1
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Ngo KH, Liew CW, Lattmann S, Winnerdy FR, Phan AT. Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A•G•G•G•G pentad in an interlocked G-quadruplex. Biochem Biophys Res Commun 2022; 613:153-158. [DOI: 10.1016/j.bbrc.2022.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 11/27/2022]
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2
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Chen XF, Zhao X, Yang Z. Aptamer-Based Antibacterial and Antiviral Therapy against Infectious Diseases. J Med Chem 2021; 64:17601-17626. [PMID: 34854680 DOI: 10.1021/acs.jmedchem.1c01567] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA molecules selected in vitro that can bind to a broad range of targets with high affinity and specificity. As promising alternatives to conventional anti-infective agents, aptamers have gradually revealed their potential in the combat against infectious diseases. This article provides an overview on the state-of-art of aptamer-based antibacterial and antiviral therapeutic strategies. Diverse aptamers targeting pathogen-related components or whole pathogenic cells are summarized according to the species of microorganisms. These aptamers exhibited remarkable in vitro and/or in vivo inhibitory effect for pathogenic invasion, enzymatic activities, or viral replication, even for some highly drug-resistant strains and biofilms. Aptamer-mediated drug delivery and controlled drug release strategies are also included herein. Critical technical barriers of therapeutic aptamers are briefly discussed, followed by some future perspectives for their implementation into clinical utility.
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Affiliation(s)
- Xiao-Fei Chen
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou 510070, PR China
| | - Xin Zhao
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou 510070, PR China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, PR China.,Guangzhou Laboratory, Guangzhou 510320, PR China.,Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, Guangzhou 510005, PR China
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3
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Xeno-Nucleic Acid (XNA) 2'-Fluoro-Arabino Nucleic Acid (FANA) Aptamers to the Receptor-Binding Domain of SARS-CoV-2 S Protein Block ACE2 Binding. Viruses 2021; 13:v13101983. [PMID: 34696413 PMCID: PMC8539646 DOI: 10.3390/v13101983] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 01/03/2023] Open
Abstract
The causative agent of COVID-19, SARS-CoV-2, gains access to cells through interactions of the receptor-binding domain (RBD) on the viral S protein with angiotensin-converting enzyme 2 (ACE2) on the surface of human host cells. Systematic evolution of ligands by exponential enrichment (SELEX) was used to generate aptamers (nucleic acids selected for high binding affinity to a target) to the RBD made from 2ʹ-fluoro-arabinonucleic acid (FANA). The best selected ~79 nucleotide aptamers bound the RBD (Arg319-Phe541) and the larger S1 domain (Val16-Arg685) of the 1272 amino acid S protein with equilibrium dissociation constants (KD,app) of ~10–20 nM, and binding half-life for the RBD, S1 domain, and full trimeric S protein of 53 ± 18, 76 ± 5, and 127 ± 7 min, respectively. Aptamers inhibited the binding of the RBD to ACE2 in an ELISA assay. Inhibition, on a per weight basis, was similar to neutralizing antibodies that were specific for RBD. Aptamers demonstrated high specificity, binding with about 10-fold lower affinity to the related S1 domain from the original SARS virus, which also binds to ACE2. Overall, FANA aptamers show affinities comparable to previous DNA aptamers to RBD and S1 protein and directly block receptor interactions while using an alternative Xeno-nucleic acid (XNA) platform.
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4
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Ferreira-Bravo IA, DeStefano JJ. Xeno-nucleic Acid (XNA) 2'-Fluoro-Arabino Nucleic Acid (FANA) Aptamers to the Receptor Binding Domain of SARS-CoV-2 S Protein Block ACE2 Binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34282416 DOI: 10.1101/2021.07.13.452259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The causative agent of COVID-19, SARS-CoV-2, gains access to cells through interactions of the receptor binding domain (RBD) on the viral S protein with angiotensin converting enzyme 2 (ACE2) on the surface of human host cells. Systematic Evolution of Ligands by Exponential Enrichment (SELEX) was used to generate aptamers (nucleic acids selected for high binding affinity to a target) to the RBD made from 2'-fluoroarabinonucleic acid (FANA). The best selected ~ 79 nucleotide aptamers bound the RBD (Arg319-Phe541) and the larger S1 domain (Val16-Arg685) of the 1272 amino acid S protein with equilibrium dissociation constants ( K D,app ) of ~ 10-20 nM and a binding half-life for the RBD of 53 ± 18 minutes. Aptamers inhibited the binding of the RBD to ACE2 in an ELISA assay. Inhibition, on a per weight basis, was similar to neutralizing antibodies that were specific for RBD. Aptamers demonstrated high specificity, binding with about 10-fold lower affinity to the related S1 domain from the original SARS virus, which also binds to ACE2. Overall, FANA aptamers show affinities comparable to previous DNA aptamers to RBD and S protein and directly block receptor interactions while using an alternative Xeno-nucleic acid (XNA) platform.
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5
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Kim TH, Lee SW. Aptamers for Anti-Viral Therapeutics and Diagnostics. Int J Mol Sci 2021; 22:ijms22084168. [PMID: 33920628 PMCID: PMC8074132 DOI: 10.3390/ijms22084168] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/16/2022] Open
Abstract
Viral infections cause a host of fatal diseases and seriously affect every form of life from bacteria to humans. Although most viral infections can receive appropriate treatment thereby limiting damage to life and livelihood with modern medicine and early diagnosis, new types of viral infections are continuously emerging that need to be properly and timely treated. As time is the most important factor in the progress of many deadly viral diseases, early detection becomes of paramount importance for effective treatment. Aptamers are small oligonucleotide molecules made by the systematic evolution of ligands by exponential enrichment (SELEX). Aptamers are characterized by being able to specifically bind to a target, much like antibodies. However, unlike antibodies, aptamers are easily synthesized, modified, and are able to target a wider range of substances, including proteins and carbohydrates. With these advantages in mind, many studies on aptamer-based viral diagnosis and treatments are currently in progress. The use of aptamers for viral diagnosis requires a system that recognizes the binding of viral molecules to aptamers in samples of blood, serum, plasma, or in virus-infected cells. From a therapeutic perspective, aptamers target viral particles or host cell receptors to prevent the interaction between the virus and host cells or target intracellular viral proteins to interrupt the life cycle of the virus within infected cells. In this paper, we review recent attempts to use aptamers for the diagnosis and treatment of various viral infections.
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Affiliation(s)
- Tae-Hyeong Kim
- Department of Molecular Biology, Dankook University, Cheonan 31116, Korea;
| | - Seong-Wook Lee
- Department of Life Convergence, Research Institute of Advanced Omics, Dankook University, Yongin 16890, Korea
- R&D Center, Rznomics Inc., Seongnam 13486, Korea
- Correspondence:
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6
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Jana J, Mohr S, Vianney YM, Weisz K. Structural motifs and intramolecular interactions in non-canonical G-quadruplexes. RSC Chem Biol 2021; 2:338-353. [PMID: 34458788 PMCID: PMC8341446 DOI: 10.1039/d0cb00211a] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/14/2021] [Indexed: 12/12/2022] Open
Abstract
Guanine(G)-rich DNA or RNA sequences can assemble or intramolecularly fold into G-quadruplexes formed through the stacking of planar G·G·G·G tetrads in the presence of monovalent cations. These secondary nucleic acid structures have convincingly been shown to also exist within a cellular environment exerting important regulatory functions in physiological processes. For identifying nucleic acid segments prone to quadruplex formation, a putative quadruplex sequence motif encompassing closely spaced tracts of three or more guanosines is frequently employed for bioinformatic search algorithms. Depending on the number and type of intervening residues as well as on solution conditions, such sequences may fold into various canonical G4 topologies with continuous G-columns. On the other hand, a growing number of sequences capable of quadruplex formation feature G-deficient guanine tracts, escaping the conservative consensus motif. By folding into non-canonical quadruplex structures, they adopt unique topologies depending on their specific sequence context. These include G-columns with only two guanines, bulges, snapback loops, D- and V-shaped loops as well as interlocked structures. This review focuses on G-quadruplex species carrying such distinct structural motifs. It evaluates characteristic features of their non-conventional scaffold and highlights principles of stabilizing interactions that also allow for their folding into stable G-quadruplex structures.
