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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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2
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Bizyaeva AA, Bunin DA, Moiseenko VL, Gambaryan AS, Balk S, Tashlitsky VN, Arutyunyan AM, Kopylov AM, Zavyalova EG. The Functional Role of Loops and Flanking Sequences of G-Quadruplex Aptamer to the Hemagglutinin of Influenza a Virus. Int J Mol Sci 2021; 22:2409. [PMID: 33673708 PMCID: PMC7957560 DOI: 10.3390/ijms22052409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/21/2021] [Accepted: 02/24/2021] [Indexed: 12/22/2022] Open
Abstract
Nucleic acid aptamers are generally accepted as promising elements for the specific and high-affinity binding of various biomolecules. It has been shown for a number of aptamers that the complexes with several related proteins may possess a similar affinity. An outstanding example is the G-quadruplex DNA aptamer RHA0385, which binds to the hemagglutinins of various influenza A virus strains. These hemagglutinins have homologous tertiary structures but moderate-to-low amino acid sequence identities. Here, the experiment was inverted, targeting the same protein using a set of related, parallel G-quadruplexes. The 5'- and 3'-flanking sequences of RHA0385 were truncated to yield parallel G-quadruplex with three propeller loops that were 7, 1, and 1 nucleotides in length. Next, a set of minimal, parallel G-quadruplexes with three single-nucleotide loops was tested. These G-quadruplexes were characterized both structurally and functionally. All parallel G-quadruplexes had affinities for both recombinant hemagglutinin and influenza virions. In summary, the parallel G-quadruplex represents a minimal core structure with functional activity that binds influenza A hemagglutinin. The flanking sequences and loops represent additional features that can be used to modulate the affinity. Thus, the RHA0385-hemagglutinin complex serves as an excellent example of the hypothesis of a core structure that is decorated with additional recognizing elements capable of improving the binding properties of the aptamer.
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Affiliation(s)
- Anastasia A. Bizyaeva
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.B.); (V.L.M.); (V.N.T.); (A.M.K.)
| | - Dmitry A. Bunin
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.B.); (V.L.M.); (V.N.T.); (A.M.K.)
| | - Valeria L. Moiseenko
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.B.); (V.L.M.); (V.N.T.); (A.M.K.)
| | - Alexandra S. Gambaryan
- Chumakov Federal Scientific Centre for Research and Development of Immune and Biological Products RAS, 108819 Moscow, Russia;
| | | | - Vadim N. Tashlitsky
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.B.); (V.L.M.); (V.N.T.); (A.M.K.)
| | - Alexander M. Arutyunyan
- Belozersky Research Institute of Physical Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Alexey M. Kopylov
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.B.); (V.L.M.); (V.N.T.); (A.M.K.)
| | - Elena G. Zavyalova
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.B.); (V.L.M.); (V.N.T.); (A.M.K.)
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3
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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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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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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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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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Noaparast Z, Hosseinimehr SJ, Piramoon M, Abedi SM. Tumor targeting with a (99m)Tc-labeled AS1411 aptamer in prostate tumor cells. J Drug Target 2015; 23:497-505. [PMID: 25673264 DOI: 10.3109/1061186x.2015.1009075] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AS1411, a 26-base guanine-rich oligonucleotide aptamer, has high affinity to nucleolin, mainly on tumor cell surfaces. In this study, a modified AS1411 was labeled with (99m)Tc and evaluated as a potential tumor-targeting agent for imaging. The AS1411 aptamer was conjugated with HYNIC and labeled with (99m)Tc in the presence a co-ligand. Radiochemical purity and stability testing of the (99m)Tc-HYNIC-AS1411 aptamer were carried out with thin layer chromatography and a size-exclusion column in normal saline and human serum. Cellular nucleolin-specific binding, cellular internalization in DU-145 cells, as high levels of nucleolin expression, were performed. Additionally, biodistribution in normal mice and DU-145 tumour-bearing mice was assessed. Radiolabeling of the aptamer resulted in a reasonable yield and radiochemical purity after purification. The aptamer was stable in normal saline and human serum, and cellular experiments demonstrated specific binding of the AS1411 aptamer to the nucleolin protein. Based on biodistribution assessment of (99m)Tc-HYNIC-AS1411, rapid blood clearance was seen after injection and it appears that the excretion route was via the urinary system at 1 h post-injection. Tumours also showed a higher accumulation of radioactivity with this labeled aptamer. (99m)Tc-AS1411 can be a potential tool for the molecular imaging of nucleolin-overexpressing cancers.
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Affiliation(s)
- Zohreh Noaparast
- Department of Radiopharmacy, Pharmaceutical Sciences Research Center, Mazandaran University of Medical Sciences , Sari , Iran and
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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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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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Li CL, Huang CC, Chen WH, Chiang CK, Chang HT. Peroxidase mimicking DNA-gold nanoparticles for fluorescence detection of the lead ions in blood. Analyst 2013; 137:5222-8. [PMID: 23032966 DOI: 10.1039/c2an35599j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Oligonucleotide (T30695) modified gold nanoparticles (T30695-Au NPs) have been prepared and employed for quantification of lead ions (Pb(2+)) in blood. The detection of Pb(2+) ions is through the formation of Au-Pb alloys and oligonucleotide-Pb(2+) complexes that catalyze the H(2)O(2)-mediated oxidation of non-fluorescent Amplex UltraRed (AUR) to form a highly fluorescent oxidized AUR product. Surface-assisted laser desorption/ionization time-of-flight mass spectrometry (SALDI-TOF MS) and inductively coupled plasma mass spectrometry (ICP-MS) revealed the formation of Au-Pb alloys on the surfaces of the 40T30695-Au NPs (i.e., the system featuring 40 molecules of T30695 per Au NP) in the presence of Pb(2+) ions, leading to increased catalytic activity for the H(2)O(2)-mediated oxidation of AUR. The fluorescence intensity (excitation/emission maxima: ca. 540/584 nm) of the oxidized AUR product is proportional to the concentration of Pb(2+) ions over the range 0.1-100 nM, with a linear correlation (R(2) = 0.99). The 40T30695-Au NP/AUR probe is highly selective toward Pb(2+) ions (by at least 200-fold over other tested metal ions). The 40T30695-Au NPs/AUR probe provided limits of detection (LOD, at a signal-to-noise ratio 3) for Pb(2+) ions of 0.05 and 0.1 nM, in Tris-acetate solution (5 mM, pH 8.0) without and with salt (150 mM NaCl, 5 mM KCl, 1 mM MgCl(2), and 1 mM CaCl(2)), respectively. Without conducting tedious sample pretreatment, the approach allows detection of Pb(2+) ions in blood samples, showing the potential of the 40T30695-Au NPs/AUR assay for on-site and real-time detection of Pb(2+) ions in biological samples.
