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Sanna C, D’Abrosca B, Fiorentino A, Giammarino F, Vicenti I, Corona A, Caredda A, Tramontano E, Esposito F. HIV-1 Integrase Inhibition Activity by Spiroketals Derived from Plagius flosculosus, an Endemic Plant of Sardinia (Italy) and Corsica (France). Pharmaceuticals (Basel) 2023; 16:1118. [PMID: 37631033 PMCID: PMC10457970 DOI: 10.3390/ph16081118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
In this work we investigated, for the first time, the effect of Plagius flosculosus (L.) Alavi & Heywood, a Sardinian-Corsican endemic plant, on HIV-1 integrase (IN) activity. The phytochemical analysis of the leaves chloroform extract led us to isolate and characterize three compounds (SPK1, SPK2, and SPK3) belonging to the spiroketals, a group of naturally occurring metabolites of phytochemical relevance with interesting biological properties. Due to their structural diversity, these cyclic ketals have attracted the interest of chemists and biologists. SPK1, SPK2, and SPK3 were evaluated here for their ability to inhibit HIV-1 integrase activity in biochemical assays. The results showed that all the compounds inhibited HIV-1 IN activity. In particular, the most active one was SPK3, which interfered in a low molecular range (IC50 of 1.46 ± 0.16 µM) with HIV-1 IN activity in the presence/absence of the LEDGF cellular cofactor. To investigate the mechanism of action, the three spiroketals were also tested on HIV-1 RT-associated Ribonuclease H (RNase H) activity, proving to be active in inhibiting this function. Although SPK3 was unable to inhibit viral replication in cell culture, it promoted the IN multimerization. We hypothesize that SPK3 inhibited HIV-1 IN through an allosteric mechanism of action.
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Affiliation(s)
- Cinzia Sanna
- Department of Life and Environmental Sciences, University of Cagliari, Via Sant’Ignazio da Laconi 13, 09123 Cagliari, Italy;
| | - Brigida D’Abrosca
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, DiSTABiF University of Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy;
| | - Antonio Fiorentino
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, DiSTABiF University of Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy;
| | - Federica Giammarino
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy; (F.G.); (I.V.)
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy; (F.G.); (I.V.)
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042 Monserrato, Italy; (A.C.); (A.C.); (E.T.)
| | - Alessia Caredda
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042 Monserrato, Italy; (A.C.); (A.C.); (E.T.)
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042 Monserrato, Italy; (A.C.); (A.C.); (E.T.)
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042 Monserrato, Italy; (A.C.); (A.C.); (E.T.)
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Serumula W, Fernandez G, Gonzalez VM, Parboosing R. Anti-HIV Aptamers: Challenges and Prospects. Curr HIV Res 2022; 20:7-19. [PMID: 34503417 DOI: 10.2174/1570162x19666210908114825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
Human Immunodeficiency Virus (HIV) infection continues to be a significant health burden in many countries around the world. Current HIV treatment through a combination of different antiretroviral drugs (cART) effectively suppresses viral replication, but drug resistance and crossresistance are significant challenges. This has prompted the search for novel targets and agents, such as nucleic acid aptamers. Nucleic acid aptamers are oligonucleotides that attach to the target sites with high affinity and specificity. This review provides a target-by-target account of research into anti-HIV aptamers and summarises the challenges and prospects of this therapeutic strategy, specifically in the unique context of HIV infection.