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Affiliation(s)
- Jagannath Jana
- Institute of Biochemistry, Universität Greifswald Felix-Hausdorff-Str. 4 D-17487 Greifswald Germany +49 3834 420-4427 +49 3834 420-4426
| | - Swantje Mohr
- Institute of Biochemistry, Universität Greifswald Felix-Hausdorff-Str. 4 D-17487 Greifswald Germany +49 3834 420-4427 +49 3834 420-4426
| | - Yoanes Maria Vianney
- Institute of Biochemistry, Universität Greifswald Felix-Hausdorff-Str. 4 D-17487 Greifswald Germany +49 3834 420-4427 +49 3834 420-4426
| | - Klaus Weisz
- Institute of Biochemistry, Universität Greifswald Felix-Hausdorff-Str. 4 D-17487 Greifswald Germany +49 3834 420-4427 +49 3834 420-4426
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7
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Search for new therapeutics against HIV-1 via dual inhibition of RNase H and integrase: current status and future challenges. Future Med Chem 2021; 13:269-286. [PMID: 33399497 DOI: 10.4155/fmc-2020-0257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Reverse transcriptase and integrase are key enzymes that play a pivotal role in HIV-1 viral maturation and replication. Reverse transcriptase consists of two active sites: RNA-dependent DNA polymerase and RNase H. The catalytic domains of integrase and RNase H share striking similarity, comprising two aspartates and one glutamate residue, also known as the catalytic DDE triad, and a Mg2+ pair. The simultaneous inhibition of reverse transcriptase and integrase can be a rational drug discovery approach for combating the emerging drug resistance problem. In the present review, the dual inhibition of RNase H and integrase is systematically discussed, including rationality of design, journey of development, advancement and future perspective.
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8
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Riccardi C, Napolitano E, Musumeci D, Montesarchio D. Dimeric and Multimeric DNA Aptamers for Highly Effective Protein Recognition. Molecules 2020; 25:E5227. [PMID: 33182593 PMCID: PMC7698228 DOI: 10.3390/molecules25225227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/14/2022] Open
Abstract
Multivalent interactions frequently occur in biological systems and typically provide higher binding affinity and selectivity in target recognition than when only monovalent interactions are operative. Thus, taking inspiration by nature, bivalent or multivalent nucleic acid aptamers recognizing a specific biological target have been extensively studied in the last decades. Indeed, oligonucleotide-based aptamers are suitable building blocks for the development of highly efficient multivalent systems since they can be easily modified and assembled exploiting proper connecting linkers of different nature. Thus, substantial research efforts have been put in the construction of dimeric/multimeric versions of effective aptamers with various degrees of success in target binding affinity or therapeutic activity enhancement. The present review summarizes recent advances in the design and development of dimeric and multimeric DNA-based aptamers, including those forming G-quadruplex (G4) structures, recognizing different key proteins in relevant pathological processes. Most of the designed constructs have shown improved performance in terms of binding affinity or therapeutic activity as anti-inflammatory, antiviral, anticoagulant, and anticancer agents and their number is certainly bound to grow in the next future.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini, 5, I-80131 Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
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9
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Virgilio A, Esposito V, Tassinari M, Nadai M, Richter SN, Galeone A. Novel monomolecular derivatives of the anti-HIV-1 G-quadruplex-forming Hotoda's aptamer containing inversion of polarity sites. Eur J Med Chem 2020; 208:112786. [PMID: 32911256 DOI: 10.1016/j.ejmech.2020.112786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 08/06/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023]
Abstract
Here we report on the design, preparation and investigation of four analogues of the anti-HIV G-quadruplex-forming Hotoda's aptamer, based on an unprecedented linear topology. In these derivatives, four TGGGAGT tracts have been joined together by exploiting 3'-3' and 5'-5' inversion of polarity sites formed by canonical phosphodiester bonds or a glycerol-based linker. Circular dichroism data suggest that all oligodeoxynucleotides fold in monomolecular G-quadruplex structures characterized by a parallel strand orientation and three side loops connecting 3'- or 5'-ends. The derivative bearing two lipophilic groups, namely HT353LGly, inhibited virus entry into the host cell, with anti-HIV-1 activity in the low nanomolar range; the other derivatives, albeit sharing the same base sequence and similar topology, were inactive. These results highlight that monomolecular Hotoda's aptamers with inversion of polarity sites represent a successful alternative strategy that merges the easiness of synthesis with the maintenance of remarkable activity. They also indicate that two lipophilic groups are necessary and sufficient for biological activity. Our data will inspire the design of further simplified derivatives with improved biophysical and antiviral properties.
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Affiliation(s)
- Antonella Virgilio
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Veronica Esposito
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Martina Tassinari
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121, Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121, Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121, Padua, Italy.
| | - Aldo Galeone
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Napoli, Italy.
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10
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Davydova AS, Timoshenko VV, Lomzov AA, Pyshnyi DV, Venyaminova AG, Vorobyeva MA. G-quadruplex 2'-F-modified RNA aptamers targeting hemoglobin: Structure studies and colorimetric assays. Anal Biochem 2020; 611:113886. [PMID: 32795455 DOI: 10.1016/j.ab.2020.113886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 10/23/2022]
Abstract
Biosensors that rely on aptamers as analyte-recognizing elements (also known as aptasensors) are gaining in popularity during recent years for analytical and biomedical applications. Among them, colorimetric ELISA-like systems seem very promising for biomarker detection in medical diagnostics. For their development, one should thoroughly consider the characteristics of the aptamers, with a particular focus on the secondary structure. In this study, we performed an in-depth structural study of previously selected hemoglobin-binding 2'-F-RNA aptamers using CD spectroscopy, enzymatic probing, and specific fluorophore binding. Only a combination of different assays allowed us to prove G-quadruplex formation for anti-hemoglobin 2'-F-RNA aptamers. We also demonstrated a possible application of these 2'-F-RNA aptamers for microplate colorimetric detection of human hemoglobin in both direct and sandwich formats.
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Affiliation(s)
- Anna S Davydova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.
| | | | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Mariya A Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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11
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Predicting Future Prospects of Aptamers in Field-Effect Transistor Biosensors. Molecules 2020; 25:molecules25030680. [PMID: 32033448 PMCID: PMC7036789 DOI: 10.3390/molecules25030680] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/26/2020] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
Aptamers, in sensing technology, are famous for their role as receptors in versatile applications due to their high specificity and selectivity to a wide range of targets including proteins, small molecules, oligonucleotides, metal ions, viruses, and cells. The outburst of field-effect transistors provides a label-free detection and ultra-sensitive technique with significantly improved results in terms of detection of substances. However, their combination in this field is challenged by several factors. Recent advances in the discovery of aptamers and studies of Field-Effect Transistor (FET) aptasensors overcome these limitations and potentially expand the dominance of aptamers in the biosensor market.
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12
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Heddi B, Cheong VV, Schmitt E, Mechulam Y, Phan AT. Recognition of different base tetrads by RHAU (DHX36): X-ray crystal structure of the G4 recognition motif bound to the 3′-end tetrad of a DNA G-quadruplex. J Struct Biol 2020; 209:107399. [DOI: 10.1016/j.jsb.2019.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 12/16/2022]
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13
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Roxo C, Kotkowiak W, Pasternak A. G-Quadruplex-Forming Aptamers-Characteristics, Applications, and Perspectives. Molecules 2019; 24:E3781. [PMID: 31640176 PMCID: PMC6832456 DOI: 10.3390/molecules24203781] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 12/31/2022] Open
Abstract
G-quadruplexes constitute a unique class of nucleic acid structures formed by G-rich oligonucleotides of DNA- or RNA-type. Depending on their chemical nature, loops length, and localization in the sequence or structure molecularity, G-quadruplexes are highly polymorphic structures showing various folding topologies. They may be formed in the human genome where they are believed to play a pivotal role in the regulation of multiple biological processes such as replication, transcription, and translation. Thus, natural G-quadruplex structures became prospective targets for disease treatment. The fast development of systematic evolution of ligands by exponential enrichment (SELEX) technologies provided a number of G-rich aptamers revealing the potential of G-quadruplex structures as a promising molecular tool targeted toward various biologically important ligands. Because of their high stability, increased cellular uptake, ease of chemical modification, minor production costs, and convenient storage, G-rich aptamers became interesting therapeutic and diagnostic alternatives to antibodies. In this review, we describe the recent advances in the development of G-quadruplex based aptamers by focusing on the therapeutic and diagnostic potential of this exceptional class of nucleic acid structures.