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Affiliation(s)
- Chi-Lin Li
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei, 10617, Taiwan
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Magbanua E, Zivkovic T, Hansen B, Beschorner N, Meyer C, Lorenzen I, Grötzinger J, Hauber J, Torda AE, Mayer G, Rose-John S, Hahn U. d(GGGT) 4 and r(GGGU) 4 are both HIV-1 inhibitors and interleukin-6 receptor aptamers. RNA Biol 2013; 10:216-27. [PMID: 23235494 PMCID: PMC3594281 DOI: 10.4161/rna.22951] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aptamers are oligonucleotides that bind targets with high specificity and affinity. They have become important tools for biosensing, target detection, drug delivery and therapy. We selected the quadruplex-forming 16-mer DNA aptamer AID-1 [d(GGGT) 4] with affinity for the interleukin-6 receptor (IL-6R) and identified single nucleotide variants that showed no significant loss of binding ability. The RNA counterpart of AID-1 [r(GGGU) 4] also bound IL-6R as quadruplex structure. AID-1 is identical to the well-known HIV inhibitor T30923, which inhibits both HIV infection and HIV-1 integrase. We also demonstrated that IL-6R specific RNA aptamers not only bind HIV-1 integrase and inhibit its 3' processing activity in vitro, but also are capable of preventing HIV de novo infection with the same efficacy as the established inhibitor T30175. All these aptamer target interactions are highly dependent on formation of quadruplex structure.
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Affiliation(s)
- Eileen Magbanua
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Tijana Zivkovic
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Björn Hansen
- Centre for Bioinformatics; Hamburg University; Hamburg, Germany
| | - Niklas Beschorner
- Heinrich Pette Institute; Leibnitz Institute for Experimental Virology; Hamburg, Germany
| | - Cindy Meyer
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Inken Lorenzen
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Joachim Grötzinger
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Joachim Hauber
- Heinrich Pette Institute; Leibnitz Institute for Experimental Virology; Hamburg, Germany
| | - Andrew E. Torda
- Centre for Bioinformatics; Hamburg University; Hamburg, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute; University of Bonn; Bonn, Germany
| | - Stefan Rose-John
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Ulrich Hahn
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
- Correspondence to: Ulrich Hahn,
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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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Pedersen EB, Nielsen JT, Nielsen C, Filichev VV. Enhanced anti-HIV-1 activity of G-quadruplexes comprising locked nucleic acids and intercalating nucleic acids. Nucleic Acids Res 2011; 39:2470-81. [PMID: 21062811 PMCID: PMC3064782 DOI: 10.1093/nar/gkq1133] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 10/21/2010] [Accepted: 10/22/2010] [Indexed: 01/23/2023] Open
Abstract
Two G-quadruplex forming sequences, 5'-TGGGAG and the 17-mer sequence T30177, which exhibit anti-HIV-1 activity on cell lines, were modified using either locked nucleic acids (LNA) or via insertions of (R)-1-O-(pyren-1-ylmethyl)glycerol (intercalating nucleic acid, INA) or (R)-1-O-[4-(1-pyrenylethynyl)phenylmethyl]glycerol (twisted intercalating nucleic acid, TINA). Incorporation of LNA or INA/TINA monomers provide as much as 8-fold improvement of anti-HIV-1 activity. We demonstrate for the first time a detailed analysis of the effect the incorporation of INA/TINA monomers in quadruplex forming oligonucleotides (QFOs) and the effect of LNA monomers in the context of biologically active QFOs. In addition, recent literature reports and our own studies on the gel retardation of the phosphodiester analogue of T30177 led to the conclusion that this sequence forms a parallel, dimeric G-quadruplex. Introduction of the 5'-phosphate inhibits dimerisation of this G-quadruplex as a result of negative charge-charge repulsion. Contrary to that, we found that attachment of the 5'-O-DMT-group produced a more active 17-mer sequence that showed signs of aggregation-forming multimeric G-quadruplex species in solution. Many of the antiviral QFOs in the present study formed more thermally stable G-quadruplexes and also high-order G-quadruplex structures which might be responsible for the increased antiviral activity observed.
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Affiliation(s)
- Erik B. Pedersen
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense, Department of Virology, Retrovirus Laboratory, State Serum Institute, 2300 Copenhagen, Denmark and Institute of Fundamental Sciences, Massey University, Palmerston North, Private Bag 11-222, New Zealand
| | - Jakob T. Nielsen
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense, Department of Virology, Retrovirus Laboratory, State Serum Institute, 2300 Copenhagen, Denmark and Institute of Fundamental Sciences, Massey University, Palmerston North, Private Bag 11-222, New Zealand
| | - Claus Nielsen
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense, Department of Virology, Retrovirus Laboratory, State Serum Institute, 2300 Copenhagen, Denmark and Institute of Fundamental Sciences, Massey University, Palmerston North, Private Bag 11-222, New Zealand
| | - Vyacheslav V. Filichev
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense, Department of Virology, Retrovirus Laboratory, State Serum Institute, 2300 Copenhagen, Denmark and Institute of Fundamental Sciences, Massey University, Palmerston North, Private Bag 11-222, New Zealand
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14
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Di Fabio G, D'Onofrio J, Chiapparelli M, Hoorelbeke B, Montesarchio D, Balzarini J, De Napoli L. Discovery of novel anti-HIV active G-quadruplex-forming oligonucleotides. Chem Commun (Camb) 2010; 47:2363-5. [PMID: 21305065 DOI: 10.1039/c0cc04751a] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of d((5')TGGGAG(3')) sequences, 5'-conjugated with a variety of aromatic groups through phosphodiester linkages, were synthesized, showing CD spectra diagnostic of parallel-stranded, tetramolecular G-quadruplex structures. When tested for anti-HIV-1 and HIV-2 activity, potent inhibition of HIV-1 infection in CEM cell cultures was found, associated with high selectivity index values. Surface Plasmon Resonance assays revealed specific binding to HIV-1 gp120 and gp41.
