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Research Center for Infectious Disease in Livestock and Poultry, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, PR China; Sino-UK Joint Laboratory for Prevention & Control of Infectious Diseases in Livestock and Poultry, Beijing 100097, PR China.
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16
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Pang KM, Castanotto D, Li H, Scherer L, Rossi JJ. Incorporation of aptamers in the terminal loop of shRNAs yields an effective and novel combinatorial targeting strategy. Nucleic Acids Res 2019; 46:e6. [PMID: 29077949 PMCID: PMC5758892 DOI: 10.1093/nar/gkx980] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/23/2017] [Indexed: 01/12/2023] Open
Abstract
Gene therapy by engineering patient's own blood cells to confer HIV resistance can potentially lead to a functional cure for AIDS. Toward this goal, we have previously developed an anti-HIV lentivirus vector that deploys a combination of shRNA, ribozyme and RNA decoy. To further improve this therapeutic vector against viral escape, we sought an additional reagent to target HIV integrase. Here, we report the development of a new strategy for selection and expression of aptamer for gene therapy. We developed a SELEX protocol (multi-tag SELEX) for selecting RNA aptamers against proteins with low solubility or stability, such as integrase. More importantly, we expressed these aptamers in vivo by incorporating them in the terminal loop of shRNAs. This novel strategy allowed efficient expression of the shRNA–aptamer fusions that targeted RNAs and proteins simultaneously. Expressed shRNA–aptamer fusions targeting HIV integrase or reverse transcriptase inhibited HIV replication in cell cultures. Viral inhibition was further enhanced by combining an anti-integrase aptamer with an anti-HIV Tat-Rev shRNA. This construct exhibited efficacy comparable to that of integrase inhibitor Raltegravir. Our strategy for the selection and expression of RNA aptamers can potentially extend to other gene therapy applications.
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Affiliation(s)
- Ka Ming Pang
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.,Department of Medical Oncology & Therapeutics Research, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Daniela Castanotto
- Department of Medical Oncology & Therapeutics Research, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Haitang Li
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Lisa Scherer
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - John J Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
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17
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Nici F, Oliviero G, Falanga AP, D'Errico S, Marzano M, Musumeci D, Montesarchio D, Noppen S, Pannecouque C, Piccialli G, Borbone N. Anti-HIV activity of new higher order G-quadruplex aptamers obtained from tetra-end-linked oligonucleotides. Org Biomol Chem 2019. [PMID: 29543291 DOI: 10.1039/c7ob02346d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
By combining the ability of short G-rich oligodeoxyribonucleotides (ODNs) containing the sequence 5'CGGA3' to form higher order G-quadruplex (G4) complexes with the tetra-end-linked (TEL) concept to produce aptamers targeting the HIV envelope glycoprotein 120 (gp120), three new TEL-ODNs (1-3) having the sequence 5'CGGAGG3' were synthesized with the aim of studying the effect of G4 dimerization on their anti-HIV activity. Furthermore, in order to investigate the effect of the groups at the 5' position, the 5' ends of 1-3 were left uncapped (1) or capped with either the lipophilic dimethoxytrityl (DMT) (2) or the hydrophilic glucosyl-4-phosphate (3) moieties. The here reported results demonstrate that only the DMT-substituted TEL-ODN 2 is effective in protecting human MT-4 cell cultures from HIV infection (76% max protection), notwithstanding all the three new aptamers proved to be capable of forming stable higher order dimeric G4s when annealed in K+-containing buffer, thus suggesting that the recognition of a hydrophobic pocket on the target glycoprotein by the aptamers represents a main structural feature for triggering their anti-HIV activity.
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Affiliation(s)
- F Nici
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - G Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Napoli, Italy
| | - A P Falanga
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - S D'Errico
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - M Marzano
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - D Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - D Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - S Noppen
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, B-3000 Leuven, Belgium
| | - C Pannecouque
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, B-3000 Leuven, Belgium
| | - G Piccialli
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - N Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
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18
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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: 6] [Impact Index Per Article: 1.2] [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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19
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Gautam LK, Sharma P, Capalash N. Bacterial Polyphosphate Kinases Revisited: Role in Pathogenesis and Therapeutic Potential. Curr Drug Targets 2019; 20:292-301. [DOI: 10.2174/1389450119666180801120231] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/02/2018] [Accepted: 07/31/2018] [Indexed: 11/22/2022]
Abstract
Bacterial infections have always been an unrestrained challenge to the medical community due to the rise of multi-drug tolerant and resistant strains. Pioneering work on Escherichia coli polyphosphate kinase (PPK) by Arthur Kornberg has generated great interest in this polyphosphate (PolyP) synthesizing enzyme. PPK has wide distribution among pathogens and is involved in promoting pathogenesis, stress management and susceptibility to antibiotics. Further, the absence of a PPK orthologue in humans makes it a potential drug target. This review covers the functional and structural aspects of polyphosphate kinases in bacterial pathogens. A description of molecules being designed against PPKs has been provided, challenges associated with PPK inhibitor design are highlighted and the strategies to enable development of efficient drug against this enzyme have also been discussed.