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Affiliation(s)
- Carolina Roxo
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Weronika Kotkowiak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Anna Pasternak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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14
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Rose KM, Alves Ferreira-Bravo I, Li M, Craigie R, Ditzler MA, Holliger P, DeStefano JJ. Selection of 2'-Deoxy-2'-Fluoroarabino Nucleic Acid (FANA) Aptamers That Bind HIV-1 Integrase with Picomolar Affinity. ACS Chem Biol 2019; 14:2166-2175. [PMID: 31560515 PMCID: PMC7005942 DOI: 10.1021/acschembio.9b00237] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Systematic Evolution
of Ligands by Exponential Enrichment (SELEX)
is the iterative process by which nucleic acids that can bind with
high affinity and specificity (termed aptamers) to specific protein
targets are selected. Using a SELEX protocol adapted for Xeno-Nucleic
Acid (XNA) as a suitable substrate for aptamer generation, 2′-fluoroarabinonucleic
acid (FANA) was used to select several related aptamers to HIV-1 integrase
(IN). IN bound FANA aptamers with equilibrium dissociation constants
(KD,app) of ∼50–100 pM in
a buffer with 200 mM NaCl and 6 mM MgCl2. Comparisons to
published HIV-1 IN RNA and DNA aptamers as well as IN genomic binding
partners indicated that FANA aptamers bound more than 2 orders of
magnitude more tightly to IN. Using a combination of RNA folding algorithms
and covariation analysis, all strong binding aptamers demonstrated
a common four-way junction structure, despite significant sequence
variation. IN aptamers were selected from the same starting library
as FA1, a FANA aptamer that binds with pM affinity to HIV-1 Reverse
Transcriptase (RT). It contains a 20-nucleotide 5′ DNA sequence
followed by 59 FANA nucleotides. IN-1.1 (one of the selected aptamers)
potently inhibited IN activity and intasome formation in vitro. Replacing
the FANA nucleotides of IN-1.1 with 2′-fluororibonucleic acid
(F-RNA), which has the same chemical formula but with a ribose rather
than arabinose sugar conformation, dramatically reduced binding, suggesting
that FANA adopts unique structural conformations that promote binding
to HIV-1 IN.
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Umar MI, Ji D, Chan CY, Kwok CK. G-Quadruplex-Based Fluorescent Turn-On Ligands and Aptamers: From Development to Applications. Molecules 2019; 24:E2416. [PMID: 31262059 PMCID: PMC6650947 DOI: 10.3390/molecules24132416] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/17/2019] [Accepted: 06/24/2019] [Indexed: 02/08/2023] Open
Abstract
Guanine (G)-quadruplexes (G4s) are unique nucleic acid structures that are formed by stacked G-tetrads in G-rich DNA or RNA sequences. G4s have been reported to play significant roles in various cellular events in both macro- and micro-organisms. The identification and characterization of G4s can help to understand their different biological roles and potential applications in diagnosis and therapy. In addition to biophysical and biochemical methods to interrogate G4 formation, G4 fluorescent turn-on ligands can be used to target and visualize G4 formation both in vitro and in cells. Here, we review several representative classes of G4 fluorescent turn-on ligands in terms of their interaction mechanism and application perspectives. Interestingly, G4 structures are commonly identified in DNA and RNA aptamers against targets that include proteins and small molecules, which can be utilized as G4 tools for diverse applications. We therefore also summarize the recent development of G4-containing aptamers and highlight their applications in biosensing, bioimaging, and therapy. Moreover, we discuss the current challenges and future perspectives of G4 fluorescent turn-on ligands and G4-containing aptamers.
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Affiliation(s)
- Mubarak I Umar
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Danyang Ji
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun-Yin Chan
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
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16
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Hotoda's Sequence and Anti-HIV Activity: Where Are We Now? Molecules 2019; 24:molecules24071417. [PMID: 30974914 PMCID: PMC6479790 DOI: 10.3390/molecules24071417] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/02/2019] [Accepted: 04/05/2019] [Indexed: 01/24/2023] Open
Abstract
The pharmacological relevance of ODNs forming G-quadruplexes as anti-HIV agents has been extensively reported in the literature over the last few years. Recent detailed studies have elucidated the peculiar arrangement adopted by many G-quadruplex-based aptamers and provided insight into their mechanism of action. In this review, we have reported the history of a strong anti-HIV agent: the 6-mer d(TGGGAG) sequence, commonly called "Hotoda's sequence". In particular, all findings reported on this sequence and its modified sequences have been discussed considering the following research phases: (i) discovery of the first 5'-modified active d(TGGGAG) sequences; (ii) synthesis of a variety of end-modified d(TGGGAG) sequences; (iii) biophysical and NMR investigations of natural and modified Hotoda's sequences; (iv); kinetic studies on the most active 5'-modified d(TGGGAG) sequences; and (v) extensive anti-HIV screening of G-quadruplexes formed by d(TGGGAG) sequences. This review aims to clarify all results obtained over the years on Hotoda's sequence, revealing its potentiality as a strong anti-HIV agent (EC50 = 14 nM).
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Rivieccio E, Tartaglione L, Esposito V, Dell'Aversano C, Koneru PC, Scuotto M, Virgilio A, Mayol L, Kvaratskhelia M, Varra M. Structural studies and biological evaluation of T30695 variants modified with single chiral glycerol-T reveal the importance of LEDGF/p75 for the aptamer anti-HIV-integrase activities. Biochim Biophys Acta Gen Subj 2018; 1863:351-361. [PMID: 30414444 DOI: 10.1016/j.bbagen.2018.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 10/18/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022]
Abstract
Some G-quadruplex (GQ) forming aptamers, such as T30695, exhibit particularly promising properties among the potential anti-HIV drugs. T30695 G-quadruplex binds to HIV-1 integrase (IN) and inhibits its activity during 3'-end processing at nanomolar concentrations. Herein we report a study concerning six T30695-GQ variants, in which the R or S chiral glycerol T, singly replaced the thymine residues at the T30695 G-quadruplex loops. CD melting, EMSA and HMRS experiments provided information about the thermal stability and the stoichiometry of T30695-GQ variants, whereas CD and 1H NMR studies were performed to evaluate the effects of the modifications on T30695-GQ topology. Furthermore, LEDGF/p75 dependent and independent integration assays were carried out to evaluate how T loop modifications impact T30695-GQ biological activities. The obtained results showed that LEDGF/p75 adversely affects the potencies of T30695 and its variants. The IN inhibitory activities of the modified aptamers also depended on the position and on the chirality (R or S) of glycerol T loop in the GQ, mostly regardless of the G-quadruplex stabilities. In view of our and literature data, we suggest that the allosteric modulation of IN tetramer conformations by LEDGF/p75 alters the interactions between the aptamers and the enzyme. Therefore, the new T30695 variants could be suitable tools in studies aimed to clarify the HIV-1 IN tetramers allostery and its role in the integration activity.
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Affiliation(s)
- Elisa Rivieccio
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Luciana Tartaglione
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Veronica Esposito
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Carmela Dell'Aversano
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - P C Koneru
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 500 West 12th Ave., Columbus, OH 43210, USA; Division of Infectious Diseases, University of Colorado School of Medicine, 12700 E. 19th Avenue, Aurora, CO 80045, USA
| | - Maria Scuotto
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Antonella Virgilio
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Luciano Mayol
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 500 West 12th Ave., Columbus, OH 43210, USA; Division of Infectious Diseases, University of Colorado School of Medicine, 12700 E. 19th Avenue, Aurora, CO 80045, USA.
| | - Michela Varra
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy.