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Affiliation(s)
- Giovanni Di Fabio
- Dipartimento di Chimica Organica e Biochimica, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte S. Angelo, via Cintia, 4, I-80126 Napoli, Italy.
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15
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Yerkes S, Vesenka J, Kmiec EB. A stable G-quartet binds to a huntingtin protein fragment containing expanded polyglutamine tracks. J Neurosci Res 2010; 88:335-45. [DOI: 10.1002/jnr.22210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Affiliation(s)
- Shinzi Ogasawara
- Bioengineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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18
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Franceschin M. G‐Quadruplex DNA Structures and Organic Chemistry: More Than One Connection. European J Org Chem 2009. [DOI: 10.1002/ejoc.200801196] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Marco Franceschin
- Dipartimento di Chimica, Sapienza – Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy, Fax: +39‐06‐4991‐3841
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Snásel J, Rosenberg I, Paces O, Pichová I. The strand transfer oligonucleotide inhibitors of HIV-integrase. J Enzyme Inhib Med Chem 2009; 24:241-6. [PMID: 18608742 DOI: 10.1080/14756360802051578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Retroviral integrase participates in two catalytic reactions, which require interactions with the two ends of the viral DNA in the 3'processing reaction, and with a targeted host DNA in the strand transfer reaction. The 3'-hydroxyl group of 2'-deoxyadenosine resulting from the specific removing of GT dinucleotide from the viral DNA in the processing reaction provides the attachment site for the host DNA in a transesterification reaction. We synthesized oligonucleotides (ONs) of various lengths that mimic the processed HIV-1 U5 terminus of the proviral long terminal repeat (LTR) and are ended by 2'-deoxyadenosine containing a 3'-O-phosphonomethyl group. The duplex stability of phosphonomethyl ONs was increased by covalent linkage of the modified strand with its complementary strand by a triethylene glycol loop (TEG). Modified ONs containing up to 10 bases inhibited in vitro the strand transfer reaction catalyzed by HIV-1 integrase at nanomolar concentrations.
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Affiliation(s)
- Jan Snásel
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic
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20
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Wang D, Bhagat L, Yu D, Zhu FG, Tang JX, Kandimalla ER, Agrawal S. Oligodeoxyribonucleotide-based antagonists for Toll-like receptors 7 and 9. J Med Chem 2009; 52:551-8. [PMID: 19102653 DOI: 10.1021/jm8014316] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Oligodeoxyribonucleotides containing unmethylated CpG motifs act as TLR9 agonists. In this study, we evaluated oligonucleotides containing an unmethylated CpG motif in which two nucleotides adjacent to the CpG dinucleotide were substituted with 2'-O-methylribonucleotides, resulting in TLR7 and TLR9 antagonists. In mouse and human cell cultures, antagonists did not stimulate immune activation but inhibited TLR7 and TLR9 agonist-induced activity. In mice, antagonists inhibited immune responses induced by TLR9 agonists for up to several days, and the inhibition was dose-dependent. Antagonists also inhibited immune responses induced by an RNA-based TLR7/8 agonist but not TLRs 2, 3, 4, or 5 agonists in mice. Additionally, antagonist inhibited TLR9 agonist-induced IL-6 in lupus-prone MRL/lpr mouse spleen cell cultures. These results indicate that antagonists described herein can suppress immune responses induced by TLR7 and TLR9 agonists. Antagonists may be suitable candidates for treating inflammatory and autoimmune diseases where inappropriate or uncontrolled TLR activation has been implicated.
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Affiliation(s)
- Daqing Wang
- Idera Pharmaceuticals, Inc., 167 Sidney Street, Cambridge, Massachusetts 02139, USA
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21
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Li H, Yuan G. Collision-induced dissociation of dimeric G-quadruplexes of HIV-1 integrase inhibitors and their complexes by tandem-in-time mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2009; 15:731-737. [PMID: 19940339 DOI: 10.1255/ejms.1033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The collision-dissociation behavior of two novel dimeric G-quadruplexes of HIV-1 integrase inhibitors and their noncovalent complex ions with a perylene derivative (Tel03), polyamides (ImImImbetaDp and PyPyPybetaDp) was investigated by tandem-in-time electrospray ionization mass spectrometry (ESI-MS). It was found that the dimeric ion loses five ammonium ions one by one at activation energy of 10%, so the loss of NH(4)(+) is the predominant fragmentation pathway at lower collision energy. When the activation amplitude is increased to 16%, the loss of guanine nucleobases from backbones of the oligonucleotide is the predominant fragmentation pathway. And the stability of the complex ion of the dimeric G-quadruplex and Tel03 is higher than that of ImImImbetaDp and PyPyPybetaDp. The results of the MS/MS spectra of the complex ion indicated that Tel03 binding molecule favor the stabilization of the novel G-quadruplex structure.