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Affiliation(s)
- Lalit Kumar Gautam
- Department of Biotechnology, Panjab University, BMS Block-I, Sector- 25, Chandigarh, 160014, India
| | - Prince Sharma
- Department of Microbiology, Panjab University, BMS Block-I, Sector- 25, Chandigarh, 160014, India
| | - Neena Capalash
- Department of Biotechnology, Panjab University, BMS Block-I, Sector- 25, Chandigarh, 160014, India
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20
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Ma Y, Li X, Li W, Liu Z. Glycan-Imprinted Magnetic Nanoparticle-Based SELEX for Efficient Screening of Glycoprotein-Binding Aptamers. ACS APPLIED MATERIALS & INTERFACES 2018; 10:40918-40926. [PMID: 30379519 DOI: 10.1021/acsami.8b14441] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nucleic acid aptamers, as useful alternatives of antibodies, have found a large range of promising applications such as affinity separation and bioassays. The screening of aptamers is critical for their applications. Aptamers are often screened by an in vitro methodology called SELEX (systematic evolution of ligands by exponential enrichment). Although numerous SELEX methods have been established to facilitate the selection, new efficient selection methods are still much needed. Molecularly imprinted polymers, which are antibody alternatives at the material level and competitors of aptamers, have not been used as a platform for aptamer selection yet so far. In this study, a glycan-imprinted magnetic nanoparticles (MNPs)-based SELEX was developed to efficiently screen aptamers against glycoproteins. Glycan-imprinted MNPs were used as an affinity interface to bind target glycoprotein, and then the target glycoprotein-bound MNPs were used as an affinity substrate for aptamer selection. The glycan-imprinted MNPs were synthesized by a state-of-the-art imprinting approach called boronate affinity controllable oriented surface imprinting. The glycan-imprinted MNPs exhibited high affinity and specificity and therefore allowed preferential binding toward target glycoproteins while excluding unwanted species. Two representative glycoproteins, including RNase B and transferrin, were employed as target glycoproteins, and aptamers with high affinity and specificity toward the two target glycoproteins were screened out in 3 rounds. This method exhibited some merits, such as high affinity, fast speed, and avoiding negative screening. Therefore, the glycan-imprinted MNP-based SELEX approach holds great values for the efficient screening of high-performance aptamers.
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Affiliation(s)
- Yanyan Ma
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Xinglin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Wei Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
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21
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Molefe PF, Masamba P, Oyinloye BE, Mbatha LS, Meyer M, Kappo AP. Molecular Application of Aptamers in the Diagnosis and Treatment of Cancer and Communicable Diseases. Pharmaceuticals (Basel) 2018; 11:ph11040093. [PMID: 30274155 PMCID: PMC6315466 DOI: 10.3390/ph11040093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 12/18/2022] Open
Abstract
Cancer and infectious diseases such as Ebola, HIV, tuberculosis, Zika, hepatitis, measles and human schistosomiasis are serious global health hazards. The increasing annual morbidities and mortalities of these diseases have been blamed on drug resistance and the inefficacy of available diagnostic tools, particularly those which are immunologically-based. Antibody-based tools rely solely on antibody production for diagnosis and for this reason they are the major cause of diagnostic delays. Unfortunately, the control of these diseases depends on early detection and administration of effective treatment therefore any diagnostic delay is a huge challenge to curbing these diseases. Hence, there is a need for alternative diagnostic tools, discovery and development of novel therapeutic agents. Studies have demonstrated that aptamers could potentially offer one of the best solutions to these problems. Aptamers are short sequences of either DNA or RNA molecules, which are identified in vitro through a SELEX process. They are sensitive and bind specifically to target molecules. Their promising features suggest they may serve as better diagnostic agents and can be used as drug carriers for therapeutic purposes. In this article, we review the applications of aptamers in the theranostics of cancer and some infectious diseases.
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Affiliation(s)
- Philisiwe Fortunate Molefe
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Priscilla Masamba
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Babatunji Emmanuel Oyinloye
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
- Department of Biochemistry, College of Sciences, Afe Babalola University, PMB 5454, Ado-Ekiti 360001, Nigeria.
| | - Londiwe Simphiwe Mbatha
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Mervin Meyer
- DST/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa.
| | - Abidemi Paul Kappo
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
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22
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Deng R, Yue J, Qu H, Liang L, Sun D, Zhang J, Liang C, Xu W, Xu S. Glucose-bridged silver nanoparticle assemblies for highly sensitive molecular recognition of sialic acid on cancer cells via surface-enhanced raman scattering spectroscopy. Talanta 2018; 179:200-206. [DOI: 10.1016/j.talanta.2017.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 10/25/2017] [Accepted: 11/03/2017] [Indexed: 01/02/2023]
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23
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Valencia-Reséndiz DG, Palomino-Vizcaino G, Tapia-Vieyra JV, Benítez-Hess ML, Leija-Montoya AG, Alvarez-Salas LM. Inhibition of Human Papillomavirus Type 16 Infection Using an RNA Aptamer. Nucleic Acid Ther 2018; 28:97-105. [PMID: 29437522 DOI: 10.1089/nat.2017.0687] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Human papillomavirus type 16 (HPV16) DNA has been found in ∼50% of cervical tumors worldwide. HPV infection starts with the binding of the virus capsid to heparan sulfate (HS) receptors exposed on the surface of epithelial basal layer keratinocytes. Previously, our group isolated a high-affinity RNA aptamer (Sc5c3) specific for HPV16 L1 virus-like particles (VLPs). In this study, we report the inhibition of HPV16 infection by Sc5c3 in a pseudovirus (PsVs) model. 293TT cells were infected by HPV16 PsVs containing the yellow fluorescent protein (YFP) as reporter gene. Incubation of HPV16 PsVs with Sc5c3 before infection resulted in a dose-dependent decrease in YFP fluorescence, suggesting infection inhibition. Aptamer degradation by RNase A restored PsVs infectivity, supporting the previous observation that Sc5c3 aptamer can inhibit infection. VLP mutants with removed HS binding sites were used in binding assays to elucidate the Sc5c3 blocking mechanism; however, no binding difference was observed between wild-type and mutant VLPs, suggesting that pseudoinfection inhibition relies on mechanisms additional to electrostatic HS binding site interaction. A DNA/RNA Sc5c3 version also inhibited HPV PsVs infection, suggesting that a modified, nuclease-resistant Sc5c3 may be used to inhibit HPV16 infection in vivo.