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Affiliation(s)
- William Serumula
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, c/o Inkosi Albert Luthuli Central Hospital, 5th Floor Laboratory Building, 800 Bellair Road, Mayville, Durban 4091, South Africa
| | - Geronimo Fernandez
- Departamento de Bioquímica-Investigación, Aptus Biotech SL, Avda. Cardenal Herrera Oria, 298-28035 Madrid. Spain
| | - Victor M Gonzalez
- Departamento de Bioquímica-Investigación, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)-Hospital Ramón y Cajal, 28034 Madrid, Spain
| | - Raveen Parboosing
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, c/o Inkosi Albert Luthuli Central Hospital, 5th Floor Laboratory Building, 800 Bellair Road, Mayville, Durban 4091, South Africa
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3
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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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4
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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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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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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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7
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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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Bala J, Chinnapaiyan S, Dutta RK, Unwalla H. Aptamers in HIV research diagnosis and therapy. RNA Biol 2018; 15:327-337. [PMID: 29431588 PMCID: PMC5927724 DOI: 10.1080/15476286.2017.1414131] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/07/2017] [Accepted: 12/03/2017] [Indexed: 12/30/2022] Open
Abstract
Aptamers are high affinity single-stranded nucleic acid or protein ligands which exhibit specificity and avidity comparable to, or exceeding that of antibodies and can be generated against most targets. The functionality of aptamers is based on their unique tertiary structure, complexity and their ability to attain unique binding pockets by folding. Aptamers are selected in vitro by a process called Systematic Evolution of Ligands by Exponential enrichment (SELEX). The Kd values for the selected aptamer are often in the picomolar to low nanomolar range. Stable and nontoxic aptamers could be selected for a wide range of ligands including small molecules to large proteins. Aptamers have shown tremendous potential and have found multipurpose application in the field of therapeutic, diagnostic, biosensor and bio-imaging. While their mechanism of action can be similar to that of monoclonal antibodies, aptamers provide additional advantages in terms of production cost, simpler regulatory approval and lower immunogenicity as they are synthesized chemically. Human immunodeficiency virus (HIV) is the primary cause of acquired immune deficiency syndrome (AIDS), which causes significant morbidity and mortality with a significant consequent decrease in the quality of patient's lives. While cART has led to good viral control, people living with HIV now suffer from non-HIV comorbidities due to viral protein expression that cannot be controlled by cART. Hence pathophysiological mechanisms that govern these comorbidities with a focus on therapies that neutralize these HIV effects gained increased attention. Recent advances in HIV/AIDS research have identified several molecular targets and for the development of therapeutic and diagnostic using aptamers against HIV/AIDS. This review presents recent advances in aptamers technology for potential application in HIV diagnostics and therapeutics towards improving the quality of life of people living with HIV.
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Affiliation(s)
- Jyoti Bala
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Srinivasan Chinnapaiyan
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Rajib Kumar Dutta
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Hoshang Unwalla
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
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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: 117] [Impact Index Per Article: 16.7] [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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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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11
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Prokofjeva M, Tsvetkov V, Basmanov D, Varizhuk A, Lagarkova M, Smirnov I, Prusakov K, Klinov D, Prassolov V, Pozmogova G, Mikhailov SN. Anti-HIV Activities of Intramolecular G4 and Non-G4 Oligonucleotides. Nucleic Acid Ther 2016; 27:56-66. [PMID: 27763826 DOI: 10.1089/nat.2016.0624] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
New natural and chemically modified DNA aptamers that inhibit HIV-1 activity at submicromolar concentrations (presumably via preventing viral entry into target cells) are reported. The new DNA aptamers were developed based on known intramolecular G-quadruplexes (G4s) that were functionally unrelated to HIV inhibition [the thrombin-binding aptamer and the fragment of the human oncogene promoter (Bcl2)]. The majority of previously described DNA inhibitors of HIV infection adopt intermolecular structures, and thus their folding variability represents an obvious disadvantage. Intramolecular architectures refold correctly after denaturation and are generally easier to handle. However, whether the G4 topology or other factors account for the anti-HIV activity of our aptamers is unknown. The impact of chemical modification (thiophosphoryl internucleotide linkages) on aptamer activity is discussed. The exact secondary structures of the active compounds and further elucidation of their mechanisms of action hopefully will be the subjects of future studies.