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Affiliation(s)
- Huihui Li
- Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Environmental Science, Nanjing Normal University, Nanjing, 210097, China
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22
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Michalowski D, Chitima-Matsiga R, Held DM, Burke DH. Novel bimodular DNA aptamers with guanosine quadruplexes inhibit phylogenetically diverse HIV-1 reverse transcriptases. Nucleic Acids Res 2008; 36:7124-35. [PMID: 18996899 PMCID: PMC2602765 DOI: 10.1093/nar/gkn891] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
DNA aptamers RT5, RT6 and RT47 form a group of related sequences that inhibit HIV-1 reverse transcriptase (RT). The essential inhibitory structure is identified here as bimodular, with a 5' stem-loop module physically connected to a 3'-guanosine quadruplex module. The stem-loop tolerates considerable sequence plasticity. Connections between the guanosine triplets in the quadruplex could be simplified to a single nucleotide or a nonnucleic acid linker, such as hexaethylene glycol. All 12 quadruplex guanosines are required in an aptamer retaining most of the original loop sequence from RT6; only 11 are required for aptamer R1T (single T residue in intra-quadruplex loops). Circular dichroism (CD) spectroscopy gave ellipticity minima and maxima at 240 nm and 264 nm, indicating a parallel arrangement of the quadruplex strands. The simplified aptamers displayed increased overall stability. An aptamer carrying the original intra-quadruplex loops from RT6 inhibited RT in K(+) buffers but not in Na(+) buffers and displayed significant CD spectral broadening in Na(+) buffers, while R1T inhibited RT in both buffers and displayed less broadening in Na(+) buffers. The bimodular ssDNA aptamers inhibited RT from diverse primate lentiviruses with low nM IC(50) values. These data provide insight into the requirements for broad-spectrum RT inhibition by nucleic acid aptamers.
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Affiliation(s)
- Daniel Michalowski
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO 65211, USA
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Weerasinghe P, Li Y, Guan Y, Zhang R, Tweardy DJ, Jing N. T40214/PEI complex: a potent therapeutics for prostate cancer that targets STAT3 signaling. Prostate 2008; 68:1430-42. [PMID: 18615483 PMCID: PMC2574665 DOI: 10.1002/pros.20807] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
BACKGROUND Prostate cancer (PC) is the most common cancer among men in American and the second leading cause of cancer death. The treatment options employed for patients with advanced and metastatic PC are limited. As a critical mediator of oncogenic signaling, STAT3 is active in 82% of patients with PC. STAT3 has become a very important molecular target for PC therapy since it upregulates the oncogenes encoding apoptosis inhibitors, cell cycle regulators, and inducers of angiogenesis. However, no anti-tumor drug whose primary mode of action is to target STAT3 has yet reached the clinic. To this end, we have laid the initial groundwork to develop the STAT3-inhibiting G-quartet oligodeoxynucleotide (GQ-ODN), T40214, for treatment of PCs. METHODS We employed in vitro and in vivo assays, including Western blots, EMSA, cell cycle analysis, TUNEL and xenograft models, to determine the drug efficacy and mechanism of T40214/PEI complex. RESULTS The results demonstrated that (i) T40214 significantly inhibited STAT3 activation and induced apoptosis in both androgen-dependent and androgen-independent PC cells; (ii) T40214 delivered by ployethylenimine (PEI) significantly suppressed prostate tumor growth in tumor-bearing nude mice due to that T40214 inhibited STAT3 activation and then greatly promoted apoptosis, reduced angiogenesis and cell proliferation in prostate tumors. CONCLUSION Our studies suggested that STAT3 is a critical oncogenic signal, which strongly influences the progression of PCs and that T40214/PEI complex is a promising candidate for treatment of patients with prostate tumors and represents a novel strategy for PC therapy.
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Affiliation(s)
- Priya Weerasinghe
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030
| | - Yifei Li
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030
| | - Yongli Guan
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030
| | - Ruiwen Zhang
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, AL
| | - David J. Tweardy
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030
- Dan Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Naijie Jing
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030
- Dan Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030
- Corresponding Author: Naijie Jing, Ph.D.*, Department of Medicine and Cancer, Center Baylor College of Medicine, One Baylor Plaza - N520, Houston, Texas 77030 USA, Tel: 713-798-3685, Fax 713-798-8948,
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Schwartz TR, Vasta CA, Bauer TL, Parekh-Olmedo H, Kmiec EB. G-rich oligonucleotides alter cell cycle progression and induce apoptosis specifically in OE19 esophageal tumor cells. Oligonucleotides 2008; 18:51-63. [PMID: 18321162 DOI: 10.1089/oli.2007.0109] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Short synthetic oligonucleotides (ODNs) can be used to block cellular processes involved in cell growth and proliferation. Often acting as aptamers, these molecules interact with critical proteins that regulate the induction of apoptosis or necrosis. We have used a specialized class of ODNs that contain a monomeric sequence of guanosine to induce apoptosis specifically in the malignant esophageal cell line, OE19, in cell culture, and in a NODscid mouse model. OE19 cells were grown in culture and treated with a stable G-rich oligonucleotide (GRO). Cells were processed and apoptosis was measured by FACS analyses, caspase activity, and Hoescht staining. Circular dichroism (CD) was used to define the structure and stability of various GROs. The GRO works by first inducing retardation in the progression of the cell cycle and then by creating a sub-G1 population of apoptotic cells. The reaction is dose dependent, and appears to rely on the capacity of the G-rich ODN to adopt a G-quartet conformation. Apoptosis was measured by determining caspase 3/7 levels and by staining for nuclear fragmentation using the Hoechst dye. Importantly, nonmalignant esophageal cells or normal human lung fibroblasts are not impeded in their cell cycle progression when incubated with the G-rich ODNs. These results suggest that a selective killing of esophageal tumor cells is directed by G-rich ODNs. Selective killing was demonstrated in the unique activity of the GRO compared to other ODNs of different sequences as well as the response of oncogenic cells compared to nononcogenic cells.
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Affiliation(s)
- Timothy R Schwartz
- Department of Biological Sciences, University of Delaware, Newark, DE 19711, USA
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25
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Li H, Yuan G, Du D. Investigation of formation, recognition, stabilization, and conversion of dimeric G-quadruplexes of HIV-1 integrase inhibitors by electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:550-559. [PMID: 18313939 DOI: 10.1016/j.jasms.2008.01.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Revised: 01/27/2008] [Accepted: 01/28/2008] [Indexed: 05/26/2023]
Abstract
The dimeric G-quadruplex structures of d(GGGTGGGTGGGTGGGT) (S1) and d(GTGGTGGGTGGGTGGGT) (S2), the potent nanomolar HIV-1 integrase inhibitors, were detected by electrospray ionization mass spectrometry (ESI-MS) for the first time. The formation and conversion of the dimers were induced by NH(4)(+), DNA concentration, pH, and the binding molecules. We directly observed the specific binding of a perylene derivative (Tel03) and ImImImbetaDp in one system consisting of the intramolecular and the dimeric G-quadruplexes of the HIV-1 integrase inhibitor, which suggested that Tel03 could shift the equilibrium to the dimeric G-quadruplex formation, while ImImImbetaDp induces preferentially a structural change from the dimer to the intramolecular G-quadruplex. The results of this study indicated that Tel03 and ImImImbetaDp favor the stabilization of the dimeric G-quadruplex structures.