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Affiliation(s)
- Diana Gabriela Valencia-Reséndiz
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. , Ciudad de México, México
| | - Giovanni Palomino-Vizcaino
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. , Ciudad de México, México
| | - Juana Virginia Tapia-Vieyra
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. , Ciudad de México, México
| | - María Luisa Benítez-Hess
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. , Ciudad de México, México
| | - Ana Gabriela Leija-Montoya
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. , Ciudad de México, México
| | - Luis Marat Alvarez-Salas
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. , Ciudad de México, México
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Zhou J, Lazar D, Li H, Xia X, Satheesan S, Charlins P, O'Mealy D, Akkina R, Saayman S, Weinberg MS, Rossi JJ, Morris KV. Receptor-targeted aptamer-siRNA conjugate-directed transcriptional regulation of HIV-1. Am J Cancer Res 2018; 8:1575-1590. [PMID: 29556342 PMCID: PMC5858168 DOI: 10.7150/thno.23085] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/09/2017] [Indexed: 12/16/2022] Open
Abstract
Gene-based therapies represent a promising therapeutic paradigm for the treatment of HIV-1, as they have the potential to maintain sustained viral inhibition with reduced treatment interventions. Such an option may represent a long-term treatment alternative to highly active antiretroviral therapy. Methods: We previously described a therapeutic approach, referred to as transcriptional gene silencing (TGS), whereby small noncoding RNAs directly inhibit the transcriptional activity of HIV-1 by targeting sites within the viral promoter, specifically the 5' long terminal repeat (LTR). TGS differs from traditional RNA interference (RNAi) in that it is characterized by concomitant silent-state epigenetic marks on histones and DNA. To deliver TGS-inducing RNAs, we developed functional RNA conjugates based on the previously reported dual function of the gp120 (A-1) aptamer conjugated to 27-mer Dicer-substrate anti-HIV-1 siRNA (dsiRNA), LTR-362. Results: We demonstrate here that high levels of processed guide RNAs localize to the nucleus in infected T lymphoblastoid CEM cell line and primary human CD4+ T-cells. Treatment of the aptamer-siRNA conjugates induced TGS with an ~10-fold suppression of viral p24 levels as measured at day 12 post infection. To explore the silencing efficacy of aptamer-siRNA conjugates in vivo, HIV-1-infected humanized NOD/SCID/IL2 rγnull mice (hu-NSG) were treated with the aptamer-siRNA conjugates. Systemic delivery of the A-1-stick-LTR-362 27-mer siRNA conjugates suppressed HIV-1 infection and protected CD4+ T cell levels in viremia hu-NSG mice. Principle conclusions: Collectively these data suggest that the gp120 aptamer-dsiRNA conjugate design is suitable for systemic delivery of small RNAs that can be used to suppress HIV-1.
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Scarborough RJ, Gatignol A. RNA Interference Therapies for an HIV-1 Functional Cure. Viruses 2017; 10:E8. [PMID: 29280961 PMCID: PMC5795421 DOI: 10.3390/v10010008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/20/2017] [Accepted: 12/22/2017] [Indexed: 12/31/2022] Open
Abstract
HIV-1 drug therapies can prevent disease progression but cannot eliminate HIV-1 viruses from an infected individual. While there is hope that elimination of HIV-1 can be achieved, several approaches to reach a functional cure (control of HIV-1 replication in the absence of drug therapy) are also under investigation. One of these approaches is the transplant of HIV-1 resistant cells expressing anti-HIV-1 RNAs, proteins or peptides. Small RNAs that use RNA interference pathways to target HIV-1 replication have emerged as competitive candidates for cell transplant therapy and have been included in all gene combinations that have so far entered clinical trials. Here, we review RNA interference pathways in mammalian cells and the design of therapeutic small RNAs that use these pathways to target pathogenic RNA sequences. Studies that have been performed to identify anti-HIV-1 RNA interference therapeutics are also reviewed and perspectives on their use in combination gene therapy to functionally cure HIV-1 infection are provided.
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Affiliation(s)
- Robert J Scarborough
- Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A0G4, Canada.
| | - Anne Gatignol
- Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A0G4, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, QC H3A0G4, Canada.
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26
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Fluorescence Sensing Using DNA Aptamers in Cancer Research and Clinical Diagnostics. Cancers (Basel) 2017; 9:cancers9120174. [PMID: 29261171 PMCID: PMC5742822 DOI: 10.3390/cancers9120174] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 12/12/2022] Open
Abstract
Among the various advantages of aptamers over antibodies, remarkable is their ability to tolerate a large number of chemical modifications within their backbone or at the termini without losing significant activity. Indeed, aptamers can be easily equipped with a wide variety of reporter groups or coupled to different carriers, nanoparticles, or other biomolecules, thus producing valuable molecular recognition tools effective for diagnostic and therapeutic purposes. This review reports an updated overview on fluorescent DNA aptamers, designed to recognize significant cancer biomarkers both in soluble or membrane-bound form. In many examples, the aptamer secondary structure switches induced by target recognition are suitably translated in a detectable fluorescent signal using either fluorescently-labelled or label-free aptamers. The fluorescence emission changes, producing an enhancement (“signal-on”) or a quenching (“signal-off”) effect, directly reflect the extent of the binding, thereby allowing for quantitative determination of the target in bioanalytical assays. Furthermore, several aptamers conjugated to fluorescent probes proved to be effective for applications in tumour diagnosis and intraoperative surgery, producing tumour-type specific, non-invasive in vivo imaging tools for cancer pre- and post-treatment assessment.
