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Falanga AP, D'Urso A, Travagliante G, Gangemi CMA, Marzano M, D'Errico S, Terracciano M, Greco F, De Stefano L, Dardano P, Rea I, Piccialli G, Oliviero G, Borbone N. Higher-order G-quadruplex structures and porphyrin ligands: Towards a non-ambiguous relationship. Int J Biol Macromol 2024; 268:131801. [PMID: 38670185 DOI: 10.1016/j.ijbiomac.2024.131801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/29/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024]
Abstract
Herein, we evaluated the interaction of the tetracationic porphyrin H2TCPPSpm4 with three distinct DNA G-quadruplex (G4) models, i.e., the tetramolecular G4 d(TGGGGT)4 (Q1), the 5'-5' stacked G4-dimer [d(CGGAGGT)4]2 (Q2), and a mixture of 5'-5' stacked G-wires [d(5'-CGGT-3'-3'-GGC-5')4]n (Qn). The combined data obtained from UV-Vis, CD, fluorescence, PAGE, RLS, AFM, NMR, and HPLC-SEC experiments allowed us to shed light on the binding mode of H2TCPPSpm4 with the three G4 models differing for the type and the number of available G4 ending faces, the length of the G4 units, and the number of stacked G4 building blocks. Specifically, we found that H2TCPPSpm4 interacted with the shortest Q1 as an end-stacking ligand, whereas the groove binding mode was ascertained in the case of the Q2 and Qn G4 models. In the case of the interaction with Q1 and Qn, we found that H2TCPPSpm4 induces the formation of supramolecular aggregates at porphyrin/G4 ratios higher than 2:1, whereas no significant aggregation was observed for the interaction with Q2 up to the 5:1 ratio. These results unambiguously demonstrated the suitability of porphyrins for the development of specific G4 ligands or G4-targeting diagnostic probes, being H2TCPPSpm4 capable to distinguish between different G4s.
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Affiliation(s)
- Andrea Patrizia Falanga
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Alessandro D'Urso
- Department of Chemical Sciences, University of Catania, viale Andrea Doria 6, 95125 Catania, Italy
| | - Gabriele Travagliante
- Department of Chemical Sciences, University of Catania, viale Andrea Doria 6, 95125 Catania, Italy
| | | | - Maria Marzano
- CESTEV, University of Naples Federico II, via Tommaso De Amicis 95, 80145 Naples, Italy
| | - Stefano D'Errico
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Monica Terracciano
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Francesca Greco
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Luca De Stefano
- Institute of Applied Sciences and Intelligent Systems, Unit of Naples, National Research Council, via Pietro Castellino 111, 80131 Naples, Italy
| | - Principia Dardano
- Institute of Applied Sciences and Intelligent Systems, Unit of Naples, National Research Council, via Pietro Castellino 111, 80131 Naples, Italy
| | - Ilaria Rea
- Institute of Applied Sciences and Intelligent Systems, Unit of Naples, National Research Council, via Pietro Castellino 111, 80131 Naples, Italy
| | - Gennaro Piccialli
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy.
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2
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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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Aptamers in Virology-A Consolidated Review of the Most Recent Advancements in Diagnosis and Therapy. Pharmaceutics 2021; 13:pharmaceutics13101646. [PMID: 34683938 PMCID: PMC8540715 DOI: 10.3390/pharmaceutics13101646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 01/05/2023] Open
Abstract
The use of short oligonucleotide or peptide molecules as target-specific aptamers has recently garnered substantial attention in the field of the detection and treatment of viral infections. Based on their high affinity and high specificity to desired targets, their use is on the rise to replace antibodies for the detection of viruses and viral antigens. Furthermore, aptamers inhibit intracellular viral transcription and translation, in addition to restricting viral entry into host cells. This has opened up a plethora of new targets for the research and development of novel vaccines against viruses. Here, we discuss the advances made in aptamer technology for viral diagnosis and therapy in the past decade.
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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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5
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Romanucci V, Oliva R, Petraccone L, Claes S, Schols D, Zarrelli A, Di Fabio G. Synthesis of new riboflavin modified ODNs: Effect of riboflavin moiety on the G-quadruplex arrangement and stability. Bioorg Chem 2020; 104:104213. [PMID: 32919132 DOI: 10.1016/j.bioorg.2020.104213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/31/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
Abstract
In the panorama of modified G-quadruplexes (G4s) with interesting proprieties, here, it has been reported the synthesis of new modified d(TGGGAG) sequences forming G-quadruplexes, with the insertion of a riboflavin unit (Rf, vitamin B2). Exploiting the flavin similarity with the hydrogen bond pattern of guanine and aiming at mimic a typical nucleoside scaffold, the synthesis of the riboflavin building block 3 it has been efficiently carried out. The effect of insertion of riboflavin mimic nucleoside on the G-quadruplex properties has been here, for the first time investigated. A biophysical characterization of Rf-modified sequences (A-D) has been carried out by circular dichroism (CD), fluorescence spectroscopy, differential scanning calorimetry (DSC) and native gel electrophoresis. CD and electrophoresis data have suggested that Rf-modified sequences are able to form parallel tetramolecular G4 structures similar to that of the unmodified sequence. Analysis of the DSC thermograms has revealed that all modified G-quadruplexes have a higher thermal stability compared with the natural sequence, particularly the stabilisation is higher when the Rf residue is introduced at the 3'-end. Further, DSC analysis has revealed that the Rf residues introduced at the 3'-end are able to form additional stabilising interactions, energetically almost comparable to the enthalpic contribution of a G-tetrad. Fluorescence measurement are consistent with this result showing that the Rf residues introduced at 3'-end are able to form stacking interactions with the adjacent bases within the G-quadruplex structure. The whole of data suggested that the introduction of Rf unit can stabilize G-quadruplex structures and can be a promising candidate for future theranostic applications.