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Affiliation(s)
- Maria Prokofjeva
- 1 Engelhardt Institute of Molecular Biology RAS , Moscow, Russia
| | - Vladimir Tsvetkov
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia .,3 Topchiev Institute of Petrochemical Synthesis Russian Academy of Sciences , Moscow, Russia
| | - Dmitry Basmanov
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | - Anna Varizhuk
- 1 Engelhardt Institute of Molecular Biology RAS , Moscow, Russia .,2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | - Maria Lagarkova
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | - Igor Smirnov
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | - Kirill Prusakov
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | - Dmitry Klinov
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia .,4 Moscow Institute of Physics and Technology (State University) , Moscow Region, Russia
| | | | - Galina Pozmogova
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
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12
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Abstract
G-quadruplexes are non-canonical secondary structures found in guanine rich regions of DNA and RNA. Reports have indicated the wide occurrence of RNA G-quadruplexes across the transcriptome in various regions of mRNAs and non-coding RNAs. RNA G-quadruplexes have been implicated in playing an important role in translational regulation, mRNA processing events and maintenance of chromosomal end integrity. In this review, we summarize the structural and functional aspects of RNA G-quadruplexes with emphasis on recent progress to understand the protein/trans factors binding these motifs. With the revelation of the importance of these secondary structures as regulatory modules in biology, we have also evaluated the various advancements towards targeting these structures and the challenges associated with them. Apart from this, numerous potential applications of this secondary motif have also been discussed.
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Affiliation(s)
- Prachi Agarwala
- Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
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13
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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, 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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15
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Costi R, Métifiot M, Esposito F, Cuzzucoli Crucitti G, Pescatori L, Messore A, Scipione L, Tortorella S, Zinzula L, Novellino E, Pommier Y, Tramontano E, Marchand C, Di Santo R. 6-(1-Benzyl-1H-pyrrol-2-yl)-2,4-dioxo-5-hexenoic acids as dual inhibitors of recombinant HIV-1 integrase and ribonuclease H, synthesized by a parallel synthesis approach. J Med Chem 2013; 56:8588-98. [PMID: 24124919 DOI: 10.1021/jm401040b] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The increasing efficiency of HAART has helped to transform HIV/AIDS into a chronic disease. Still, resistance and drug-drug interactions warrant the development of new anti-HIV agents. We previously discovered hit 6, active against HIV-1 replication and targeting RNase H in vitro. Because of its diketo-acid moiety, we speculated that this chemotype could serve to develop dual inhibitors of both RNase H and integrase. Here, we describe a new series of 1-benzyl-pyrrolyl diketohexenoic derivatives, 7a-y and 8a-y, synthesized following a parallel solution-phase approach. Those 50 analogues have been tested on recombinant enzymes (RNase H and integrase) and in cell-based assays. Approximately half (22) exibited inhibition of HIV replication. Compounds 7b, 7u, and 8g were the most active against the RNase H activity of reverse-transcriptase, with IC50 values of 3, 3, and 2.5 μM, respectively. Compound 8g was also the most potent integrase inhibitor with an IC50 value of 26 nM.
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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, Rome I-00185, Italy
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16
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Faure-Perraud A, Métifiot M, Reigadas S, Recordon-Pinson P, Parissi V, Ventura M, Andréola ML. The guanine-quadruplex aptamer 93del inhibits HIV-1 replication ex vivo by interfering with viral entry, reverse transcription and integration. Antivir Ther 2011; 16:383-94. [PMID: 21555821 DOI: 10.3851/imp1756] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND We have previously identified the guanine-rich oligonucleotide (ODN) 93del as a potent inhibitor in vitro of HIV-1 integrase. Moreover, low nanomolar concentrations of ODN 93del have been shown to inhibit HIV-1 replication in infected cells. METHODS To investigate the ex vivo mechanism of ODN 93del inhibition, we analysed its antiviral effects on the early steps of HIV-1 replication such as viral entry, reverse transcription and integration using quantitative PCR. RESULTS In addition to the effect on viral entry previously described for other guanine-quadruplex ODNs, transfection experiments showed that ODN 93del severely affects the proviral integration step independently of the effect on viral entry. Moreover, incubation of viral particles with ODN 93del revealed a potential microbicide activity of the aptamer. CONCLUSIONS Our data point to an original multimodal inhibition of HIV-1 replication by ODN 93del, strongly suggesting that targets of guanine-quartet-forming ODNs involve entry as well as other intracellular early steps of HIV-1 replication.
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Reshetnikov RV, Sponer J, Rassokhina OI, Kopylov AM, Tsvetkov PO, Makarov AA, Golovin AV. Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process. Nucleic Acids Res 2011; 39:9789-802. [PMID: 21893589 PMCID: PMC3239185 DOI: 10.1093/nar/gkr639] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange.