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Luo CH, Yeh CS. Construction of Deoxyribonucleic Acid Decorated Gold Nanostructures as Nanomedical Agents. J CHIN CHEM SOC-TAIP 2017. [DOI: 10.1002/jccs.201700255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Cheng-Hung Luo
- Department of Chemistry; National Cheng Kung University; Tainan 701 Taiwan
| | - Chen-Sheng Yeh
- Department of Chemistry; National Cheng Kung University; Tainan 701 Taiwan
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Komorowska B, Hasiów-Jaroszewska B, Minicka J. Application of nucleic acid aptamers for detection of Apple stem pitting virus isolates. Mol Cell Probes 2017; 36:62-65. [PMID: 29050990 DOI: 10.1016/j.mcp.2017.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/30/2017] [Accepted: 10/12/2017] [Indexed: 12/19/2022]
Abstract
DNA aptamers (PSA-H and MT32) were applied for the detection of Apple stem pitting virus (ASPV) isolates using an Enzyme-Linked Oligonucleotide Assay (ELONA) and Western blot analysis. The specificity and effectiveness of aptamers were verified in comparison to a conventional Enzyme Linked Immunosorbent Assay (ELISA). A genetically diverse group of ASPV isolates was tested. The results showed that aptamer MT32 detected a wider range of ASPV isolates than an aptamer PSA-H and proved to be superior to commercially available monoclonal antibodies. Aptamer MT32 produced higher signal intensity in ELONA with a virus-infected plant extracts than antibodies in ELISA. Moreover, the ELISA method failed to detect ASPV in six samples. The results presented in this study indicated that aptamer MT32 can be used as a receptor molecule of various immunoassay protocols for ASPV detection.
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Affiliation(s)
- Beata Komorowska
- Research Institute of Horticulture, Department of Phytopathology, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland.
| | - Beata Hasiów-Jaroszewska
- Institute of Plant Protection-National Research Institute, Department of Virology and Bacteriology, Wł. Węgorka 20, 60-318 Poznań, Poland
| | - Julia Minicka
- Institute of Plant Protection-National Research Institute, Department of Virology and Bacteriology, Wł. Węgorka 20, 60-318 Poznań, Poland
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Discovery and Characterization of a Novel CD4-Binding Adnectin with Potent Anti-HIV Activity. Antimicrob Agents Chemother 2017; 61:AAC.00508-17. [PMID: 28584151 DOI: 10.1128/aac.00508-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/30/2017] [Indexed: 02/08/2023] Open
Abstract
A novel fibronectin-based protein (Adnectin) HIV-1 inhibitor was generated using in vitro selection. This inhibitor binds to human CD4 with a high affinity (3.9 nM) and inhibits viral entry at a step after CD4 engagement and preceding membrane fusion. The progenitor sequence of this novel inhibitor was selected from a library of trillions of Adnectin variants using mRNA display and then further optimized for improved antiviral and physical properties. The final optimized inhibitor exhibited full potency against a panel of 124 envelope (gp160) proteins spanning 11 subtypes, indicating broad-spectrum activity. Resistance profiling studies showed that this inhibitor required 30 passages (151 days) in culture to acquire sufficient resistance to result in viral titer breakthrough. Resistance mapped to the loss of multiple potential N-linked glycosylation sites in gp120, suggesting that inhibition is due to steric hindrance of CD4-binding-induced conformational changes.
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Chen K, Liu B, Yu B, Zhong W, Lu Y, Zhang J, Liao J, Liu J, Pu Y, Qiu L, Zhang L, Liu H, Tan W. Advances in the development of aptamer drug conjugates for targeted drug delivery. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2017; 9:10.1002/wnan.1438. [PMID: 27800663 PMCID: PMC5507701 DOI: 10.1002/wnan.1438] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 08/29/2016] [Accepted: 09/06/2016] [Indexed: 12/20/2022]
Abstract
A key goal of modern medicine is target-specific therapeutic intervention. However, most drugs lack selectivity, resulting in 'off-target' side effects. To address the requirements of 'targeted therapy,' aptamers, which are artificial oligonucleotides, have been used as novel targeting ligands to construct aptamer drug conjugates (ApDC) that can specifically bind to a broad spectrum of targets, including diseased cells. Accordingly, the application of aptamers in targeted drug delivery has attracted broad interest due to their impressive selectivity and affinity, low immunogenicity, easy synthesis with high reproducibility, facile modification, and relatively rapid tissue penetration with no toxicity. Functionally, aptamers themselves can be used as macromolecular drugs, and they are also commonly used in biomarker discovery and targeted drug delivery. In this review, we will highlight the most recent advances in the development of aptamers and aptamer conjugates, and discuss their potential in targeted therapy. WIREs Nanomed Nanobiotechnol 2017, 9:e1438. doi: 10.1002/wnan.1438 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ke Chen
- Xiangya Hospital, Central South University, Changsha, China
| | - Bo Liu
- Xiangya Hospital, Central South University, Changsha, China
| | - Bo Yu
- Xiangya Hospital, Central South University, Changsha, China
| | - Wen Zhong
- Xiangya Hospital, Central South University, Changsha, China
| | - Yi Lu
- Xiangya Hospital, Central South University, Changsha, China
| | - Jiani Zhang
- Xiangya Hospital, Central South University, Changsha, China
| | - Jie Liao
- Xiangya Hospital, Central South University, Changsha, China
| | - Jun Liu
- Xiangya Hospital, Central South University, Changsha, China
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha, China
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, Hunan University, Changsha, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Ying Pu
- Xiangya Hospital, Central South University, Changsha, China
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha, China
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, Hunan University, Changsha, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Liqin Zhang
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha, China
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, Hunan University, Changsha, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Huixia Liu
- Xiangya Hospital, Central South University, Changsha, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha, China
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, Hunan University, Changsha, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, University of Florida, Gainesville, FL, USA
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Abstract
Nucleic acid aptamers, often termed 'chemical antibodies', are functionally comparable to traditional antibodies, but offer several advantages, including their relatively small physical size, flexible structure, quick chemical production, versatile chemical modification, high stability and lack of immunogenicity. In addition, many aptamers are internalized upon binding to cellular receptors, making them useful targeted delivery agents for small interfering RNAs (siRNAs), microRNAs and conventional drugs. However, several crucial factors have delayed the clinical translation of therapeutic aptamers, such as their inherent physicochemical characteristics and lack of safety data. This Review discusses these challenges, highlighting recent clinical developments and technological advances that have revived the impetus for this promising class of therapeutics.