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Affiliation(s)
- Huihui Li
- Beijing National Laboratory for Molecular Sciences, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
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Famulok M, Hartig JS, Mayer G. Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem Rev 2007; 107:3715-43. [PMID: 17715981 DOI: 10.1021/cr0306743] [Citation(s) in RCA: 666] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael Famulok
- LIMES Institute, Program Unit Chemical Biology and Medicinal Chemistry, c/o Kekulé-Institut für Organische Chemie und Biochemie, Gerhard Domagk-Strasse 1, 53121 Bonn, Germany.
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27
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Li J, Trent JO, Bates PJ, Ng CK. Factors affecting the labeling yield of F-18-labeled AS1411. J Labelled Comp Radiopharm 2007. [DOI: 10.1002/jlcr.1457] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Skogen M, Roth J, Yerkes S, Parekh-Olmedo H, Kmiec E. Short G-rich oligonucleotides as a potential therapeutic for Huntington's Disease. BMC Neurosci 2006; 7:65. [PMID: 17014717 PMCID: PMC1609172 DOI: 10.1186/1471-2202-7-65] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Accepted: 10/02/2006] [Indexed: 11/28/2022] Open
Abstract
Background Huntington's Disease (HD) is an inherited autosomal dominant genetic disorder in which neuronal tissue degenerates. The pathogenesis of the disease appears to center on the development of protein aggregates that arise initially from the misfolding of the mutant HD protein. Mutant huntingtin (Htt) is produced by HD genes that contain an increased number of glutamine codons within the first exon and this expansion leads to the production of a protein that misfolds. Recent studies suggest that mutant Htt can nucleate protein aggregation and interfere with a multitude of normal cellular functions. Results As such, efforts to find a therapy for HD have focused on agents that disrupt or block the mutant Htt aggregation pathway. Here, we report that short guanosine monotonic oligonucleotides capable of adopting a G-quartet structure, are effective inhibitors of aggregation. By utilizing a biochemical/immunoblotting assay as an initial screen, we identified a 20-mer, all G-oligonucleotide (HDG) as an active molecule. Subsequent testing in a cell-based assay revealed that HDG was an effective inhibitor of aggregation of a fusion protein, comprised of a mutant Htt fragment and green fluorescent protein (eGFP). Taken together, our results suggest that a monotonic G-oligonucleotide, capable of adopting a G-quartet conformation is an effective inhibitor of aggregation. This oligonucleotide can also enable cell survival in PC12 cells overexpressing a mutant Htt fragment fusion gene. Conclusion Single-stranded DNA oligonucleotides capable of forming stable G-quartets can inhibit aggregation of the mutant Htt fragment protein. This activity maybe an important part of the pathogenecity of Huntington's Disease. Our results reveal a new class of agents that could be developed as a therapeutic approach for Huntington's Disease.
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Affiliation(s)
- Michael Skogen
- Department of Biological Sciences, University of Delaware, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA
| | - Jennifer Roth
- Department of Biological Sciences, University of Delaware, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA
| | - Sarah Yerkes
- Department of Biological Sciences, University of Delaware, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA
| | - Hetal Parekh-Olmedo
- Department of Biological Sciences, University of Delaware, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA
| | - Eric Kmiec
- Department of Biological Sciences, University of Delaware, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA
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Lee DS, Jung KE, Yoon CH, Lim H, Bae YS. Newly designed six-membered azasugar nucleotide-containing phosphorothioate oligonucleotides as potent human immunodeficiency virus type 1 inhibitors. Antimicrob Agents Chemother 2006; 49:4110-20. [PMID: 16189087 PMCID: PMC1251495 DOI: 10.1128/aac.49.10.4110-4120.2005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A series of modified oligonucleotides (ONs), characterized by a phosphorothioate (P S) backbone and a six-membered azasugar (6-AZS) as a sugar substitute in a nucleotide, were newly synthesized and assessed for their ability to inhibit human immunodeficiency virus type 1 (HIV-1) via simple treatment of HIV-1-infected cultures, without any transfection process. While unmodified P S ONs exhibited only minor anti-HIV-1 activity, the six-membered azasugar nucleotide (6-AZN)-containing P S oligonucleotides (AZPSONs) exhibited remarkable antiviral activity against HIV-1/simian-human immunodeficiency virus (SHIV) replication and syncytium formation (50% effective concentration = 0.02 to 0.2 microM). The AZPSONs exhibited little cytotoxicity at concentrations of up to 100 microM. DBM 2198, one of the most effective AZPSONs, exhibited antiviral activity against a broad spectrum of HIV-1, including T-cell-tropic, monotropic, and even drug-resistant HIV-1 variants. The anti-HIV-1 activities of DBM 2198 were similarly maintained in HIV-1-infected cultures of peripheral blood mononuclear cells. When we treated severely infected cultures with DBM 2198, syncytia disappeared completely within 2 days. Taken together, our results indicate that DBM 2198 and other AZPSONs may prove useful in the further development of safe and effective AIDS-therapeutic drugs against a broad spectrum of HIV-1 variants.