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Affiliation(s)
- Valeria Romanucci
- Department of Chemical Sciences, University of Napoli Federico II, Complesso di Monte Sant'Angelo, Via Cintia 4, I-80126 Napoli, Italy.
| | - Rosario Oliva
- Department of Chemical Sciences, University of Napoli Federico II, Complesso di Monte Sant'Angelo, Via Cintia 4, I-80126 Napoli, Italy; Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Otto-Hahn Strasse 4a, D-44227 Dortmund, Germany
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Napoli Federico II, Complesso di Monte Sant'Angelo, Via Cintia 4, I-80126 Napoli, Italy
| | - Sandra Claes
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Dominique Schols
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Armando Zarrelli
- Department of Chemical Sciences, University of Napoli Federico II, Complesso di Monte Sant'Angelo, Via Cintia 4, I-80126 Napoli, Italy
| | - Giovanni Di Fabio
- Department of Chemical Sciences, University of Napoli Federico II, Complesso di Monte Sant'Angelo, Via Cintia 4, I-80126 Napoli, Italy.
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6
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Virgilio A, Esposito V, Tassinari M, Nadai M, Richter SN, Galeone A. Novel monomolecular derivatives of the anti-HIV-1 G-quadruplex-forming Hotoda's aptamer containing inversion of polarity sites. Eur J Med Chem 2020; 208:112786. [PMID: 32911256 DOI: 10.1016/j.ejmech.2020.112786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 08/06/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023]
Abstract
Here we report on the design, preparation and investigation of four analogues of the anti-HIV G-quadruplex-forming Hotoda's aptamer, based on an unprecedented linear topology. In these derivatives, four TGGGAGT tracts have been joined together by exploiting 3'-3' and 5'-5' inversion of polarity sites formed by canonical phosphodiester bonds or a glycerol-based linker. Circular dichroism data suggest that all oligodeoxynucleotides fold in monomolecular G-quadruplex structures characterized by a parallel strand orientation and three side loops connecting 3'- or 5'-ends. The derivative bearing two lipophilic groups, namely HT353LGly, inhibited virus entry into the host cell, with anti-HIV-1 activity in the low nanomolar range; the other derivatives, albeit sharing the same base sequence and similar topology, were inactive. These results highlight that monomolecular Hotoda's aptamers with inversion of polarity sites represent a successful alternative strategy that merges the easiness of synthesis with the maintenance of remarkable activity. They also indicate that two lipophilic groups are necessary and sufficient for biological activity. Our data will inspire the design of further simplified derivatives with improved biophysical and antiviral properties.
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Affiliation(s)
- Antonella Virgilio
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Veronica Esposito
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Martina Tassinari
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121, Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121, Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121, Padua, Italy.
| | - Aldo Galeone
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Napoli, Italy.
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Roxo C, Kotkowiak W, Pasternak A. G-Quadruplex-Forming Aptamers-Characteristics, Applications, and Perspectives. Molecules 2019; 24:E3781. [PMID: 31640176 PMCID: PMC6832456 DOI: 10.3390/molecules24203781] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 12/31/2022] Open
Abstract
G-quadruplexes constitute a unique class of nucleic acid structures formed by G-rich oligonucleotides of DNA- or RNA-type. Depending on their chemical nature, loops length, and localization in the sequence or structure molecularity, G-quadruplexes are highly polymorphic structures showing various folding topologies. They may be formed in the human genome where they are believed to play a pivotal role in the regulation of multiple biological processes such as replication, transcription, and translation. Thus, natural G-quadruplex structures became prospective targets for disease treatment. The fast development of systematic evolution of ligands by exponential enrichment (SELEX) technologies provided a number of G-rich aptamers revealing the potential of G-quadruplex structures as a promising molecular tool targeted toward various biologically important ligands. Because of their high stability, increased cellular uptake, ease of chemical modification, minor production costs, and convenient storage, G-rich aptamers became interesting therapeutic and diagnostic alternatives to antibodies. In this review, we describe the recent advances in the development of G-quadruplex based aptamers by focusing on the therapeutic and diagnostic potential of this exceptional class of nucleic acid structures.