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Affiliation(s)
- Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
| | - John Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
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32
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Repression of the Internal Ribosome Entry Site-dependent Translation of Hepatitis C Virus by an Engineered PUF Protein. HEPATITIS MONTHLY 2017. [DOI: 10.5812/hepatmon.45022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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33
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Davydova AS, Vorobyeva MA, Kabilov MR, Tikunova NV, Pyshnyi DV, Venyaminova AG. In vitro selection of cell-internalizing 2′-modified RNA aptamers against Pseudomonas aeruginosa. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162016060030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Mirian M, Khanahmad H, Darzi L, Salehi M, Sadeghi-Aliabadi H. Oligonucleotide aptamers: potential novel molecules against viral hepatitis. Res Pharm Sci 2017; 12:88-98. [PMID: 28515761 PMCID: PMC5385733 DOI: 10.4103/1735-5362.202447] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Viral hepatitis, as an international public health concern, seriously affects communities and health system. In recent years, great strides have been taken for development of new potential tools against viral hepatitis. Among these efforts, a valuable strategy introduced new molecules called “aptamers”. Aptamers as potential alternatives for antibodies could be directed against any protein in infected cells and any components of viral particles. In this review, we will focus on recent advances in the diagnosis and treatment of viral hepatitis based on aptamer technology. In recent years, various types of aptamers including RNA and DNA were introduced against viral hepatitis. Some of these aptamers can be utilized for early and precise diagnosis of hepatitis infections and other group selected as therapeutic tools against viral targets. Designing diagnostic and therapeutic platforms based on aptamer technology is a promising approach in viral infections. The obtained aptamers in the recent years showed obvious potential for use as diagnostic and therapeutic tools against viral hepatitis. Although some modifications to increase the biostability and half-life of aptamers are underway, it seems these molecules will be a favorable substitute for monoclonal antibody in near future.
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Affiliation(s)
- Mina Mirian
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran.,Department of Pharmaceutical Chemistry and Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Leila Darzi
- Department of Pharmaceutical Chemistry and Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Mansour Salehi
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Hojjat Sadeghi-Aliabadi
- Department of Pharmaceutical Chemistry and Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
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35
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Surface Plasmon Resonance: A Boon for Viral Diagnostics. REFERENCE MODULE IN LIFE SCIENCES 2017. [PMCID: PMC7157476 DOI: 10.1016/b978-0-12-809633-8.12245-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Rapidly evolving viral strains leading to epidemics and pandemics necessitates quick diagnostics and treatment to halt the progressive march of the disease. Optical biosensors like surface plasmon resonance (SPR) have emerged in recent times as a most reliable diagnostic device owing to their portability, reproducibility, sensitivity and specificity. SPR analyzes the kinetics of biomolecular interactions in a label-free manner. It has surpassed the conventional virus detection methods in its utility, particularly in medical diagnostics and healthcare. However, the requirement of high-end infrastructure setup and trained manpower are some of the roadblocks in realizing the true potential of SPR. This platform needs further improvisation in terms of simplicity, affordability and portability before it could be utilized in need-based remote areas of under-developed and developing countries with limited infrastructure.
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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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37
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Kumar PKR. Monitoring Intact Viruses Using Aptamers. BIOSENSORS-BASEL 2016; 6:bios6030040. [PMID: 27527230 PMCID: PMC5039659 DOI: 10.3390/bios6030040] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 12/13/2022]
Abstract
Viral diagnosis and surveillance are necessary steps in containing the spread of viral diseases, and they help in the deployment of appropriate therapeutic interventions. In the past, the commonly employed viral detection methods were either cell-culture or molecule-level assays. Most of these assays are laborious and expensive, require special facilities, and provide a slow diagnosis. To circumvent these limitations, biosensor-based approaches are becoming attractive, especially after the successful commercialization of glucose and other biosensors. In the present article, I have reviewed the current progress using the biosensor approach for detecting intact viruses. At the time of writing this review, three types of bioreceptor surfaces (antibody-, glycan-, and aptamer-based) have been explored on different sensing platforms for detecting intact viruses. Among these bioreceptors, aptamer-based sensors have been increasingly explored for detecting intact viruses using surface plasmon resonance (SPR) and other platforms. Special emphasis is placed on the aptamer-based SPR platform in the present review.
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Affiliation(s)
- Penmetcha K R Kumar
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba City 305-8566, Ibaraki, Japan.
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38
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Alexandre KB, Mufhandu HT, London GM, Chakauya E, Khati M. Progress and Perspectives on HIV-1 microbicide development. Virology 2016; 497:69-80. [PMID: 27429040 DOI: 10.1016/j.virol.2016.07.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 12/12/2022]
Abstract
The majority of HIV-1 infections occur via sexual intercourse. Women are the most affected by the epidemic, particularly in developing countries, due to their socio-economic dependence on men and the fact that they are often victims of gender based sexual violence. Despite significant efforts that resulted in the reduction of infection rates in some countries, there is still need for effective prevention methods against the virus. One of these methods for preventing sexual transmission in women is the use of microbicides. In this review we provide a summary of the progress made toward the discovery of affordable and effective HIV-1 microbicides and suggest future directions. We show that there is a wide range of compounds that have been proposed as potential microbicides. Although most of them have so far failed to show protection in humans, there are many promising ones currently in pre-clinical studies and in clinical trials.