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Affiliation(s)
- Dong-Seong Lee
- Department of Biological Science, Sungkyunkwan University, Jangan-gu, Suwon, Gyounggi-do, South Korea
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Jason TLH, Koropatnick J, Berg RW. Toxicology of antisense therapeutics. Toxicol Appl Pharmacol 2004; 201:66-83. [PMID: 15519609 DOI: 10.1016/j.taap.2004.04.017] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2003] [Accepted: 04/28/2004] [Indexed: 12/24/2022]
Abstract
Targeting unique mRNA molecules using antisense approaches, based on sequence specificity of double-stranded nucleic acid interactions should, in theory, allow for design of drugs with high specificity for intended targets. Antisense-induced degradation or inhibition of translation of a target mRNA is potentially capable of inhibiting the expression of any target protein. In fact, a large number of proteins of widely varied character have been successfully downregulated using an assortment of antisense-based approaches. The most prevalent approach has been to use antisense oligonucleotides (ASOs), which have progressed through the preclinical development stages including pharmacokinetics and toxicological studies. A small number of ASOs are currently in human clinical trials. These trials have highlighted several toxicities that are attributable to the chemical structure of the ASOs, and not to the particular ASO or target mRNA sequence. These include mild thrombocytopenia and hyperglycemia, activation of the complement and coagulation cascades, and hypotension. Dose-limiting toxicities have been related to hepatocellular degeneration leading to decreased levels of albumin and cholesterol. Despite these toxicities, which are generally mild and readily treatable with available standard medications, the clinical trials have clearly shown that ASOs can be safely administered to patients. Alternative chemistries of ASOs are also being pursued by many investigators to improve specificity and antisense efficacy and to reduce toxicity. In the design of ASOs for anticancer therapeutics in particular, the goal is often to enhance the cytotoxicity of traditional drugs toward cancer cells or to reduce the toxicity to normal cells to improve the therapeutic index of existing clinically relevant cancer chemotherapy drugs. We predict that use of antisense ASOs in combination with small molecule therapeutics against the target protein encoded by the antisense-targeted mRNA, or an alternate target in the same or a connected biological pathway, will likely be the most beneficial application of this emerging class of therapeutic agent.
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Affiliation(s)
- Tracey L H Jason
- Cancer Research Laboratories, London Regional Cancer Centre, London, Ontario, Canada N6A 4L6
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Jing N, Li Y, Xiong W, Sha W, Jing L, Tweardy DJ. G-quartet oligonucleotides: a new class of signal transducer and activator of transcription 3 inhibitors that suppresses growth of prostate and breast tumors through induction of apoptosis. Cancer Res 2004; 64:6603-9. [PMID: 15374974 DOI: 10.1158/0008-5472.can-03-4041] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Stat3 is a signaling molecular and oncogene activated frequently in many human malignancies including the majority of prostate, breast, and head and neck cancers; yet, no current chemotherapeutic approach has been implemented clinically that specifically targets Stat3. We recently developed G-rich oligodeoxynucleotides, which form intramolecular G-quartet structures (GQ-ODN), as a new class of Stat3 inhibitor. GQ-ODN targeted Stat3 protein directly inhibiting its ability to bind DNA. When delivered into cells using polyethyleneimine as vehicle, GQ-ODN blocked ligand-induced Stat3 activation and Stat3-mediated transcription of antiapoptotic genes. To establish the effectiveness of GQ-ODN as a potential new chemotherapeutic agent, we systemically administered GQ-ODN (T40214 or T40231) plus polyethyleneimine or polyethyleneimine alone (placebo) by tail-vein injection into nude mice with prostate and breast tumor xenografts. Whereas the mean volume of breast tumor xenografts in placebo-treated mice increased >7-fold over 18 days, xenografts in the GQ-ODN-treated mice remained unchanged. Similarly, whereas the mean volume of prostate tumor xenografts in placebo-treated mice increased 9-fold over 10 days, xenografts in GQ-ODN-treated mice increased by only 2-fold. Biochemical examination of tumors from GQ-ODN-treated mice demonstrated a significant reduction in Stat3 activation, levels of the antiapoptotic proteins Bcl-2 and Bcl-xL, and an 8-fold increase in the number of apoptotic cells compared with the tumors of placebo-treated mice. Thus, GQ-ODN targeting Stat3 induces tumor cell apoptosis when delivered into tumor xenografts and represents a novel class of chemotherapeutic agents that holds promise for the systemic treatment of many forms of metastatic cancer.
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Affiliation(s)
- Naijie Jing
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX, USA.
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Jing N, Li Y, Xu X, Sha W, Li P, Feng L, Tweardy DJ. Targeting Stat3 with G-quartet oligodeoxynucleotides in human cancer cells. DNA Cell Biol 2004; 22:685-96. [PMID: 14659041 DOI: 10.1089/104454903770946665] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Stat3 is an oncogene that is activated in many human cancer cells. Genetic approaches that disrupt Stat3 activity result in inhibition of cancer cell growth and enhanced cell apoptosis supporting the development of novel drugs targeting Stat3 for cancer therapy. G-quartet oligodeoxynucleotides (ODNs) were demonstrated to be potent inhibitors of Stat3 DNA binding activity in vitro with the G-quartet ODN, T40214, having an IC(50) of 7 microM. Computer-simulated docking studies indicated that G-quartet ODNs mainly interacted with the SH2 domain of Stat3 and were capable of inserting between the SH2 domains of Stat3 dimers bound to DNA. We demonstrated that the G-rich ODN T40214, which forms a G-quartet structure at intracellular but not extracellular K+ ion concentrations, is delivered efficiently into the cytoplasm and nucleus of cancer cells where it inhibited IL-6-stimulated Stat3 activation and suppressed Stat3-mediated upregulation of bcl-x and mcl-1 gene expression. Thus, G-quartet represents a new class of drug for targeting of Stat3 within cancer cells.
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Affiliation(s)
- Naijie Jing
- Section of Infectious Diseases, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
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33
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Esposito V, Galeone A, Mayol L, Messere A, Piccialli G, Randazzo A. PNA-DNA chimeras forming quadruplex structures. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:1681-4. [PMID: 14565494 DOI: 10.1081/ncn-120023112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
1H-NMR, CD, and UV spectroscopy have been used to investigate the structure of PNA/DNA chimeras forming quadruplex structures. In particular, we synthesized 5'TGGG3'-t (1) and 5'TGG3'-gt (2), where lower and upper case letters indicate PNA and DNA residues, respectively. CD spectrum and all NMR data of (1) are typical of quadruplexes involving four parallel strands. UV melting profile of (1) indicates that its thermal stability is quite similar to that observed for the reference structure [d(TGGGT)]4. 1H-NMR spectrum for 5'TGG3'-gt (2) shows that this oligonucleotide is not able to fold into a single, well-defined species.