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Affiliation(s)
- Roman V Reshetnikov
- Department of Boiengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, 119991, Russian Federation
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Marchand C, Maddali K, Métifiot M, Pommier Y. HIV-1 IN inhibitors: 2010 update and perspectives. Curr Top Med Chem 2010; 9:1016-37. [PMID: 19747122 DOI: 10.2174/156802609789630910] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 06/13/2009] [Indexed: 12/29/2022]
Abstract
Integrase (IN) is the newest validated target against AIDS and retroviral infections. The remarkable activity of raltegravir (Isentress((R))) led to its rapid approval by the FDA in 2007 as the first IN inhibitor. Several other IN strand transfer inhibitors (STIs) are in development with the primary goal to overcome resistance due to the rapid occurrence of IN mutations in raltegravir-treated patients. Thus, many scientists and drug companies are actively pursuing clinically useful IN inhibitors. The objective of this review is to provide an update on the IN inhibitors reported in the last two years, including second generation STI, recently developed hydroxylated aromatics, natural products, peptide, antibody and oligonucleotide inhibitors. Additionally, the targeting of IN cofactors such as LEDGF and Vpr will be discussed as novel strategies for the treatment of AIDS.
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Affiliation(s)
- Christophe Marchand
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Abstract
PURPOSE OF REVIEW Most of the studies investigating inhibition of human immunodeficiency virus integration have focused on blocking the enzymatic functions of HIV integrase, with the predominant judgment that integration inhibitors need to block at least one of the integrase-catalyzed reactions. Recent studies, however, have highlighted the importance of other proteins and their contacts with integrase in the preintegration complex, and their involvement in chromosomal integration of the viral DNA. RECENT FINDINGS Promising results of clinical trials for two new integrase inhibitors were announced recently, providing the proof of the concept for using HIV-1 integrase inhibitors as antiretroviral therapy. Two strategies are currently employed for the development of novel inhibitors of HIV integrase: synthesis of hybrid molecules comprising core structures of two or more known inhibitors, and three-dimensional pharmacophore searches based on previously discovered compounds. By highlighting the role of the cellular cofactor LEDGF/p75 in HIV integration, novel approaches are indicated that aim to develop compounds altering contact between HIV integrase and integration cofactors. SUMMARY By the discovery of novel inhibitors and targets for HIV integration, coupled with recent studies in characterizing preintegration complex formation, new insight is provided for the rational design of anti-HIV integration inhibitors.
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Wendeler M, Beilhartz GL, Beutler JA, Götte M, Le Grice SFJ. HIV ribonuclease H: continuing the search for small molecule antagonists. HIV THERAPY 2008; 3:39-53. [PMID: 38961883 PMCID: PMC11221599 DOI: 10.2217/17584310.3.1.39] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Members of the ribonuclease H (RNase H) family of enzymes (EC 3.1.26.4), which are found in nearly all organisms, are endoribonucleases that specifically hydrolyze the phosphodiester bond of RNA in a RNA-DNA hybrid. In retroviruses such as HIV-1, the RNase H activity is part of reverse transcriptase, the enzyme that converts the viral ssRNA into dsDNA suitable for integration into the host cell genome. In HIV-1, RNase H plays an essential role in various stages of reverse transcription, and it has been known for 20 years that inhibiting RNase H activity renders HIV noninfectious. However, the development of potent and selective antagonists of HIV RNase H has made surprisingly slow progress, and so far no RNase H inhibitor is in clinical trial, rendering this enzyme an important, but as yet underexplored, drug target. The recently described crystal structure of human RNase H in complex with a RNA-DNA hybrid provides new insight into the mechanism of HIV RNase H activity, with the potential to unveil new niches for therapeutic intervention. The current status of RNase H screening efforts is reviewed here.