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Affiliation(s)
- Kabamba B Alexandre
- Council for Scientific and Industrial Research, Pioneering Health Sciences Laboratory, Biosciences Unit, Pretoria, Gauteng, South Africa.
| | - Hazel T Mufhandu
- Council for Scientific and Industrial Research, Pioneering Health Sciences Laboratory, Biosciences Unit, Pretoria, Gauteng, South Africa
| | - Grace M London
- Department of Health Free State District Health Services and Health Programs, South Africa
| | - E Chakauya
- Council for Scientific and Industrial Research, Pioneering Health Sciences Laboratory, Biosciences Unit, Pretoria, Gauteng, South Africa
| | - M Khati
- Council for Scientific and Industrial Research, Pioneering Health Sciences Laboratory, Biosciences Unit, Pretoria, Gauteng, South Africa; University of Cape Town and Groote Schuur Hospital, Department of Medicine, Cape Town, South Africa
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Wang CC, Wu SM, Li HW, Chang HT. Biomedical Applications of DNA-Conjugated Gold Nanoparticles. Chembiochem 2016; 17:1052-62. [PMID: 26864481 DOI: 10.1002/cbic.201600014] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 01/07/2023]
Abstract
Gold nanoparticles (AuNPs) are useful for diagnostic and biomedical applications, mainly because of their ease in preparation and conjugation, biocompatibility, and size-dependent optical properties. However, bare AuNPs do not possess specificity for targets. AuNPs conjugated with DNA aptamers offer specificity for various analytes, such as proteins and small molecules/ions. Although DNA aptamers themselves have therapeutic and target-recognizing properties, they are susceptible to degradation in vivo. When DNA aptamers are conjugated to AuNPs, their stability and cell uptake efficiency both increase, making aptamer-AuNPs suitable for biomedical applications. Additionally, drugs can be efficiently conjugated with DNA aptamer-AuNPs to further enhance their therapeutic efficiency. This review focuses on the applications of DNA aptamer-based AuNPs in several biomedical areas, including anticoagulation, anticancer, antibacterial, and antiviral applications.
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Affiliation(s)
- Chun-Chi Wang
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei, 10617, Taiwan
| | - Shou-Mei Wu
- School of Pharmacy, Kaohsiung Medical University, 100, Shih-Chuan 1st Road, Kaohsiung, 80708, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei, 10617, Taiwan
| | - Huan-Tsung Chang
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei, 10617, Taiwan.
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40
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Li W, Feng X, Yan X, Liu K, Deng L. A DNA Aptamer Against Influenza A Virus: An Effective Inhibitor to the Hemagglutinin-Glycan Interactions. Nucleic Acid Ther 2016; 26:166-72. [PMID: 26904922 DOI: 10.1089/nat.2015.0564] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Most therapeutical nucleic acid aptamers tend to inhibit protein-protein interactions and thereby function as antagonists. Attachment of the influenza virus surface glycoprotein hemagglutinin (HA) to sialic acid-containing host cell receptors (glycan) facilitates the initial stage of viral infection. Inhibition of the attachment may result in an antiviral effect on the proliferation of the influenza virus. To develop therapeutically interesting agents, we selected two single-stranded DNA (ssDNA) aptamers specific to the HA protein of H1N1 influenza virus (A/Puerto Rico/8/1934) through a procedure of systematic evolution of ligands by exponential enrichment. As it showed a higher binding affinity for HA protein (Kd = 78 ± 1 nM), aptamer 1 was tested for its ability to interfere with HA-glycan interactions using chicken red blood cell hemagglutination and microneutralization assays, which demonstrated that it significantly suppressed the viral infection in host cells. These results indicate that the isolated ssDNA aptamer may be developed as an antiviral agent against influenza through appropriate therapeutic formulation.
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Affiliation(s)
- Wenkai Li
- 1 Department of Microbiology, College of Life Science, Hunan Normal University , Changsha, China .,2 Department of Biochemistry, the State Key Laboratory of Medical Genetics and School of Life Science, Central South University , Changsha, China
| | - Xinru Feng
- 1 Department of Microbiology, College of Life Science, Hunan Normal University , Changsha, China .,3 The Second Xiangya Hospital, Central South University , Changsha, China
| | - Xing Yan
- 1 Department of Microbiology, College of Life Science, Hunan Normal University , Changsha, China
| | - Keyi Liu
- 1 Department of Microbiology, College of Life Science, Hunan Normal University , Changsha, China
| | - Le Deng
- 1 Department of Microbiology, College of Life Science, Hunan Normal University , Changsha, China
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Oliviero G, Stornaiuolo M, D'Atri V, Nici F, Yousif AM, D'Errico S, Piccialli G, Mayol L, Novellino E, Marinelli L, Grieco P, Carotenuto A, Noppen S, Liekens S, Balzarini J, Borbone N. Screening Platform toward New Anti-HIV Aptamers Set on Molecular Docking and Fluorescence Quenching Techniques. Anal Chem 2016; 88:2327-34. [PMID: 26810800 DOI: 10.1021/acs.analchem.5b04268] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
By using a new rapid screening platform set on molecular docking simulations and fluorescence quenching techniques, three new anti-HIV aptamers targeting the viral surface glycoprotein 120 (gp120) were selected, synthesized, and assayed. The use of the short synthetic fluorescent peptide V35-Fluo mimicking the V3 loop of gp120, as the molecular target for fluorescence-quenching binding affinity studies, allowed one to measure the binding affinities of the new aptamers for the HIV-1 gp120 without the need to obtain and purify the full recombinant gp120 protein. The almost perfect correspondence between the calculated Kd and the experimental EC50 on HIV-infected cells confirmed the reliability of the platform as an alternative to the existing methods for aptamer selection and measuring of aptamer-protein equilibria.