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Affiliation(s)
- Carolina Roxo
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Weronika Kotkowiak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Anna Pasternak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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8
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Carvalho J, Paiva A, Cabral Campello MP, Paulo A, Mergny JL, Salgado GF, Queiroz JA, Cruz C. Aptamer-based Targeted Delivery of a G-quadruplex Ligand in Cervical Cancer Cells. Sci Rep 2019; 9:7945. [PMID: 31138870 PMCID: PMC6538641 DOI: 10.1038/s41598-019-44388-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/27/2019] [Indexed: 02/02/2023] Open
Abstract
AS1411 is a G-rich DNA oligonucleotide that functions as an aptamer of the protein nucleolin, found at high levels on the surface of cancer cells but not on the surface of normal cells. Herein, we have studied AS1411 as a supramolecular carrier for the delivery of an acridine-based G-quadruplex ligand, C8, to HeLa cancer cells. Two AS1411 derivatives, LNA-AS1411 and U-AS1411, were also tested, in an attempt to compare AS1411 pharmacological properties. The results showed that AS1411-C8 complexation was made with great binding strength and that it lowered the ligand's cytotoxicity towards non-malignant cells. This effect was suggested to be due to a decreased internalization of the complexed versus free C8 as shown by flow cytometry. The AS1411 derivatives, despite forming a stable complex with C8, lacked the necessary tumour-selective behaviour. The binding of C8 to AS1411 G-quadruplex structure did not negatively affect the recognition of nucleolin by the aptamer. The AS1411-C8 repressed c-MYC expression at the transcriptional level, possibly due to C8 ability to stabilize the c-MYC promoter G-quadruplexes. Overall, this study demonstrates the usefulness of AS1411 as a supramolecular carrier of the G-quadruplex binder C8 and the potential of using its tumour-selective properties for the delivery of ligands for cancer therapy.
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Affiliation(s)
- Josué Carvalho
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal
| | - Artur Paiva
- Unidade de Gestão Operacional em Citometria, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
- CIMAGO/iCBR/CIBB, Faculdade de Medicina da Universidade de Coimbra, Coimbra, Portugal
- Instituto Politécnico de Coimbra, ESTESC-Coimbra Health School, Ciências Biomédicas Laboratoriais, Coimbra, Portugal
| | - Maria Paula Cabral Campello
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139,7), 2695-066, Bobadela, LRS, Portugal
| | - António Paulo
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139,7), 2695-066, Bobadela, LRS, Portugal
| | - Jean-Louis Mergny
- Univ. Bordeaux, ARNA laboratory, INSERM, U1212, CNRS UMR 5320, IECB, F-33600, Pessac, France
- Institute of Biophysics, AS CR, v.v.i. Kralovopolska 135, 612 65, Brno, Czech Republic
| | - Gilmar F Salgado
- Univ. Bordeaux, ARNA laboratory, INSERM, U1212, CNRS UMR 5320, IECB, F-33600, Pessac, France
| | - João A Queiroz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal.
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9
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Hotoda's Sequence and Anti-HIV Activity: Where Are We Now? Molecules 2019; 24:molecules24071417. [PMID: 30974914 PMCID: PMC6479790 DOI: 10.3390/molecules24071417] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/02/2019] [Accepted: 04/05/2019] [Indexed: 01/24/2023] Open
Abstract
The pharmacological relevance of ODNs forming G-quadruplexes as anti-HIV agents has been extensively reported in the literature over the last few years. Recent detailed studies have elucidated the peculiar arrangement adopted by many G-quadruplex-based aptamers and provided insight into their mechanism of action. In this review, we have reported the history of a strong anti-HIV agent: the 6-mer d(TGGGAG) sequence, commonly called "Hotoda's sequence". In particular, all findings reported on this sequence and its modified sequences have been discussed considering the following research phases: (i) discovery of the first 5'-modified active d(TGGGAG) sequences; (ii) synthesis of a variety of end-modified d(TGGGAG) sequences; (iii) biophysical and NMR investigations of natural and modified Hotoda's sequences; (iv); kinetic studies on the most active 5'-modified d(TGGGAG) sequences; and (v) extensive anti-HIV screening of G-quadruplexes formed by d(TGGGAG) sequences. This review aims to clarify all results obtained over the years on Hotoda's sequence, revealing its potentiality as a strong anti-HIV agent (EC50 = 14 nM).
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10
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Nici F, Oliviero G, Falanga AP, D'Errico S, Marzano M, Musumeci D, Montesarchio D, Noppen S, Pannecouque C, Piccialli G, Borbone N. Anti-HIV activity of new higher order G-quadruplex aptamers obtained from tetra-end-linked oligonucleotides. Org Biomol Chem 2019. [PMID: 29543291 DOI: 10.1039/c7ob02346d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
By combining the ability of short G-rich oligodeoxyribonucleotides (ODNs) containing the sequence 5'CGGA3' to form higher order G-quadruplex (G4) complexes with the tetra-end-linked (TEL) concept to produce aptamers targeting the HIV envelope glycoprotein 120 (gp120), three new TEL-ODNs (1-3) having the sequence 5'CGGAGG3' were synthesized with the aim of studying the effect of G4 dimerization on their anti-HIV activity. Furthermore, in order to investigate the effect of the groups at the 5' position, the 5' ends of 1-3 were left uncapped (1) or capped with either the lipophilic dimethoxytrityl (DMT) (2) or the hydrophilic glucosyl-4-phosphate (3) moieties. The here reported results demonstrate that only the DMT-substituted TEL-ODN 2 is effective in protecting human MT-4 cell cultures from HIV infection (76% max protection), notwithstanding all the three new aptamers proved to be capable of forming stable higher order dimeric G4s when annealed in K+-containing buffer, thus suggesting that the recognition of a hydrophobic pocket on the target glycoprotein by the aptamers represents a main structural feature for triggering their anti-HIV activity.