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18
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Tang Y, Han Z, Ren H, Guo J, Chong H, Tian Y, Liu K, Xu L. A novel multivalent DNA helix-based inhibitor showed enhanced anti-HIV-1 fusion activity. Eur J Pharm Sci 2018; 125:244-253. [PMID: 30292749 DOI: 10.1016/j.ejps.2018.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/26/2018] [Accepted: 10/04/2018] [Indexed: 11/27/2022]
Abstract
DNA helix-based HIV-1 fusion inhibitors have been discovered as potent drug candidates, but further research is required to enhance their efficiency. The trimeric structure of the HIV-1 envelope glycoprotein provides a structural basis for multivalent drug design. In this work, a "multi-domain" strategy was adopted for design of an oligodeoxynucleotide with assembly, linkage, and activity domains. Built on the self-assembly of higher-order nucleic acid structure, a novel category of multivalent DNA helix-based HIV-1 fusion inhibitor could be easily obtained by a simple annealing course in solution buffer, with no other chemical synthesis for multivalent connection. An optimized multivalent molecule, M4, showed significantly higher anti-HIV-1 fusion activity than did corresponding monovalent inhibitors. Examination of the underlying mechanism indicated that M4 could interact with HIV-1 glycoproteins gp120 and gp41, thereby inhibiting 6HB formation in the fusion course. M4 also showed anti-RDDP and anti-RNase H activity of reverse transcriptase. Besides, these assembled molecules showed improved in vitro metabolic stability in liver homogenate, kidney homogenate, and rat plasma. Moreover, little acute toxicity was observed. Our findings aid in the structural design and understanding of the mechanisms of DNA helix-based HIV-1 inhibitors. This study also provides a general strategy based on a new structural paradigm for the design of other multivalent nucleic acid drugs.
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Affiliation(s)
- Yongjia Tang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, 27 Taiping road, Beijing 100850, China
| | - Zeye Han
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, 27 Taiping road, Beijing 100850, China
| | - Hongqian Ren
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, 27 Taiping road, Beijing 100850, China
| | - Jiamei Guo
- Beijing Key laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, , Institute of Materia Medica, , Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Huihui Chong
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yangli Tian
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, 27 Taiping road, Beijing 100850, China
| | - Keliang Liu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, 27 Taiping road, Beijing 100850, China.
| | - Liang Xu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, 27 Taiping road, Beijing 100850, China.
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19
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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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20
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Therapeutic aptamers in discovery, preclinical and clinical stages. Adv Drug Deliv Rev 2018; 134:51-64. [PMID: 30125605 DOI: 10.1016/j.addr.2018.08.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/11/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023]
Abstract
The aptamer field witnessed steady growth during the past 28 years as evident from the exponentially increasing number of related publications. The field is "coming of age", but like other biomedical research areas facing a global push towards translational research to carry ideas from bench- to bedside, there is pressure to show impact for aptamers at the clinical end. Being easy-to-make, non-immunogenic, stable and high-affinity nano-ligands, aptamers are perfectly poised to move in this direction. They can specifically bind targets ranging from small molecules to complex multimeric structures, making them potentially useful in a limitless variety of therapeutic approaches. This review will summarize efforts made to accomplish the therapeutic promise of aptamers, with a focus on aptamers directly acting as therapeutic molecules, rather than those used in targeted delivery of other drugs. The review will showcase representative examples at various stages of development, covering different disease categories.
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21
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Kaboudin B, Saghatchi F, Kazemi F, Akbari-Birgani S. A Novel Magnetic Carbon Nanotubes Functionalized with Pyridine Groups: Synthesis, Characterization and Their Application as an Efficient Carrier for Plasmid DNA and Aptamer. ChemistrySelect 2018. [DOI: 10.1002/slct.201800708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Babak Kaboudin
- Department of Chemistry; Institute for Advanced Studies in Basic Sciences (IASBS), Gava Zang; Zanjan 45137-66731 Iran
- Center for Research in Basic Sciences and Contemporary Technologies
| | - Fatemeh Saghatchi
- Department of Chemistry; Institute for Advanced Studies in Basic Sciences (IASBS), Gava Zang; Zanjan 45137-66731 Iran
| | - Foad Kazemi
- Department of Chemistry; Institute for Advanced Studies in Basic Sciences (IASBS), Gava Zang; Zanjan 45137-66731 Iran
| | - Shiva Akbari-Birgani
- Center for Research in Basic Sciences and Contemporary Technologies
- Faculty of Biological Sciences; Institute for Advanced Studies in Basic Sciences (IASBS), GavaZang; Zanjan 45137-66731 Iran
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22
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Pan Q, Luo F, Liu M, Zhang XL. Oligonucleotide aptamers: promising and powerful diagnostic and therapeutic tools for infectious diseases. J Infect 2018; 77:83-98. [PMID: 29746951 PMCID: PMC7112547 DOI: 10.1016/j.jinf.2018.04.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 01/02/2018] [Accepted: 04/08/2018] [Indexed: 12/21/2022]
Abstract
The entire human population is at risk of infectious diseases worldwide. Thus far, the diagnosis and treatment of human infectious diseases at the molecular and nanoscale levels have been extremely challenging tasks because of the lack of effective probes to identify and recognize biomarkers of pathogens. Oligonucleotide aptamers are a class of small nucleic acid ligands that are composed of single-stranded DNA (ssDNA) or RNA and act as affinity probes or molecular recognition elements for a variety of targets. These aptamers have an exciting potential for diagnose and/or treatment of specific diseases. In this review, we highlight areas where aptamers have been developed as diagnostic and therapeutic agents for both bacterial and viral infectious diseases as well as aptamer-based detection.
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Affiliation(s)
- Qin Pan
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Fengling Luo
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Min Liu
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China.
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23
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Tuma Sabah J, Zulkifli RM, Shahir S, Ahmed F, Abdul Kadir MR, Zakaria Z. In vitro selection and characterization of single stranded DNA aptamers for luteolin: A possible recognition tool. Anal Biochem 2018. [PMID: 29524380 DOI: 10.1016/j.ab.2018.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Distinctive bioactivities possessed by luteolin (3', 4', 5, 7-tetrahydroxy-flavone) are advantageous for sundry practical applications. This paper reports the in vitro selection and characterization of single stranded-DNA (ssDNA) aptamers, specific for luteolin (LUT). 76-mer library containing 1015 randomized ssDNA were screened via systematic evolution of ligands by exponential enrichment (SELEX). The recovered ssDNA pool from the 8th round was amplified with unlabeled primers and cloned into PSTBlue-1 vector prior to sequencing. 22 of LUT-binding aptamer variants were further classified into one of the seven groups based on their N40 random sequence regions, wherein one representative from each group was characterized. The dissociation constant of aptamers designated as LUT#28, LUT#20 and LUT#3 was discerned to be 107, 214 and 109 nM, respectively with high binding affinity towards LUT. Prediction analysis of the secondary structure suggested discrete features with typical loop and stem motifs. Furthermore, LUT#3 displayed higher specificity with insignificant binding toward kaempferol and quercetin despite its structural and functional similarity compared to LUT#28 and LUT#20. Further LUT#3 can detect free luteolin within 0.2-1 mM in solution. It was suggested that LUT#3 aptamer were the most suitable for LUT recognition tool at laboratory scale based on the condition tested.
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Affiliation(s)
- Jinan Tuma Sabah
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Malaysia
| | | | - Shafinaz Shahir
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Malaysia
| | - Farediah Ahmed
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Malaysia
| | | | - Zarita Zakaria
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Malaysia
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24
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Romanucci V, Zarrelli A, Liekens S, Noppen S, Pannecouque C, Di Fabio G. New findings on the d(TGGGAG) sequence: Surprising anti-HIV-1 activity. Eur J Med Chem 2018; 145:425-430. [PMID: 29335208 DOI: 10.1016/j.ejmech.2018.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 12/12/2017] [Accepted: 01/02/2018] [Indexed: 10/18/2022]
Abstract
The biological relevance of tetramolecular G-quadruplexes especially as anti-HIV agents has been extensively reported in the literature over the last years. In the light of our recent results regarding the slow G-quadruplex folding kinetics of ODNs based on d(TGGGAG) sequence, here we report a systematic anti-HIV screening to investigate the impact of the G-quadruplex folding on their anti-HIV activity. In particular, varying the single stranded concentrations of ODNs, it has been tested a pool of ODN sample solutions with different G-quadruplex concentrations. The anti-HIV assays have been designed favouring the limited kinetics involved in the tetramolecular G4-association based on the d(TGGGAG) sequence. Aiming to determine the stoichiometry of G-quadruplex structures in the same experimental conditions of the anti-HIV assays, a native gel electrophoresis was performed. The gel confirmed the G-quadruplex formation for almost all sample solutions while showing the formation of high order G4 structures for the more concentrated ODNs solutions. The most significant result is the discovery of a potent anti-HIV activity of the G-quadruplex formed by the natural d(TGGGAG) sequence (IC50 = 14 nM) that, until now, has been reported to be completely inactive against HIV infection.