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Affiliation(s)
- Michaela Wendeler
- HIV Drug Resistance Program, National Cancer Institute-Frederick, Frederick, MD, USA
| | - Greg L Beilhartz
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - John A Beutler
- Molecular Targets Discovery Program, National Cancer Institute-Frederick, Frederick, MD, USA
| | - Matthias Götte
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Stuart FJ Le Grice
- HIV Drug Resistance Program, National Cancer Institute-Frederick, Frederick, MD, USA
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DeStefano JJ, Nair GR. Novel aptamer inhibitors of human immunodeficiency virus reverse transcriptase. Oligonucleotides 2008; 18:133-44. [PMID: 18637731 DOI: 10.1089/oli.2008.0103] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Primer-template-based double-stranded nucleic acids capable of binding human immunodeficiency virus reverse transcriptase (HIV-RT) with high affinity were used as starting material to develop small single-stranded loop-back DNA aptamers. The original primer-templates were selected using a SELEX (Systematic Evolution of Ligands by EXponential enrichment) approach and consisted of 46- and 50-nt primer and template strands, respectively. The major determinant of the approximately 10-fold tighter binding in selected sequences relative to control primer-templates was a run of 6.8 G residues at the 3' primer end. Sixty, thirty-seven, twenty-seven, and twenty-two nucleotide loop-back single-stranded versions that retained the base pairs near the 3' primer terminus were constructed. Both the 60- and 37-nt versions retained high affinity for RT with K(d) values of approximately 0.44 nM and 0.66 nM, respectively. Random sequence primer-templates of the same length had K(d)s of approximately 20 nM and approximately 161 nM. The shorter 27- and 22-nt aptamers bound with reduced affinity. Several modifications of the 37-nt aptamer were also tested including changes to the terminal 3' G nucleotide and internal bases in the G run, replacement of specific nucleotides with phosphothioates, and alterations to the 5' overhang. Optimal binding required a 4- to 5-nt overhang, and internal changes within the G run had a pronounced negative effect on binding. Phosphothioate nucleotides or the presence of a 3' dideoxy G residue did not alter affinity. The 37-nt aptamer was a potent inhibitor of HIV-RT in vitro and functioned by blocking binding of other primer-templates.
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Affiliation(s)
- Jeffrey J DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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Métifiot M, Faure A, Guyonnet-Duperat V, Bellecave P, Litvak S, Ventura M, Andréola ML. Cellular uptake of ODNs in HIV-1 human-infected cells: a role for viral particles in DNA delivery? Oligonucleotides 2007; 17:151-65. [PMID: 17638520 DOI: 10.1089/oli.2006.0061] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We have previously described how a 16 nucleotides ODN (termed 93del) is capable of inhibiting the activity of recombinant integrase in a cell-free system as well as HIV-1 replication in human-infected cells with IC(50) in the low nanomolar range. Intracellular HIV-1 replication was inhibited when the ODN was added at the onset of infection. These results raise several questions. Is a naked ODN able to enter the cell? Does the virus play a role in ODN entry? The uptake of several ODNs (93del, 60del(sc), TBA, T30923) was evaluated and then tracked by labeling the ODN with a fluorescent dye and assessing its intracellular localization by confocal microscopy. A significant level of cellular uptake of free ODN was observed in several cell lines: HeLa epithelial cells, Huh7 hepatic cells, and H9 lymphocytes, and was detected for all ODNs tested except for TBA. Striking differences were observed when naked ODNs were added to cell in the presence or absence of the virus. When HIV-1 virions were present a sharp increase in cellular fluorescence was observed. These results strongly suggest a role for HIV-1 virions in the uptake of certain ODNs.
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Affiliation(s)
- Mathieu Métifiot
- UMR 5097 CNRS, Université Victor Segalen Bordeaux 2, 33076 Bordeaux cedex, France
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Savarino A. A historical sketch of the discovery and development of HIV-1 integrase inhibitors. Expert Opin Investig Drugs 2006; 15:1507-22. [PMID: 17107277 DOI: 10.1517/13543784.15.12.1507] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The long process of HIV-1 integrase inhibitor discovery and development can be attributed to both the complexity of HIV-1 integration and poor 'integration' of these researches into mainstream investigations on antiretroviral therapy in the mid-1990s. Of note, some fungal extracts investigated during this period contain the beta-hydroxyketo group, later recognised to be a key structural requirement for keto-enol acids (also referred to as diketo acids) and other integrase inhibitors. This review reconstructs (in the general context of the history of AIDS research) the principal steps that led to the integrase inhibitors currently in clinical trials, and discusses possible future directions.
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Affiliation(s)
- Andrea Savarino
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità Viale Regina Elena, 299. 00161- Rome, Italy.
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