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Affiliation(s)
- F Nici
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - G Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Napoli, Italy
| | - A P Falanga
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - S D'Errico
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - M Marzano
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - D Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - D Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - S Noppen
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, B-3000 Leuven, Belgium
| | - C Pannecouque
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, B-3000 Leuven, Belgium
| | - G Piccialli
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - N Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
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11
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DNA Quadruplex-Based Inhibitor With Flexible Fragments at the 3' Terminal Shows Enhanced Anti-HIV-1 Fusion Activity. J Pharm Sci 2019; 108:2243-2246. [PMID: 30797782 DOI: 10.1016/j.xphs.2019.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/14/2019] [Accepted: 02/08/2019] [Indexed: 12/20/2022]
Abstract
Chemically optimizing the molecular structure of aptamers may enhance properties such as biological activity or metabolic stability. DNA quadruplex-based HIV-1 fusion inhibitors were found to interact with HIV-1 surface glycoprotein in aptamer mode. In this work, a series of quadruplex-based HIV-1 fusion inhibitors with flexible oligodeoxynucleotide fragments at the 3' terminal was discovered. The flexible extension did not greatly influence quadruplex formation at the 5'-end. Increasing the length of the flexible fragment may increase antifusion activity. Compared with a traditional inhibitor, d(5'TGGGAG3')4, these novel inhibitors showed enhanced interaction with HIV-1 glycoproteins gp120 and gp41, which increased inhibition of 6-helical bundle formation during the course of virus fusion. These inhibitors also showed improved stability, compared with natural oligodeoxynucleotide. This work may inform the design of anti-HIV-1 DNA helix-based inhibitors with new structures or mechanisms.
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12
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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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13
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Tang Y, Han Z, Guo J, Tian Y, Liu K, Xu L. Synthesis, biophysical characterization, and anti-HIV-1 fusion activity of DNA helix-based inhibitors with a p-benzyloxyphenyl substituent at the 5'-nucleobase site. Bioorg Med Chem Lett 2018; 28:1842-1845. [PMID: 29680665 DOI: 10.1016/j.bmcl.2018.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 11/17/2022]
Abstract
DNA helix-based HIV-1 fusion inhibitors have been discovered as potent drug candidates. Introduction of hydrophobic groups to a nucleobase provides an opportunity to design inhibitors with novel structures and mechanisms of action. In this work, two novel nucleoside analogues (1 and 2) were synthesized and incorporated into four DNA duplex- and quadruplex-based inhibitors. All the molecules showed anti-HIV-1 fusion activity. The effect of the p-benzyloxyphenyl group and the attached linker on the helix formation and thermal stability were fully compared and discussed. Surface plasmon resonance analysis further indicated that inhibitors with the same DNA helix may still have variable reaction targets, mainly attributed to the different hydrophobic modifications.
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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
| | - 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
| | - 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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14
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Park Y, Kim KT, Kim BH. G-Quadruplex formation using fluorescent oligonucleotides as a detection method for discriminating AGG trinucleotide repeats. Chem Commun (Camb) 2018; 52:12757-12760. [PMID: 27722273 DOI: 10.1039/c6cc06566j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We have developed a simple and sensitive system for detecting AGG trinucleotide repeats through the formation of intermolecular G-quadruplexes using a fluorescent oligonucleotide. The fluorescence signal increased rapidly and dramatically by 44.7-fold with respect to the low background signal in the presence of RNA agg repeats and by 35.0-fold in the presence of DNA AGG repeats.
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Affiliation(s)
- Yoojin Park
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTEH), Pohang 37673, Republic of Korea.
| | - Ki Tae Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTEH), Pohang 37673, Republic of Korea.
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTEH), Pohang 37673, Republic of Korea.
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15
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Romanucci V, Zarrelli A, Liekens S, Noppen S, Pannecouque C, Di Fabio G. New findings on the d(TGGGAG) sequence: Surprising anti-HIV-1 activity. Eur J Med Chem 2018; 145:425-430. [PMID: 29335208 DOI: 10.1016/j.ejmech.2018.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 12/12/2017] [Accepted: 01/02/2018] [Indexed: 10/18/2022]
Abstract
The biological relevance of tetramolecular G-quadruplexes especially as anti-HIV agents has been extensively reported in the literature over the last years. In the light of our recent results regarding the slow G-quadruplex folding kinetics of ODNs based on d(TGGGAG) sequence, here we report a systematic anti-HIV screening to investigate the impact of the G-quadruplex folding on their anti-HIV activity. In particular, varying the single stranded concentrations of ODNs, it has been tested a pool of ODN sample solutions with different G-quadruplex concentrations. The anti-HIV assays have been designed favouring the limited kinetics involved in the tetramolecular G4-association based on the d(TGGGAG) sequence. Aiming to determine the stoichiometry of G-quadruplex structures in the same experimental conditions of the anti-HIV assays, a native gel electrophoresis was performed. The gel confirmed the G-quadruplex formation for almost all sample solutions while showing the formation of high order G4 structures for the more concentrated ODNs solutions. The most significant result is the discovery of a potent anti-HIV activity of the G-quadruplex formed by the natural d(TGGGAG) sequence (IC50 = 14 nM) that, until now, has been reported to be completely inactive against HIV infection.