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Affiliation(s)
- Valeria Romanucci
- Department of Chemical Sciences, University of Napoli 'Federico II', Via Cintia 4, I-80126, Napoli, Italy
| | - Armando Zarrelli
- Department of Chemical Sciences, University of Napoli 'Federico II', Via Cintia 4, I-80126, Napoli, Italy
| | - Sandra Liekens
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, B-3000, Leuven, Belgium
| | - Sam Noppen
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, B-3000, Leuven, Belgium
| | - Christophe Pannecouque
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, B-3000, Leuven, Belgium.
| | - Giovanni Di Fabio
- Department of Chemical Sciences, University of Napoli 'Federico II', Via Cintia 4, I-80126, Napoli, Italy.
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25
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Lech CJ, Phan AT. Ball with hair: modular functionalization of highly stable G-quadruplex DNA nano-scaffolds through N2-guanine modification. Nucleic Acids Res 2017; 45:6265-6274. [PMID: 28499037 PMCID: PMC5499775 DOI: 10.1093/nar/gkx243] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 05/10/2017] [Indexed: 12/13/2022] Open
Abstract
Functionalized nanoparticles have seen valuable applications, particularly in the delivery of therapeutic and diagnostic agents in biological systems. However, the manufacturing of such nano-scale systems with the consistency required for biological application can be challenging, as variation in size and shape have large influences in nanoparticle behavior in vivo. We report on the development of a versatile nano-scaffold based on the modular functionalization of a DNA G-quadruplex. DNA sequences are functionalized in a modular fashion using well-established phosphoramidite chemical synthesis with nucleotides containing modification of the amino (N2) position of the guanine base. In physiological conditions, these sequences fold into well-defined G-quadruplex structures. The resulting DNA nano-scaffolds are thermally stable, consistent in size, and functionalized in a manner that allows for control over the density and relative orientation of functional chemistries on the nano-scaffold surface. Various chemistries including small modifications (N2-methyl-guanine), bulky aromatic modifications (N2-benzyl-guanine), and long chain-like modifications (N2-6-amino-hexyl-guanine) are tested and are found to be generally compatible with G-quadruplex formation. Furthermore, these modifications stabilize the G-quadruplex scaffold by 2.0–13.3 °C per modification in the melting temperature, with concurrent modifications producing extremely stable nano-scaffolds. We demonstrate the potential of this approach by functionalizing nano-scaffolds for use within the biotin–avidin conjugation approach.
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Affiliation(s)
- Christopher Jacques Lech
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Anh Tuân Phan
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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26
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Do NQ, Chung WJ, Truong THA, Heddi B, Phan AT. G-quadruplex structure of an anti-proliferative DNA sequence. Nucleic Acids Res 2017; 45:7487-7493. [PMID: 28549181 PMCID: PMC5499593 DOI: 10.1093/nar/gkx274] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/24/2017] [Indexed: 01/06/2023] Open
Abstract
AGRO100 (also known as AS1411) is a G-rich oligonucleotide that has long been established as a potent anti-cancer aptamer. However, the structure of AGRO100 remained unresolved, due to the co-existence of multiple different G-quadruplex conformations. We identified a DNA sequence named AT11, derived from AGRO100, which formed a single major G-quadruplex conformation and exhibited a similar anti-proliferative activity as AGRO100. The solution structure of AT11 revealed a four-layer G-quadruplex comprising of two propeller-type parallel-stranded subunits connected through a central linker. The stacking between the two subunits occurs at the 3΄-end of the first block and the 5΄-end of the second block. The structure of the anti-proliferative DNA sequence AT11 will allow greater understanding on the G-quadruplex folding principles and aid in structural optimization of anti-proliferative oligonucleotides.
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Affiliation(s)
- Ngoc Quang Do
- School of Physical and Mathematical Sciences.,School of Biological Sciences, Nanyang Technological University, Singapore
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27
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Kwok CK, Merrick CJ. G-Quadruplexes: Prediction, Characterization, and Biological Application. Trends Biotechnol 2017; 35:997-1013. [PMID: 28755976 DOI: 10.1016/j.tibtech.2017.06.012] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/14/2017] [Accepted: 06/15/2017] [Indexed: 02/08/2023]
Abstract
Guanine (G)-rich sequences in nucleic acids can assemble into G-quadruplex structures that involve G-quartets linked by loop nucleotides. The structural and topological diversity of G-quadruplexes have attracted great attention for decades. Recent methodological advances have advanced the identification and characterization of G-quadruplexes in vivo as well as in vitro, and at a much higher resolution and throughput, which has greatly expanded our current understanding of G-quadruplex structure and function. Accumulating knowledge about the structural properties of G-quadruplexes has helped to design and develop a repertoire of molecular and chemical tools for biological applications. This review highlights how these exciting methods and findings have opened new doors to investigate the potential functions and applications of G-quadruplexes in basic and applied biosciences.
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Affiliation(s)
- Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
| | - Catherine J Merrick
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, UK.
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28
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Yokoyama T, Tsukakoshi K, Yoshida W, Saito T, Teramoto K, Savory N, Abe K, Ikebukuro K. Development of HGF-binding aptamers with the combination of G4 promoter-derived aptamer selection and in silico maturation. Biotechnol Bioeng 2017. [PMID: 28627727 DOI: 10.1002/bit.26354] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We describe the selection of aptamers based on bioinformatics-based approaches without Systematic Evolution of Ligands by EXponential enrichment (SELEX). SELEX is a potent method; however, it is time intensive and the PCR-amplification step, which is essential step for SELEX, leads to the loss of good aptamers. We have developed an aptamer-screening method, G4 promoter-derived aptamer selection (G4PAS), and an aptamer-improving method, in silico maturation (ISM). They are based on in silico sequence selection and computer assisted directed evolution, respectively. In this study, we succeeded in identifying new aptamers against hepatocyte growth factor (HGF) by G4PAS as well as improving the specificity of the HGF aptamers by ISM. Using ISM improved the specificity of the aptamer for HGF by up to 45-fold in comparison with the original aptamer. These methods enable easy and efficient identification of good aptamers, and the combination of G4PAS with ISM can thus serve as a potent approach for aptamer identification. Biotechnol. Bioeng. 2017;114: 2196-2203. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Tomomi Yokoyama
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Wataru Yoshida
- School of Biotechnology and Bioscience, Tokyo University of Technology, Hachioji, Tokyo, Japan
| | - Taiki Saito
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kentaro Teramoto
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Nasa Savory
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koichi Abe
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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29
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Platella C, Riccardi C, Montesarchio D, Roviello GN, Musumeci D. G-quadruplex-based aptamers against protein targets in therapy and diagnostics. Biochim Biophys Acta Gen Subj 2017; 1861:1429-1447. [PMID: 27865995 PMCID: PMC7117017 DOI: 10.1016/j.bbagen.2016.11.027] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 12/17/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA molecules identified to recognize with high affinity specific targets including proteins, small molecules, ions, whole cells and even entire organisms, such as viruses or bacteria. They can be identified from combinatorial libraries of DNA or RNA oligonucleotides by SELEX technology, an in vitro iterative selection procedure consisting of binding (capture), partitioning and amplification steps. Remarkably, many of the aptamers selected against biologically relevant protein targets are G-rich sequences that can fold into stable G-quadruplex (G4) structures. Aiming at disseminating novel inspiring ideas within the scientific community in the field of G4-structures, the emphasis of this review is placed on: 1) recent advancements in SELEX technology for the efficient and rapid identification of new candidate aptamers (introduction of microfluidic systems and next generation sequencing); 2) recurrence of G4 structures in aptamers selected by SELEX against biologically relevant protein targets; 3) discovery of several G4-forming motifs in important regulatory regions of the human or viral genome bound by endogenous proteins, which per se can result into potential aptamers; 4) an updated overview of G4-based aptamers with therapeutic potential and 5) a discussion on the most attractive G4-based aptamers for diagnostic applications. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | | | - Domenica Musumeci
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy; Institute of Biostructures and Bioimages, CNR, Napoli, Italy.