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Affiliation(s)
- Giorgia Oliviero
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Mariano Stornaiuolo
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Valentina D'Atri
- University of Bordeaux , IECB, ARNA laboratory, Pessac, 33600, France.,INSERM , U869, ARNA laboratory, Bordeaux, 33000, France
| | - Fabrizia Nici
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Ali Munaim Yousif
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Stefano D'Errico
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Gennaro Piccialli
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy.,CNR , Institute of Protein Biochemistry, Napoli, 80131, Italy
| | - Luciano Mayol
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Ettore Novellino
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Luciana Marinelli
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Paolo Grieco
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Alfonso Carotenuto
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Sam Noppen
- KU Leuven , Rega Institute for Medical Research, Leuven, 3000, Belgium
| | - Sandra Liekens
- KU Leuven , Rega Institute for Medical Research, Leuven, 3000, Belgium
| | - Jan Balzarini
- KU Leuven , Rega Institute for Medical Research, Leuven, 3000, Belgium
| | - Nicola Borbone
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
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42
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Wang T, Gantier MP, Xiang D, Bean AG, Bruce M, Zhou SF, Khasraw M, Ward A, Wang L, Wei MQ, AlShamaileh H, Chen L, She X, Lin J, Kong L, Shigdar S, Duan W. EpCAM Aptamer-mediated Survivin Silencing Sensitized Cancer Stem Cells to Doxorubicin in a Breast Cancer Model. Am J Cancer Res 2015; 5:1456-72. [PMID: 26681989 PMCID: PMC4672025 DOI: 10.7150/thno.11692] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 07/30/2015] [Indexed: 12/23/2022] Open
Abstract
Understanding the molecular basis of drug resistance and utilising this information to overcome chemoresistance remains a key challenge in oncology. Here we report that survivin, a key protein implicated in drug resistance, is overexpressed in cancer stem cell pool of doxorubicin-resistant breast cancer cells. Moreover, by utilising an active targeting system consisting of an RNA aptamer targeted against the epithelial cell adhesion molecule and a Dicer substrate survivin siRNA, we could deliver a high dose of the siRNA to cancer stem cells in xenograft tumours. Importantly, silencing of survivin with this aptamer-siRNA chimera in cancer stem cell population led to the reversal of chemoresistance, such that combined treatment with low dose of doxorubicin inhibited stemness, eliminated cancer stem cells via apoptosis, suppressed tumour growth, and prolonged survival in mice bearing chemoresistant tumours. This strategy for in vivo cancer stem cell targeting has wide application for future effective silencing of anti-death genes and in fact any dysregulated genes involved in chemoresistance and tumour relapse.
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43
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Musumeci D, Riccardi C, Montesarchio D. G-Quadruplex Forming Oligonucleotides as Anti-HIV Agents. Molecules 2015; 20:17511-32. [PMID: 26402662 PMCID: PMC6332060 DOI: 10.3390/molecules200917511] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/10/2015] [Accepted: 09/16/2015] [Indexed: 12/21/2022] Open
Abstract
Though a variety of different non-canonical nucleic acids conformations have been recognized, G-quadruplex structures are probably the structural motifs most commonly found within known oligonucleotide-based aptamers. This could be ascribed to several factors, as their large conformational diversity, marked responsiveness of their folding/unfolding processes to external stimuli, high structural compactness and chemo-enzymatic and thermodynamic stability. A number of G-quadruplex-forming oligonucleotides having relevant in vitro anti-HIV activity have been discovered in the last two decades through either SELEX or rational design approaches. Improved aptamers have been obtained by chemical modifications of natural oligonucleotides, as terminal conjugations with large hydrophobic groups, replacement of phosphodiester linkages with phosphorothioate bonds or other surrogates, insertion of base-modified monomers, etc. In turn, detailed structural studies have elucidated the peculiar architectures adopted by many G-quadruplex-based aptamers and provided insight into their mechanism of action. An overview of the state-of-the-art knowledge of the relevance of putative G-quadruplex forming sequences within the viral genome and of the most studied G-quadruplex-forming aptamers, selectively targeting HIV proteins, is here presented.
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Affiliation(s)
- Domenica Musumeci
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, Napoli I-80126, Italy.
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, Napoli I-80126, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, Napoli I-80126, Italy.
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44
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Kun Á, Szathmáry E. Fitness Landscapes of Functional RNAs. Life (Basel) 2015; 5:1497-517. [PMID: 26308059 PMCID: PMC4598650 DOI: 10.3390/life5031497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/26/2015] [Accepted: 08/03/2015] [Indexed: 11/16/2022] Open
Abstract
The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world.
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Affiliation(s)
- Ádám Kun
- Parmenides Center for the Conceptual Foundations of Science, Kirchplatz 1, 82049 Munich/Pullach, Germany.
- MTA-ELTE-MTMT Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
| | - Eörs Szathmáry
- Parmenides Center for the Conceptual Foundations of Science, Kirchplatz 1, 82049 Munich/Pullach, Germany.
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
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45
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Davydova A, Vorobjeva M, Pyshnyi D, Altman S, Vlassov V, Venyaminova A. Aptamers against pathogenic microorganisms. Crit Rev Microbiol 2015; 42:847-65. [PMID: 26258445 PMCID: PMC5022137 DOI: 10.3109/1040841x.2015.1070115] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An important current issue of modern molecular medicine and biotechnology is the search for new approaches to early diagnostic assays and adequate therapy of infectious diseases. One of the promising solutions to this problem might be a development of nucleic acid aptamers capable of interacting specifically with bacteria, protozoa, and viruses. Such aptamers can be used for the specific recognition of infectious agents as well as for blocking of their functions. The present review summarizes various modern SELEX techniques used in this field, and of several currently identified aptamers against viral particles and unicellular organisms, and their applications. The prospects of applying nucleic acid aptamers for the development of novel detection systems and antibacterial and antiviral drugs are discussed.