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Affiliation(s)
- Veronica Esposito
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Napoli, Italy
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Abstract
The use of antisense (AS) oligonucleotides as therapeutic agents was proposed as far back as the 1960s/1970s when the AS strategy was initially developed. However, it has taken almost a quarter of a century for this potential to be realized. The last few years has seen a rapid increase in the number of AS molecules progressing past Phase I in clinical trials, due in part to our increased knowledge of their structure and chemistry. Here, we describe the most prominent of these modifications with respect to clinical applicability. However, the main focus of this review is clinical application, with a focus on cancer. We will discuss in detail both the status of the current AS clinical trials and the molecules that are likely to be the targets of the next group of AS molecules entering the clinic.
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Affiliation(s)
- Kathleen F Pirollo
- Department of Oncology, Georgetown University Medical Center, Washington, DC 20007, USA
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Petraccone L, Erra E, Nasti L, Galeone A, Randazzo A, Mayol L, Barone G, Giancola C. Effect of a modified thymine on the structure and stability of [d(TGGGT)]4 quadruplex. Int J Biol Macromol 2003; 31:131-7. [PMID: 12568920 DOI: 10.1016/s0141-8130(02)00073-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Telomeric guanine-rich sequence can adopt quadruplex structures that are important for their biological role in chromosomal stabilisation. G quartets are characterised by the cyclic hydrogen bonding of four guanine bases in a coplanar arrangement and their stability is ion-dependent. In this work we compare the stability of [d(TGGGT)](4) and [d(T*GGGT)](4) quadruplexes. The last one contains a modified thymine, where the hydroxyl group substitutes one hydrogen atom of the methyl group of the thymine in the [d(TGGGT)](4) sequence. We used a combination of spectroscopic, calorimetric and computational techniques to characterise the G-quadruplex formation. NMR and CD spectra of [d(T*GGGT)](4) were characteristic of parallel-stranded, tetramolecular quadruplex. CD and DSC melting experiments reveal that [d(T*GGGT)](4) is less stable that unmodified quadruplex. Molecular models suggest possible explanation for the observed behaviour.
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Affiliation(s)
- Luigi Petraccone
- Dipartimento di Chimica, Via Cintia, Università Federico II di Napoli, Monte Sant' Angelo, 80126 Naples, Italy
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Torrence PF, Powell LD. The quest for an efficacious antiviral for respiratory syncytial virus. Antivir Chem Chemother 2002; 13:325-44. [PMID: 12718405 DOI: 10.1177/095632020201300601] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Respiratory syncytial virus (RSV) continues as an emerging infectious disease not only among infants and children, but also for the immune-suppressed, hospitalized and the elderly. To date, ribavirin (Virazole) remains the only therapeutic agent approved for the treatment of RSV. The prophylactic administration of palivizumab is problematic and costly. The quest for an efficacious RSV antiviral has produced a greater understanding of the viral fusion process, a new hypothesis for the mechanism of action of ribavirin, and a promising antisense strategy combining the 2'-5' oligoadenylate antisense (2-5A-antisense) approach and RSV genomics.
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Affiliation(s)
- Paul F Torrence
- Department of Chemistry, Northern Arizona University, Flagstaff, Ariz., USA.
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Suzuki JI, Miyano-Kurosaki N, Kuwasaki T, Takeuchi H, Kawai G, Takaku H. Inhibition of human immunodeficiency virus type 1 activity in vitro by a new self-stabilized oligonucleotide with guanosine-thymidine quadruplex motifs. J Virol 2002; 76:3015-22. [PMID: 11861867 PMCID: PMC135965 DOI: 10.1128/jvi.76.6.3015-3022.2002] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An oligonucleotide with a dimeric hairpin guanosine quadruplex (basket type structure) (dG3T4G3-s), containing phosphorothioate groups, was able to inhibit human immunodeficiency virus type 1 (HIV-1)-induced syncytium formation and virus production (as measured by p24 core antigen expression) in peripheral blood mononuclear cells. This oligonucleotide lacks primary sequence homology with the complementary (antisense) sequences to the HIV-1 genome. Furthermore, this oligonucleotide may have increased nuclease resistance. The activity of this oligonucleotide was increased when the phosphodiester backbone was replaced with a phosphorothioate backbone. In vivo results showed that dG3T4G3-s was capable of blocking the interaction between gp120 and CD4. We also found that dG3T4G3-s specifically inhibits the entry of T-cell line-tropic HIV-1 into cells. This compound is a viable candidate for evaluation as a therapeutic agent against HIV-1 in humans.
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Affiliation(s)
- Jun-ichiro Suzuki
- Department of Industrial Chemistry, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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Jing N, Marchand C, Guan Y, Liu J, Pallansch L, Lackman-Smith C, De Clercq E, Pommier Y. Structure-activity of inhibition of HIV-1 integrase and virus replication by G-quartet oligonucleotides. DNA Cell Biol 2001; 20:499-508. [PMID: 11560782 DOI: 10.1089/104454901316976136] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
As novel anti-HIV agents, the G-tetrad-forming oligonucleotides have been explored for their structure-activity relations with regard to inhibition of integrase (IN) (N. Jing, Expert Opin. Investig. Drugs (2000) 9, 1777-1785). We have now developed two families of G-quartet oligonucleotides: T40217-T40222, with potential formation of a tail-to-tail G-quartet dimer, and T40224-T40227, with phosphorothioate (PT) linkages in the guanine loops. The results obtained from biophysical measurements and the assays of the inhibition of HIV-1 IN and virus replication demonstrated that an increase in the length of the G-quartet structure from a monomer (15A) to a tail-to-tail dimer (47A) does not distinctly disrupt the inhibition of HIV-1 IN activity or the inhibition of HIV-1 replication in cell cultures. G-quartet oligonucleotides were observed to induce molecular aggregation of HIV-1 IN and interrupt the binding of viral DNA to HIV-1 IN. Also, PT substitutions did not confer any advantages compared with the regular phosphodiesters for the inhibition of HIV-1 replication by intramolecular G-quartets. The G-quartet motif is the primary requirement for the remarkable nuclease resistance and pronounced biological efficacy of these oligonucleotides.