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Korolev SP, Zatsepin TS, Gottikh MB. Oligonucleotide inhibitors of HIV-1 integrase efficiently inhibit HIV-1 reverse transcriptase. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017020078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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Voges M, Schneider C, Sinn M, Hartig JS, Reimer R, Hauber J, Moelling K. Abolishing HIV-1 infectivity using a polypurine tract-specific G-quadruplex-forming oligonucleotide. BMC Infect Dis 2016; 16:358. [PMID: 27450669 PMCID: PMC4957839 DOI: 10.1186/s12879-016-1713-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 07/12/2016] [Indexed: 02/04/2023] Open
Abstract
Background HIV is primarily transmitted by sexual intercourse and predominantly infects people in Third World countries. Here an important medical need is self-protection for women, particularly in societies where condoms are not widely accepted. Therefore, availability of antiviral microbicides may significantly reduce sexual HIV transmission in such environments. Methods Here, we investigated structural characteristics and the antiviral activity of the polypurine tract (PPT)-specific ODN A, a 54-mer oligodeoxynucleotide (ODN) that has been previously shown to trigger the destruction of viral RNA genomes by prematurely activating the retroviral RNase H. The stability of ODN A and mutants thereof was tested at various storage conditions. Furthermore, antiviral effects of ODN A were analyzed in various tissue culture HIV-1 infection models. Finally, circular dichroism spectroscopy was employed to gain insight into the structure of ODN A. Results We show here that ODN A is a powerful tool to abolish HIV-1 particle infectivity, as required for a candidate compound in vaginal microbicide applications. We demonstrate that ODN A is not only capable to prematurely activate the retroviral RNase H, but also prevents HIV-1 from entering host cells. ODN A also exhibited extraordinary stability lasting several weeks. Notably, ODN A is biologically active under various storage conditions, as well as in the presence of carboxymethylcellulose CMC (K-Y Jelly), a potential carrier for application as a vaginal microbicide. ODN A’s remarkable thermostability is apparently due to its specific, guanosine-rich sequence. Interestingly, these residues can form G-quadruplexes and may lead to G-based DNA hyperstructures. Importantly, the pronounced antiviral activity of ODN A is maintained in the presence of human semen or semen-derived enhancer of virus infection (SEVI; i.e. amyloid fibrils), both known to enhance HIV infectivity and reduce the efficacy of some antiviral microbicides. Conclusions Since ODN A efficiently inactivates HIV-1 and also displays high stability and resistance against semen, it combines unique and promising features for its further development as a vaginal microbicide against HIV.
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Affiliation(s)
- Maike Voges
- Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany
| | - Carola Schneider
- Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany
| | - Malte Sinn
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Rudolph Reimer
- Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany
| | - Joachim Hauber
- Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany. .,German Center for Infection Research (DZIF), partner site, Hamburg, Germany.
| | - Karin Moelling
- Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany.,Institute of Medical Virology, University of Zurich, Gloriastrasse 32, 8006, Zurich, Switzerland.,Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany
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Alves Ferreira-Bravo I, Cozens C, Holliger P, DeStefano JJ. Selection of 2'-deoxy-2'-fluoroarabinonucleotide (FANA) aptamers that bind HIV-1 reverse transcriptase with picomolar affinity. Nucleic Acids Res 2015; 43:9587-99. [PMID: 26476448 PMCID: PMC4751925 DOI: 10.1093/nar/gkv1057] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/02/2015] [Indexed: 11/17/2022] Open
Abstract
Using a Systematic Evolution of Ligands by Exponential Enrichment (SELEX) protocol capable of selecting xeno-nucleic acid (XNA) aptamers, a 2′-deoxy-2′-fluoroarabinonucleotide (FANA) aptamer (referred to as FA1) to HIV-1 reverse transcriptase (HIV-1 RT) was selected. FA1 bound HIV-1 RT with KD,app values in the low pM range under different ionic conditions. Comparisons to published HIV-1 RT RNA and DNA aptamers indicated that FA1 bound at least as well as these aptamers. FA1 contained a 20 nucleotide 5′ DNA sequence followed by a 57 nucleotide region of FANA nucleotides. Removal of the fourteen 5′ DNA nucleotides did not affect binding. FA1's predicted structure was composed of four stems and four loops. All stem nucleotides could be modified to G-C base pairs (14 total changes) with a small effect on binding. Eliminating or altering most loop sequences reduced or abolished tight binding. Overall, results suggested that the structure and the sequence of FA1 were important for binding. FA1 showed strong inhibition of HIV-1 RT in extension assays while no specific binding to avian myeloblastosis or Moloney murine leukemia RTs was detected. A complete DNA version of FA1 showed low binding to HIV-1 RT, emphasizing the unique properties of FANA in HIV-1 RT binding.
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Affiliation(s)
- Irani Alves Ferreira-Bravo
- Cell Biology and Molecular Genetics, Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Maryland Pathogen Research Institute, College Park, MD 20742, USA
| | - Christopher Cozens
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Jeffrey J DeStefano
- Cell Biology and Molecular Genetics, Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Maryland Pathogen Research Institute, College Park, MD 20742, USA
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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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Métifiot M, Amrane S, Mergny JL, Andreola ML. Anticancer molecule AS1411 exhibits low nanomolar antiviral activity against HIV-1. Biochimie 2015; 118:173-5. [PMID: 26363100 DOI: 10.1016/j.biochi.2015.09.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/07/2015] [Indexed: 11/29/2022]
Abstract
During clinical trials, a number of fully characterized molecules are dropped along the way because they do not provide enough benefit for the patient. Some of them show limited side effects and might be of great use for other applications. AS1411 is a nucleolin-targeting aptamer that underwent phase II clinical trials as anticancer agent. Here, we show that AS1411 exhibits extremely potent antiviral activity and is therefore an attractive new lead as anti-HIV agent.
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Affiliation(s)
- Mathieu Métifiot
- Laboratoire MFP, CNRS UMR-5234, Université de Bordeaux, FR Transbiomed, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Samir Amrane
- INSERM U869, IECB, ARNA Laboratory, Université de Bordeaux, 2 Rue Robert Escarpit, 33600 Pessac, France
| | - Jean-Louis Mergny
- INSERM U869, IECB, ARNA Laboratory, Université de Bordeaux, 2 Rue Robert Escarpit, 33600 Pessac, France.
| | - Marie-Line Andreola
- Laboratoire MFP, CNRS UMR-5234, Université de Bordeaux, FR Transbiomed, 146 Rue Léo Saignat, 33076 Bordeaux, France.
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Ogloblina AM, Bannikova VA, Khristich AN, Oretskaya TS, Yakubovskaya MG, Dolinnaya NG. Parallel G-quadruplexes formed by guanine-rich microsatellite repeats inhibit human topoisomerase I. BIOCHEMISTRY (MOSCOW) 2015; 80:1026-38. [DOI: 10.1134/s0006297915080088] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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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: 67] [Impact Index Per Article: 7.4] [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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Su M, Tan J, Lin CY. Development of HIV-1 integrase inhibitors: recent molecular modeling perspectives. Drug Discov Today 2015. [PMID: 26220090 DOI: 10.1016/j.drudis.2015.07.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Of the three viral enzymes essential to HIV replication, HIV-1 integrase (IN) is gaining popularity as a target for the antiviral therapy of AIDS. Substantial work focusing on IN has been done over the past three decades, which has facilitated and led to the approval of three drugs. Here, we discuss in detail the development of IN inhibitors between January 2012 and May 2014, with a particular focus on molecular simulation. We highlight controversial aspects of computational drug design and refer to alternative practices where appropriate. The analysis of these computational approaches provides some useful clues to the possible future discovery of novel IN inhibitors.
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Affiliation(s)
- Min Su
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Jianjun Tan
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Chun-Yuan Lin
- Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan 33302, Taiwan.
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Single-Stranded DNA Aptamers against Pathogens and Toxins: Identification and Biosensing Applications. BIOMED RESEARCH INTERNATIONAL 2015. [PMID: 26199940 PMCID: PMC4493287 DOI: 10.1155/2015/419318] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Molecular recognition elements (MREs) can be short sequences of single-stranded DNA, RNA, small peptides, or antibody fragments. They can bind to user-defined targets with high affinity and specificity. There has been an increasing interest in the identification and application of nucleic acid molecular recognition elements, commonly known as aptamers, since they were first described in 1990 by the Gold and Szostak laboratories. A large number of target specific nucleic acids MREs and their applications are currently in the literature. This review first describes the general methodologies used in identifying single-stranded DNA (ssDNA) aptamers. It then summarizes advancements in the identification and biosensing application of ssDNA aptamers specific for bacteria, viruses, their associated molecules, and selected chemical toxins. Lastly, an overview of the basic principles of ssDNA aptamer-based biosensors is discussed.