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Affiliation(s)
- Valeria Romanucci
- Department of Chemical Sciences, University of Napoli 'Federico II', Via Cintia 4, I-80126, Napoli, Italy
| | - Armando Zarrelli
- Department of Chemical Sciences, University of Napoli 'Federico II', Via Cintia 4, I-80126, Napoli, Italy
| | - Sandra Liekens
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, B-3000, Leuven, Belgium
| | - Sam Noppen
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, B-3000, Leuven, Belgium
| | - Christophe Pannecouque
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, B-3000, Leuven, Belgium.
| | - Giovanni Di Fabio
- Department of Chemical Sciences, University of Napoli 'Federico II', Via Cintia 4, I-80126, Napoli, Italy.
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16
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D'Urso A, Randazzo R, Rizzo V, Gangemi CMA, Romanucci V, Zarrelli A, Tomaselli G, Milardi D, Borbone N, Purrello R, Piccialli G, Di Fabio G, Oliviero G. Stabilization vs. destabilization of G-quadruplex superstructures: the role of the porphyrin derivative having spermine arms. Phys Chem Chem Phys 2017. [PMID: 28650039 DOI: 10.1039/c7cp02816d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of the porphyrin derivative H2TCPPSpm4, having spermine pendants in the four meso positions, with the G-quadruplex (GQ) structure formed by the DNA aptamer TGGGAG has been investigated by means of UV, electronic circular dichroism and PAGE studies. The results reported here demonstrate that the porphyrin derivative is capable of stabilizing or destabilizing the higher-ordered structures of parallel GQs, depending on the method used to reach their relative stoichiometry (titration vs. single addition). Noteworthily, when two equivalents of H2TCPPSpm4 were mixed directly with one equivalent of the (TGGGAG)4 GQ to reach a 2 : 1 H2TCPPSpm4 : GQ ratio T1/2 higher than 80 °C was also observed confirming the presence of higher-ordered GQ structures.
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Affiliation(s)
- A D'Urso
- Department of Chemical Science, University of Catania, V.le A Doria 6, 95125, Catania, Italy.
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17
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Platella C, Riccardi C, Montesarchio D, Roviello GN, Musumeci D. G-quadruplex-based aptamers against protein targets in therapy and diagnostics. Biochim Biophys Acta Gen Subj 2017; 1861:1429-1447. [PMID: 27865995 PMCID: PMC7117017 DOI: 10.1016/j.bbagen.2016.11.027] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 12/17/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA molecules identified to recognize with high affinity specific targets including proteins, small molecules, ions, whole cells and even entire organisms, such as viruses or bacteria. They can be identified from combinatorial libraries of DNA or RNA oligonucleotides by SELEX technology, an in vitro iterative selection procedure consisting of binding (capture), partitioning and amplification steps. Remarkably, many of the aptamers selected against biologically relevant protein targets are G-rich sequences that can fold into stable G-quadruplex (G4) structures. Aiming at disseminating novel inspiring ideas within the scientific community in the field of G4-structures, the emphasis of this review is placed on: 1) recent advancements in SELEX technology for the efficient and rapid identification of new candidate aptamers (introduction of microfluidic systems and next generation sequencing); 2) recurrence of G4 structures in aptamers selected by SELEX against biologically relevant protein targets; 3) discovery of several G4-forming motifs in important regulatory regions of the human or viral genome bound by endogenous proteins, which per se can result into potential aptamers; 4) an updated overview of G4-based aptamers with therapeutic potential and 5) a discussion on the most attractive G4-based aptamers for diagnostic applications. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | | | - Domenica Musumeci
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy; Institute of Biostructures and Bioimages, CNR, Napoli, Italy.
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18
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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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19
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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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20
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Xu L, Zhang T, Xu X, Chong H, Lai W, Jiang X, Wang C, He Y, Liu K. DNA Triplex-Based Complexes Display Anti-HIV-1-Cell Fusion Activity. Nucleic Acid Ther 2016; 25:219-25. [PMID: 26192705 DOI: 10.1089/nat.2015.0535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
DNA triplexes with hydrophobic modifications were designed and evaluated for their activity as inhibitors of the cell fusion of human immunodeficiency virus type 1 (HIV-1). Triplex inhibitors displayed low micromolar activities in the cell-cell fusion assay and nanomolar activities in the anti-HIV-1 pseudovirus test. Helix structure and the presence of sufficient numbers of hydrophobic regions were essential for the antifusion activity. Results from native polyacrylamide gel electrophoresis and a fluorescent resonance energy transfer-based inhibitory assay indicated that these triplexes may interact with the primary pocket at the glycoprotein 41 (gp41) N-heptad repeat, thereby inhibiting formation of the HIV-1 gp41 6-helical bundle. Triplex-based complexes may represent a novel category of HIV-1 inhibitors in anti-HIV-1 drug discovery.