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Affiliation(s)
- Anna Davydova
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Maria Vorobjeva
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Dmitrii Pyshnyi
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Sidney Altman
- b Department of Molecular, Cellular and Developmental Biology , Yale University , New Haven , CT , USA
| | - Valentin Vlassov
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Alya Venyaminova
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
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46
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Scuotto M, Rivieccio E, Varone A, Corda D, Bucci M, Vellecco V, Cirino G, Virgilio A, Esposito V, Galeone A, Borbone N, Varra M, Mayol L. Site specific replacements of a single loop nucleoside with a dibenzyl linker may switch the activity of TBA from anticoagulant to antiproliferative. Nucleic Acids Res 2015; 43:7702-16. [PMID: 26250112 PMCID: PMC4652776 DOI: 10.1093/nar/gkv789] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/23/2015] [Indexed: 12/20/2022] Open
Abstract
Many antiproliferative G-quadruplexes (G4s) arise from the folding of GT-rich strands. Among these, the Thrombin Binding Aptamer (TBA), as a rare example, adopts a monomolecular well-defined G4 structure. Nevertheless, the potential anticancer properties of TBA are severely hampered by its anticoagulant action and, consequently, no related studies have appeared so far in the literature. We wish to report here that suitable chemical modifications in the TBA sequence can preserve its antiproliferative over anticoagulant activity. Particularly, we replaced one residue of the TT or TGT loops with a dibenzyl linker to develop seven new quadruplex-forming TBA based sequences (TBA-bs), which were studied for their structural (CD, CD melting, 1D NMR) and biological (fibrinogen, PT and MTT assays) properties. The three-dimensional structures of the TBA-bs modified at T13 (TBA-bs13) or T12 (TBA-bs12), the former endowed with selective antiproliferative activity, and the latter acting as potently as TBA in both coagulation and MTT assays, were further studied by 2D NMR restrained molecular mechanics. The comparative structural analyses indicated that neither the stability, nor the topology of the G4s, but the different localization of the two benzene rings of the linker was responsible for the loss of the antithrombin activity for TBA-bs13.
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Affiliation(s)
- Maria Scuotto
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Elisa Rivieccio
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Alessia Varone
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Daniela Corda
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Mariarosaria Bucci
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Valentina Vellecco
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Giuseppe Cirino
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Antonella Virgilio
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Veronica Esposito
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Aldo Galeone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Michela Varra
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Luciano Mayol
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
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47
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Predicting the Uncertain Future of Aptamer-Based Diagnostics and Therapeutics. Molecules 2015; 20:6866-87. [PMID: 25913927 PMCID: PMC6272696 DOI: 10.3390/molecules20046866] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/04/2015] [Accepted: 04/07/2015] [Indexed: 01/07/2023] Open
Abstract
Despite the great promise of nucleic acid aptamers in the areas of diagnostics and therapeutics for their facile in vitro development, lack of immunogenicity and other desirable properties, few truly successful aptamer-based products exist in the clinical or other markets. Core reasons for these commercial deficiencies probably stem from industrial commitment to antibodies including a huge financial investment in humanized monoclonal antibodies and a general ignorance about aptamers and their performance among the research and development community. Given the early failures of some strong commercial efforts to gain government approval and bring aptamer-based products to market, it may seem that aptamers are doomed to take a backseat to antibodies forever. However, the key advantages of aptamers over antibodies coupled with niche market needs that only aptamers can fill and more recent published data still point to a bright commercial future for aptamers in areas such as infectious disease and cancer diagnostics and therapeutics. As more researchers and entrepreneurs become familiar with aptamers, it seems inevitable that aptamers will at least be considered for expanded roles in diagnostics and therapeutics. This review also examines new aptamer modifications and attempts to predict new aptamer applications that could revolutionize biomedical technology in the future and lead to marketed products.
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48
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Lao YH, Phua KKL, Leong KW. Aptamer nanomedicine for cancer therapeutics: barriers and potential for translation. ACS NANO 2015; 9:2235-54. [PMID: 25731717 DOI: 10.1021/nn507494p] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Aptamer nanomedicine, including therapeutic aptamers and aptamer nanocomplexes, is beginning to fulfill its potential in both clinical trials and preclinical studies. Especially in oncology, aptamer nanomedicine may perform better than conventional or antibody-based chemotherapeutics due to specificity compared to the former and stability compared to the latter. Many proof-of-concept studies on applying aptamers to drug delivery, gene therapy, and cancer imaging have shown promising efficacy and impressive safety in vivo toward translation. Yet, there remains ample room for improvement and critical barriers to be addressed. In this review, we will first introduce the recent progress in clinical trials of aptamer nanomedicine, followed by a discussion of the barriers at the design and in vivo application stages. We will then highlight recent advances and engineering strategies proposed to tackle these barriers. Aptamer cancer nanomedicine has the potential to address one of the most important healthcare issues of the society.
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Affiliation(s)
- Yeh-Hsing Lao
- †Department of Biomedical Engineering, Columbia University, New York 10027, New York, United States
| | | | - Kam W Leong
- †Department of Biomedical Engineering, Columbia University, New York 10027, New York, United States
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49
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Cell-specific RNA aptamer against human CCR5 specifically targets HIV-1 susceptible cells and inhibits HIV-1 infectivity. ACTA ACUST UNITED AC 2015; 22:379-90. [PMID: 25754473 DOI: 10.1016/j.chembiol.2015.01.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/29/2014] [Accepted: 01/25/2015] [Indexed: 11/21/2022]
Abstract
The C-C chemokine receptor type 5 (CCR5) is a receptor expressed by T cells and macrophages that serves as a coreceptor for macrophage-tropic HIV-1. Loss of CCR5 is associated with resistance to HIV-1. Here, we combine the live-cell-based SELEX with high-throughput sequencing technology to generate CCR5 RNA aptamers capable of specifically targeting HIV-1 susceptible cells (as small interfering RNA [siRNA] delivery agent) and inhibiting HIV-1 infectivity (as antiviral agent) via block of the CCR5 required for HIV-1 to enter cells. One of the best candidates, G-3, efficiently bound and was internalized into human CCR5-expressing cells. The G-3 specifically neutralized R5 virus infection in primary peripheral blood mononuclear cells, and in vivo generated human CD4(+) T cells with a nanomolar inhibitory concentration 50%. G-3 was also capable of transferring functional siRNAs to CCR5-expressing cells. Collectively, the cell-specific, internalizing, CCR5-targeted aptamers and aptamer-siRNA conjugates offer promise for overcoming some of the current challenges of drug resistance in HIV-1 by providing cell-type- or tissue-specific delivery of various therapeutic moieties.
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50
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Takahashi M, Burnett JC, Rossi JJ. Aptamer–siRNA Chimeras for HIV. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 848:211-34. [DOI: 10.1007/978-1-4939-2432-5_11] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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