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Pescatori L, Métifiot M, Chung S, Masoaka T, Cuzzucoli Crucitti G, Messore A, Pupo G, Madia VN, Saccoliti F, Scipione L, Tortorella S, Di Leva FS, Cosconati S, Marinelli L, Novellino E, Le Grice SFJ, Pommier Y, Marchand C, Costi R, Di Santo R. N-Substituted Quinolinonyl Diketo Acid Derivatives as HIV Integrase Strand Transfer Inhibitors and Their Activity against RNase H Function of Reverse Transcriptase. J Med Chem 2015; 58:4610-23. [PMID: 25961960 DOI: 10.1021/acs.jmedchem.5b00159] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bifunctional quinolinonyl DKA derivatives were first described as nonselective inhibitors of 3'-processing (3'-P) and strand transfer (ST) functions of HIV-1 integrase (IN), while 7-aminosubstituted quinolinonyl derivatives were proven IN strand transfer inhibitors (INSTIs) that also displayed activity against ribonuclease H (RNase H). In this study, we describe the design, synthesis, and biological evaluation of new quinolinonyl diketo acid (DKA) derivatives characterized by variously substituted alkylating groups on the nitrogen atom of the quinolinone ring. Removal of the second DKA branch of bifunctional DKAs, and the amino group in position 7 of quinolinone ring combined with a fine-tuning of the substituents on the benzyl group in position 1 of the quinolinone, increased selectivity for IN ST activity. In vitro, the most potent compound was 11j (IC50 = 10 nM), while the most active compounds against HIV infected cells were ester derivatives 10j and 10l. In general, the activity against RNase H was negligible, with only a few compounds active at concentrations higher than 10 μM. The binding mode of the most potent IN inhibitor 11j within the IN catalytic core domain (CCD) is described as well as its binding mode within the RNase H catalytic site to rationalize its selectivity.
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Affiliation(s)
- Luca Pescatori
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Mathieu Métifiot
- ‡Laboratory of Molecular Pharmacology and Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 5068, Bethesda, Maryland 20892-4255, United States
| | - Suhman Chung
- §Resistance Mechanisms Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Takashi Masoaka
- §Resistance Mechanisms Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Giuliana Cuzzucoli Crucitti
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Antonella Messore
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Giovanni Pupo
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Valentina Noemi Madia
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Francesco Saccoliti
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Luigi Scipione
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Silvano Tortorella
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Francesco Saverio Di Leva
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Sandro Cosconati
- ⊥DiSTABiF, Seconda Università di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luciana Marinelli
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Ettore Novellino
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Stuart F J Le Grice
- §Resistance Mechanisms Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Yves Pommier
- ‡Laboratory of Molecular Pharmacology and Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 5068, Bethesda, Maryland 20892-4255, United States
| | - Christophe Marchand
- ‡Laboratory of Molecular Pharmacology and Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 5068, Bethesda, Maryland 20892-4255, United States
| | - Roberta Costi
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Roberto Di Santo
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
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Novel 3'-Processing Integrase Activity Assay by Real-Time PCR for Screening and Identification of HIV-1 Integrase Inhibitors. BIOMED RESEARCH INTERNATIONAL 2015; 2015:853891. [PMID: 26064960 PMCID: PMC4439469 DOI: 10.1155/2015/853891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/13/2015] [Accepted: 04/17/2015] [Indexed: 11/25/2022]
Abstract
The 3′-end processing (3′P) of each viral long terminal repeat (LTR) during human immunodeficiency virus type-1 (HIV-1) integration is a vital step in the HIV life cycle. Blocking the 3′P using 3′P inhibitor has recently become an attractive strategy for HIV-1 therapeutic intervention. Recently, we have developed a novel real-time PCR based assay for the detection of 3′P activity in vitro. The methodology usually involves biotinylated HIV-1 LTR, HIV-1 integrase (IN), and specific primers and probe. In this novel assay, we designed the HIV-1 LTR substrate based on a sequence with a homology to HIV-1 LTR labeled at its 3′ end with biotin on the sense strand. Two nucleotides at the 3′ end were subsequently removed by IN activity. Only two nucleotides labeled biotin were captured on an avidin-coated tube; therefore, inhibiting the binding of primers and probe results in late signals in the real-time PCR. This novel assay has successfully detected both the 3′P activity of HIV-1 IN and the anti-IN activity by Raltegravir and sodium azide agent. This real-time PCR assay has been shown to be effective and inexpensive for a high-throughput screening of novel IN inhibitors.
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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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Ren J, Wang T, Wang E, Wang J. Versatile G-quadruplex-mediated strategies in label-free biosensors and logic systems. Analyst 2015; 140:2556-72. [DOI: 10.1039/c4an02282c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review addresses how G-quadruplex (G4)-mediated biosensors convert the events of target recognition into a measurable physical signal. The application of label-free G4-strategies in the construction of logic systems is also discussed.
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Affiliation(s)
- Jiangtao Ren
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Tianshu Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
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Mahmood MAI, Wan Y, Islam M, Ali W, Hanif M, Kim YT, Iqbal SM. Micro+nanotexturing of substrates to enhance ligand-assisted cancer cell isolation. NANOTECHNOLOGY 2014; 25:475102. [PMID: 25379988 DOI: 10.1088/0957-4484/25/47/475102] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This paper presents a simple approach to create a two-tiered surface for superior cancer cell isolation. The idea is inspired by the interactions of cells with a nanotextured basement membrane. The texture mimicked the extracellular matrix and basement membrane for superior target cell adhesion. Prepared micro+nanotextured surfaces showed enhanced cell capture. Preparation of the two-tiered surface was done using micro- and nanotexturing and was easily reproducible. It has been shown before that the larger surface area of a nanotextured surface assists the cell's attachment through surface-anchored ligands. Taking it a step further, ligand functionalized two-level micro+nanotextured surfaces improved the sensitivity of the cancer cell isolation over simple flat nanotexturing. The isolation efficiency increased by 208% compared to the surface with a single-level nanotexture. The two-tiered surface was compatible with previously reported nanotextured devices used for cancer cell isolation. Micro-texture on the glass surface was created using simple sand gritting, followed by reactive ion etching (RIE) of the entire surface. The approach could create large surface areas within a short time while maintaining superior cell isolation efficiency.
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Affiliation(s)
- Mohammed Arif I Mahmood
- Nano-Bio Lab, University of Texas at Arlington, Texas, USA. Department of Electrical Engineering, University of Texas at Arlington, Texas, USA. Nanotechnology Research Center, Shimadzu Institute for Research Technologies, University of Texas at Arlington, Texas, USA
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45
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Métifiot M, Amrane S, Litvak S, Andreola ML. G-quadruplexes in viruses: function and potential therapeutic applications. Nucleic Acids Res 2014; 42:12352-66. [PMID: 25332402 PMCID: PMC4227801 DOI: 10.1093/nar/gku999] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/26/2014] [Accepted: 10/06/2014] [Indexed: 12/15/2022] Open
Abstract
G-rich nucleic acids can form non-canonical G-quadruplex structures (G4s) in which four guanines fold in a planar arrangement through Hoogsteen hydrogen bonds. Although many biochemical and structural studies have focused on DNA sequences containing successive, adjacent guanines that spontaneously fold into G4s, evidence for their in vivo relevance has recently begun to accumulate. Complete sequencing of the human genome highlighted the presence of ∼300,000 sequences that can potentially form G4s. Likewise, the presence of putative G4-sequences has been reported in various viruses genomes [e.g., Human immunodeficiency virus (HIV-1), Epstein-Barr virus (EBV), papillomavirus (HPV)]. Many studies have focused on telomeric G4s and how their dynamics are regulated to enable telomere synthesis. Moreover, a role for G4s has been proposed in cellular and viral replication, recombination and gene expression control. In parallel, DNA aptamers that form G4s have been described as inhibitors and diagnostic tools to detect viruses [e.g., hepatitis A virus (HAV), EBV, cauliflower mosaic virus (CaMV), severe acute respiratory syndrome virus (SARS), simian virus 40 (SV40)]. Here, special emphasis will be given to the possible role of these structures in a virus life cycle as well as the use of G4-forming oligonucleotides as potential antiviral agents and innovative tools.