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Affiliation(s)
- Liang Xu
- 1 State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology , Beijing, China
| | - Tao Zhang
- 1 State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology , Beijing, China
| | - Xiaoyu Xu
- 1 State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology , Beijing, China
| | - Huihui Chong
- 2 Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing, China
| | - Wenqing Lai
- 1 State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology , Beijing, China
| | - Xifeng Jiang
- 1 State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology , Beijing, China
| | - Chao Wang
- 1 State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology , Beijing, China
| | - Yuxian He
- 2 Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing, China
| | - Keliang Liu
- 1 State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology , Beijing, China
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21
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Romanucci V, Marchand A, Mendoza O, D’Alonzo D, Zarrelli A, Gabelica V, Di Fabio G. Kinetic ESI-MS Studies of Potent Anti-HIV Aptamers Based on the G-Quadruplex Forming Sequence d(TGGGAG). ACS Med Chem Lett 2016; 7:256-60. [PMID: 26985311 DOI: 10.1021/acsmedchemlett.5b00408] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/26/2016] [Indexed: 12/24/2022] Open
Abstract
To investigate what properties make tetramolecular G-quadruplex ODNs good anti-HIV aptamers, we studied the stoichiometry and the self-assembly kinetics of the highly active 5'-end modified G-quadruplexes based on the d(TGGGAG) sequence. Our results demonstrate that the 5'-end conjugation does not necessarily increase the folding rate of the G-quadruplex; indeed, it ascribes anti-HIV activity. Unexpectedly, the G4-folding kinetics of the inactive G4 is similar to that of the 5'-end modified sequences. ESI-MS studies also revealed the formation of higher order G4 structures identified as octameric complexes along with tetramolecular G-quadruplexes.
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Affiliation(s)
- Valeria Romanucci
- Department
of Chemical Sciences, University of Napoli Federico II, Via Cintia, I-80126 Napoli, Italy
| | - Adrien Marchand
- IECB,
ARNA Laboratory, University of Bordeaux, 33600 Pessac, France
- Inserm,
U869, ARNA Laboratory, Institut National de la Santé et de la Recherche Médicale, 33000 Bordeaux, France
| | - Oscar Mendoza
- IECB,
ARNA Laboratory, University of Bordeaux, 33600 Pessac, France
- Inserm,
U869, ARNA Laboratory, Institut National de la Santé et de la Recherche Médicale, 33000 Bordeaux, France
| | - Daniele D’Alonzo
- Department
of Chemical Sciences, University of Napoli Federico II, Via Cintia, I-80126 Napoli, Italy
| | - Armando Zarrelli
- Department
of Chemical Sciences, University of Napoli Federico II, Via Cintia, I-80126 Napoli, Italy
| | - Valérie Gabelica
- IECB,
ARNA Laboratory, University of Bordeaux, 33600 Pessac, France
- Inserm,
U869, ARNA Laboratory, Institut National de la Santé et de la Recherche Médicale, 33000 Bordeaux, France
| | - Giovanni Di Fabio
- Department
of Chemical Sciences, University of Napoli Federico II, Via Cintia, I-80126 Napoli, Italy
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22
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Oliviero G, Stornaiuolo M, D'Atri V, Nici F, Yousif AM, D'Errico S, Piccialli G, Mayol L, Novellino E, Marinelli L, Grieco P, Carotenuto A, Noppen S, Liekens S, Balzarini J, Borbone N. Screening Platform toward New Anti-HIV Aptamers Set on Molecular Docking and Fluorescence Quenching Techniques. Anal Chem 2016; 88:2327-34. [PMID: 26810800 DOI: 10.1021/acs.analchem.5b04268] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
By using a new rapid screening platform set on molecular docking simulations and fluorescence quenching techniques, three new anti-HIV aptamers targeting the viral surface glycoprotein 120 (gp120) were selected, synthesized, and assayed. The use of the short synthetic fluorescent peptide V35-Fluo mimicking the V3 loop of gp120, as the molecular target for fluorescence-quenching binding affinity studies, allowed one to measure the binding affinities of the new aptamers for the HIV-1 gp120 without the need to obtain and purify the full recombinant gp120 protein. The almost perfect correspondence between the calculated Kd and the experimental EC50 on HIV-infected cells confirmed the reliability of the platform as an alternative to the existing methods for aptamer selection and measuring of aptamer-protein equilibria.