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Affiliation(s)
- N Jing
- Section of Infectious Diseases, Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA.
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Catalanotti B, Galeone A, Gomez-Paloma L, Mayol L, Pepe A. 2'-Deoxy-8-(propyn-1-yl)adenosine-containing oligonucleotides: effects on stability of duplex and quadruplex structures. Bioorg Med Chem Lett 2000; 10:2005-9. [PMID: 10987437 DOI: 10.1016/s0960-894x(00)00381-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
2'-Deoxy-8-(propyn-1-yl)adenosine has been incorporated in synthetic oligodeoxyribonucleotides and its influence on thermal stability of duplex and quadruplex structures investigated by UV, CD and 1H NMR. The obtained results seem to indicate that the presence of the modified base negatively affects the stability of double stranded DNA whereas remarkably increases the stability of parallel quadruplex structures.
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Affiliation(s)
- B Catalanotti
- Dip. di Chimica delle Sostanze Naturali, Univ. di Napoli Federico II, Italy
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Pommier Y, Marchand C, Neamati N. Retroviral integrase inhibitors year 2000: update and perspectives. Antiviral Res 2000; 47:139-48. [PMID: 10974366 DOI: 10.1016/s0166-3542(00)00112-1] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
HIV-1 integrase is an essential enzyme for retroviral replication and a rational target for the design of anti-AIDS drugs. A number of inhibitors have been reported in the past 8 years. This review focuses on the recent developments in the past 2 years. There are now several inhibitors with known sites of actions and antiviral activity. The challenge is to convert these leads into drugs that will selectively target integrase in vivo, and can be added to our antiviral armamentarium.
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Affiliation(s)
- Y Pommier
- Laboratory of Molecular Pharmacology, Division of Basic Sciences, National Cancer Institute, Bethesda, MD 20892-4255, USA.
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Jing N, Marchand C, Liu J, Mitra R, Hogan ME, Pommier Y. Mechanism of inhibition of HIV-1 integrase by G-tetrad-forming oligonucleotides in Vitro. J Biol Chem 2000; 275:21460-7. [PMID: 10801812 DOI: 10.1074/jbc.m001436200] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The G-tetrad-forming oligonucleotides and have been identified as potent inhibitors of human immunodeficiency virus type 1 integrase (HIV-1 IN) activity (Rando, R. F., Ojwang, J., Elbaggari, A., Reyes, G. R., Tinder, R., McGrath, M. S., and Hogan, M. E. (1995) J. Biol. Chem. 270, 1754-1760; Mazumder, A., Neamati, N., Ojwang, J. O., Sunder, S., Rando, R. F., and Pommier, Y. (1996) Biochemistry 35, 13762-13771; Jing, N., and Hogan, M. E. (1998) J. Biol. Chem. 273, 34992-34999). To understand the inhibition of HIV-1 IN activity by the G-quartet inhibitors, we have designed the oligonucleotides and, composed of three and four G-quartets with stem lengths of 19 and 24 A, respectively. The fact that increasing the G-quartet stem length from 15 to 24 A kept inhibition of HIV-1 IN activity unchanged suggests that the binding interaction occurs between a GTGT loop domain of the G-quartet inhibitors and a catalytic site of HIV-1 IN, referred to as a face-to-face interaction. Docking the NMR structure of (Jing and Hogan (1998)) into the x-ray structure of the core domain of HIV-1 IN, HIV-1 IN-(51-209) (Maignan, S., Guilloteau, J.-P. , Qing, Z.-L., Clement-Mella, C., and Mikol, V. (1998) J. Mol. Biol. 282, 359-368), was performed using the GRAMM program. The statistical distributions of hydrogen bonding between HIV-1 IN and were obtained from the analyses of 1000 random docking structures. The docking results show a high probability of interaction between the GTGT loop residues of the G-quartet inhibitors and the catalytic site of HIV-1 IN, in agreement with the experimental observation.
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Affiliation(s)
- N Jing
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.
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Abstract
Virtually all the compounds that are currently used, or under advanced clinical trial, for the treatment of HIV infections, belong to one of the following classes: (i) nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs), (ii) non-nucleoside reverse transcriptase inhibitors (NNRTIs) and (iii) protease inhibitors (PIs). In addition to the reverse transcriptase and protease step, various other events in the HIV replicative cycle are potential targets for chemotherapeutic intervention: (i) viral adsorption, through binding to the viral envelope glycoprotein gp120 (polysulphates, polysulphonates, polyoxometalates, zintevir, negatively charged albumins); (ii) viral entry, through blockade of the viral coreceptors CXCR4 and CCR5 [bicyclams (AMD3100), polyphemusins (T22), TAK-779]; (iii) virus-cell fusion, through binding to the viral glycoprotein gp41 [T-20 (DP-178), siamycins, betulinic acid derivatives]; (iv) viral assembly and disassembly, through NCp7 zinc finger-targeted agents [2,2'-dithiobisbenzamides (DIBAs), azadicarbonamide (ADA)]; (v) proviral DNA integration, through integrase inhibitors such as L-chicoric acid; (vi) viral mRNA transcription, through inhibitors of the transcription (transactivation) process (peptoid CGP64222, fluoroquinolone K-12, Streptomyces product EM2487). Also, in recent years new NRTIs, NNRTIs and PIs have been developed that possess, respectively, improved metabolic characteristics (i.e. phosphoramidate and cyclosaligenyl pronucleotides of d4T), or increased activity against NNRTI-resistant HIV strains, or, in the case of PIs, a different, non-peptidic scaffold. Given the multitude of molecular targets with which anti-HIV agents can interact, one should be cautious in extrapolating from cell-free enzymatic assays to the mode of action of these agents in intact cells. A number of compounds (i.e. zintevir and L-chicoric acid, on the one hand; and CGP64222 on the other hand) have recently been found to interact with virus-cell binding and viral entry in contrast to their proposed modes of action targeted at the integrase and transactivation process, respectively.
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Affiliation(s)
- E De Clercq
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Belgium
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