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Affiliation(s)
- Mathieu Métifiot
- CNRS UMR-5234, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Samir Amrane
- INSERM, U869, IECB, ARNA laboratory, Université de Bordeaux, 2 Rue Robert Escarpit 33600 Pessac, France
| | - Simon Litvak
- CNRS UMR-5234, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Marie-Line Andreola
- CNRS UMR-5234, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
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46
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Sirous H, Zabihollahi R, Aghasadeghi MR, Sadat SM, Saghaie L, Fassihi A. Docking studies of some 5-hydroxypyridine-4-one derivatives: evaluation of integrase and ribonuclease H domain of reverse transcriptase as possible targets for anti-HIV-1 activity. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1289-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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47
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Romanucci V, Gaglione M, Messere A, Potenza N, Zarrelli A, Noppen S, Liekens S, Balzarini J, Di Fabio G. Hairpin oligonucleotides forming G-quadruplexes: new aptamers with anti-HIV activity. Eur J Med Chem 2014; 89:51-8. [PMID: 25462225 DOI: 10.1016/j.ejmech.2014.10.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 09/20/2014] [Accepted: 10/12/2014] [Indexed: 12/31/2022]
Abstract
We describe the facile syntheses of new modified oligonucleotides based on d(TG3AG) that form bimolecular G-quadruplexes and possess a HEG loop as an inversion of polarity site 3'-3' or 5'-5' and aromatic residues conjugated to the 5'-end through phosphodiester bonds. The conjugated hairpin G-quadruplexes exhibited parallel orientation, high thermal stability, elevated resistance in human serum and high or moderate anti-HIV-1 activity with low cytotoxicity. Further, these molecules showed significant binding to HIV envelope glycoproteins gp120, gp41 and HSA, as revealed by SPR assays. As a result, these conjugated hairpins represent the first active anti-HIV-1 bimolecular G-quadruplexes based on the d(TG3AG) sequence.
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Affiliation(s)
- Valeria Romanucci
- Department of Chemical Sciences, University of Napoli 'Federico II', Via Cintia 4, I-80126 Napoli, Italy
| | - Maria Gaglione
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università̀ di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Anna Messere
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università̀ di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Nicoletta Potenza
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università̀ di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Armando Zarrelli
- Department of Chemical Sciences, University of Napoli 'Federico II', Via Cintia 4, I-80126 Napoli, Italy
| | - Sam Noppen
- Rega Institute for Medical Research, KU Leuven, 10 Minderbroedersstraat, B-3000 Leuven, Belgium
| | - Sandra Liekens
- Rega Institute for Medical Research, KU Leuven, 10 Minderbroedersstraat, B-3000 Leuven, Belgium
| | - Jan Balzarini
- Rega Institute for Medical Research, KU Leuven, 10 Minderbroedersstraat, B-3000 Leuven, Belgium
| | - Giovanni Di Fabio
- Department of Chemical Sciences, University of Napoli 'Federico II', Via Cintia 4, I-80126 Napoli, Italy.
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Aptamer-facilitated Protection of Oncolytic Virus from Neutralizing Antibodies. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e167. [PMID: 24892725 PMCID: PMC4078759 DOI: 10.1038/mtna.2014.19] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/23/2014] [Indexed: 12/12/2022]
Abstract
Oncolytic viruses promise to significantly improve current cancer treatments through their tumor-selective replication and multimodal attack against cancer cells. However, one of the biggest setbacks for oncolytic virus therapy is the intravenous delivery of the virus, as it can be cleared from the bloodstream by neutralizing antibodies before it reaches the tumor cells. We have selected DNA aptamers against an oncolytic virus, vesicular stomatitis virus, using a competitive binding approach, as well as against the antigen binding fragment (Fab) of antivesicular stomatitis virus polyclonal antibodies, in order to shield the virus from nAbs and enhance its in vivo survival. We used flow cytometry to identify these aptamers and evaluated their efficiency to shield vesicular stomatitis virus in a cell-based plaque forming assay. These oligonucleotides were then modified to obtain multivalent binders, which led to a decrease of viral aggregation, an increase in its infectivity and an increase in its stability in serum. The aptamers were also incubated in nondiluted serum, showing their effectiveness under conditions mimicking those in vivo. With this approach, we were able to increase viral infectivity by more than 70% in the presence of neutralizing antibodies. Thus, this method has the potential to enhance the delivery of vesicular stomatitis virus through the bloodstream without compromising the patient's immune system.
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Costi R, Métifiot M, Chung S, Cuzzucoli Crucitti G, Maddali K, Pescatori L, Messore A, Madia VN, Pupo G, Scipione L, Tortorella S, Di Leva FS, Cosconati S, Marinelli L, Novellino E, Le Grice SFJ, Corona A, Pommier Y, Marchand C, Di Santo R. Basic quinolinonyl diketo acid derivatives as inhibitors of HIV integrase and their activity against RNase H function of reverse transcriptase. J Med Chem 2014; 57:3223-34. [PMID: 24684270 PMCID: PMC4203401 DOI: 10.1021/jm5001503] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
A series
of antiviral basic quinolinonyl diketo acid derivatives
were developed as inhibitors of HIV-1 IN. Compounds 12d,f,i inhibited HIV-1 IN with IC50 values below 100 nM for strand transfer and showed a 2 order of
magnitude selectivity over 3′-processing. These strand transfer
selective inhibitors also inhibited HIV-1 RNase H with low micromolar
potencies. Molecular modeling studies based on both the HIV-1 IN and
RNase H catalytic core domains provided new structural insights for
the future development of these compounds as dual HIV-1 IN and RNase
H inhibitors.
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Affiliation(s)
- Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma , P.le Aldo Moro 5, I-00185 Roma, Italy
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50
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Romanucci V, Milardi D, Campagna T, Gaglione M, Messere A, D'Urso A, Crisafi E, La Rosa C, Zarrelli A, Balzarini J, Di Fabio G. Synthesis, biophysical characterization and anti-HIV activity of d(TG3AG) Quadruplexes bearing hydrophobic tails at the 5'-end. Bioorg Med Chem 2014; 22:960-6. [PMID: 24433967 DOI: 10.1016/j.bmc.2013.12.051] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Revised: 12/17/2013] [Accepted: 12/21/2013] [Indexed: 01/24/2023]
Abstract
Novel conjugated G-quadruplex-forming d(TG3AG) oligonucleotides, linked to hydrophobic groups through phosphodiester bonds at 5'-end, have been synthesized as potential anti-HIV aptamers, via a fully automated, online phosphoramidite-based solid-phase strategy. Conjugated quadruplexes showed pronounced anti-HIV activity with some preference for HIV-1, with inhibitory activity invariably in the low micromolar range. The CD and DSC monitored thermal denaturation studies on the resulting quadruplexes, indicated the insertion of lipophilic residue at the 5'-end, conferring always improved stability to the quadruplex complex (20<ΔTm<40°C). The data suggest no direct functional relationship between the thermal stability and anti-HIV activity of the folded conjugated G-quartets. It would appear that the nature of the residue at 5' end of the d(TG3AG) quadruplexes plays an important role in the thermodynamic stabilization but a minor influence on the anti-HIV activity. Moreover, a detailed CD and DSC analyses indicate a monophasic behaviour for sequences I and V, while for ODNs (II-IV) clearly show that these quadruplex structures deviate from simple two-state melting, supporting the hypothesis that intermediate states along the dissociation pathway may exist.
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Affiliation(s)
- Valeria Romanucci
- Department of Chemical Sciences, University of Napoli 'Federico II', Via Cintia 4, I-80126 Napoli, Italy
| | - Danilo Milardi
- Istituto di Biostrutture e Bioimmagini-Catania, Consiglio Nazionale delle Ricerche, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Tiziana Campagna
- Istituto di Biostrutture e Bioimmagini-Catania, Consiglio Nazionale delle Ricerche, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Maria Gaglione
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università̀ di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Anna Messere
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università̀ di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Alessandro D'Urso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Emanuela Crisafi
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Armando Zarrelli
- Department of Chemical Sciences, University of Napoli 'Federico II', Via Cintia 4, I-80126 Napoli, Italy
| | - Jan Balzarini
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Giovanni Di Fabio
- Department of Chemical Sciences, University of Napoli 'Federico II', Via Cintia 4, I-80126 Napoli, Italy.
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