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Affiliation(s)
- Giorgia Oliviero
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Mariano Stornaiuolo
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Valentina D'Atri
- University of Bordeaux , IECB, ARNA laboratory, Pessac, 33600, France.,INSERM , U869, ARNA laboratory, Bordeaux, 33000, France
| | - Fabrizia Nici
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Ali Munaim Yousif
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Stefano D'Errico
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Gennaro Piccialli
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy.,CNR , Institute of Protein Biochemistry, Napoli, 80131, Italy
| | - Luciano Mayol
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Ettore Novellino
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Luciana Marinelli
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Paolo Grieco
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Alfonso Carotenuto
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
| | - Sam Noppen
- KU Leuven , Rega Institute for Medical Research, Leuven, 3000, Belgium
| | - Sandra Liekens
- KU Leuven , Rega Institute for Medical Research, Leuven, 3000, Belgium
| | - Jan Balzarini
- KU Leuven , Rega Institute for Medical Research, Leuven, 3000, Belgium
| | - Nicola Borbone
- University of Naples Federico II , Department of Pharmacy, Napoli, 80131, Italy
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23
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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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24
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Salgado GF, Cazenave C, Kerkour A, Mergny JL. G-quadruplex DNA and ligand interaction in living cells using NMR spectroscopy. Chem Sci 2015; 6:3314-3320. [PMID: 28706695 PMCID: PMC5490339 DOI: 10.1039/c4sc03853c] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/13/2015] [Indexed: 12/31/2022] Open
Abstract
Using in-cell NMR spectroscopy to probe ligand binding to a G-quadruplex nucleic acid.
Gathering structural information from biologically relevant molecules inside living cells has always been a challenging task. In this work, we have used multidimensional NMR spectroscopy to probe DNA G-quadruplexes inside living Xenopus laevis oocytes. Some of these structures can be found in key regions of chromosomes. G-quadruplexes are considered potential anticancer therapeutic targets and several lines of evidence indirectly point out roles in key biological processes, such as cell proliferation, genomic instability or replication initiation. However, direct demonstrations of the existence of G-quadruplexes in vivo are scarce. Using SOFAST-HMQC type spectra, we probed a tetramolecular G-quadruplex model made of d(TG4T)4 inside living Xenopus laevis oocytes. Our observations lead us to conclude that the quadruplex structure is formed within the cell and that the intracellular environment preferentially selects a conformation that most resembles the one found in vitro under KCl conditions. We also show for the first time that specific ligands targeting G-quadruplexes can be studied using high resolution NMR directly inside living cells, opening new avenues to study ligand binding discrimination under physiologically relevant conditions with atomic detail.
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Affiliation(s)
- Gilmar F Salgado
- Univ. Bordeaux , ARNA Laboratory , F-33000 Bordeaux , France . .,INSERM , U869 , IECB , F-33600 Pessac , France
| | - Christian Cazenave
- CNRS , Microbiologie Fondamentale et Pathogénicité , UMR 5234 , F-33000 Bordeaux , France.,Univ. Bordeaux , Microbiologie Fondamentale et Pathogénicité , UMR 5234 , F-33000 Bordeaux , France
| | - Abdelaziz Kerkour
- Univ. Bordeaux , ARNA Laboratory , F-33000 Bordeaux , France . .,INSERM , U869 , IECB , F-33600 Pessac , France
| | - Jean-Louis Mergny
- Univ. Bordeaux , ARNA Laboratory , F-33000 Bordeaux , France . .,INSERM , U869 , IECB , F-33600 Pessac , France
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25
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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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26
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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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27
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Altieri A, Alvino A, Ohnmacht S, Ortaggi G, Neidle S, Nocioni D, Franceschin M, Bianco A. Xanthene and xanthone derivatives as G-quadruplex stabilizing ligands. Molecules 2013; 18:13446-70. [PMID: 24177701 PMCID: PMC6269716 DOI: 10.3390/molecules181113446] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 10/21/2013] [Accepted: 10/23/2013] [Indexed: 12/14/2022] Open
Abstract
Following previous studies on anthraquinone and acridine-based G-quadruplex ligands, here we present a study of similar aromatic cores, with the specific aim of increasing G-quadruplex binding and selectivity with respect to duplex DNA. Synthesized compounds include two and three-side chain xanthone and xanthene derivatives, as well as a dimeric “bridged” form. ESI and FRET measurements suggest that all the studied molecules are good G-quadruplex ligands, both at telomeres and on G-quadruplex forming sequences of oncogene promoters. The dimeric compound and the three-side chain xanthone derivative have been shown to represent the best compounds emerging from the different series of ligands presented here, having also high selectivity for G-quadruplex structures with respect to duplex DNA. Molecular modeling simulations are in broad agreement with the experimental data.
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Affiliation(s)
- Alessandro Altieri
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, Roma 00185, Italy; E-Mails: (A.A.); (G.O.); (D.N.); (M.F.)
- Authors to whom correspondence should be addressed; E-Mails: (A.A.); (A.B.); Tel.: +39-064-991-3229/3622 (A.A. & A.B.) Fax: +39-064-991-3841 (A.A. & A.B.)
| | - Antonello Alvino
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, Roma 00185, Italy; E-Mails: (A.A.); (G.O.); (D.N.); (M.F.)
| | - Stephan Ohnmacht
- The UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; E-Mails: (S.O.); (S.N.)
| | - Giancarlo Ortaggi
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, Roma 00185, Italy; E-Mails: (A.A.); (G.O.); (D.N.); (M.F.)
| | - Stephen Neidle
- The UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; E-Mails: (S.O.); (S.N.)
| | - Daniele Nocioni
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, Roma 00185, Italy; E-Mails: (A.A.); (G.O.); (D.N.); (M.F.)
| | - Marco Franceschin
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, Roma 00185, Italy; E-Mails: (A.A.); (G.O.); (D.N.); (M.F.)
| | - Armandodoriano Bianco
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, Roma 00185, Italy; E-Mails: (A.A.); (G.O.); (D.N.); (M.F.)
- Authors to whom correspondence should be addressed; E-Mails: (A.A.); (A.B.); Tel.: +39-064-991-3229/3622 (A.A. & A.B.) Fax: +39-064-991-3841 (A.A. & A.B.)
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28
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DNA duplexes with hydrophobic modifications inhibit fusion between HIV-1 and cell membranes. Antimicrob Agents Chemother 2013; 57:4963-70. [PMID: 23896466 DOI: 10.1128/aac.00758-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Discovery of new drugs for the treatment of AIDS typically possessing unique structures associated with novel mechanisms of action has been of great importance due to the quick drug-resistant mutations of HIV-1 strains. The work presented in this report describes a novel class of DNA duplex-based HIV-1 fusion inhibitors. Hydrophobic groups were introduced into a DNA duplex skeleton either at one end, at both ends, or in the middle. These modified DNA duplexes inhibited fusion between HIV-1 and human cell membranes at micro- or submicromolar concentrations. Respective inhibitors adopted an aptamer pattern instead of a base-pairing interaction pattern. Structure-activity relationship studies of the respective DNA duplexes showed that the rigid and negatively charged DNA skeletons, in addition to the presence of hydrophobic groups, were crucial to the anti-HIV-1 activity of these compounds. A fluorescent resonance energy transfer (FRET)-based inhibitory assay showed that these duplex inhibitors interacted with the primary pocket in the gp41 N-terminal heptad repeat (NHR) instead of interacting with the lipid bilayers.
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29
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Pagano B, Randazzo A, Fotticchia I, Novellino E, Petraccone L, Giancola C. Differential scanning calorimetry to investigate G-quadruplexes structural stability. Methods 2013; 64:43-51. [PMID: 23500655 DOI: 10.1016/j.ymeth.2013.02.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/19/2013] [Accepted: 02/25/2013] [Indexed: 01/20/2023] Open
Abstract
Differential Scanning Calorimetry (DSC) is a straightforward methodology to characterize the energetics of thermally-induced transitions of DNA and other biological macromolecules. Therefore, DSC has been used to study the thermodynamic stability of several nucleic acids structures. G-quadruplexes are among the most important non-canonical nucleic acid architectures that are receiving great consideration. This article reports examples on the contribution of DSC to the knowledge of G-quadruplex structures. The selected case studies show the potential of this method in investigating the structure stability of G-quadruplex forming nucleic acids, and in providing information on their structural complexity. Indeed, DSC can determine thermodynamic parameters of G-quadruplex folding/unfolding processes, but it can also be useful to reveal the formation of multiple conformations or the presence of intermediate states along the unfolding pathway, and to evaluate the impact of chemical modifications on their structural stability. This article aims to show that DSC is an important complementary methodology to structural techniques, such as NMR and X-ray crystallography, in the study of G-quadruplex forming nucleic acids.
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Affiliation(s)
- Bruno Pagano
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, I-80131 Napoli, Italy
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30
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Doluca O, Withers JM, Filichev VV. Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes. Chem Rev 2013; 113:3044-83. [PMID: 23391174 DOI: 10.1021/cr300225q] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osman Doluca
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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31
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Vaddula BR, Varma RS, Leazer J. One-Pot Catalyst-Free Synthesis of β- and γ-Hydroxy Sulfides Using Diaryliodonium Salts and Microwave Irradiation. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201313] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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32
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Musumeci D, Montesarchio D. Synthesis of a cholesteryl-HEG phosphoramidite derivative and its application to lipid-conjugates of the anti-HIV 5'TGGGAG³' Hotoda's sequence. Molecules 2012; 17:12378-92. [PMID: 23090019 PMCID: PMC6268758 DOI: 10.3390/molecules171012378] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 10/16/2012] [Accepted: 10/17/2012] [Indexed: 02/07/2023] Open
Abstract
A novel phosphoramidite derivative of cholesterol, with an ether-linked hexaethylene glycol (HEG) spacer arm, has been obtained through simple and reproducible solid phase modified oligonucleotide synthesis manipulations. This building block and the known phosphoramidite derivative of 3b-(2-hydroxyethoxy)cholesterol have been exploited in standard oligonucleotide synthesis protocols for the preparation of 5'- conjugates of the G-quadruplex-forming ⁵'TGGGAG³' oligomer, known as the Hotoda's sequence, to produce new potential anti-HIV agents.
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Affiliation(s)
| | - Daniela Montesarchio
- Dipartimento di Scienze Chimiche, Università di Napoli “Federico II”, Complesso Universitario di Monte Sant’Angelo, via Cintia 21, I-80126, Napoli, Italy
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33
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Virgilio A, Esposito V, Citarella G, Mayol L, Galeone A. Structural investigations on the anti-HIV G-quadruplex-forming oligonucleotide TGGGAG and its analogues: evidence for the presence of an A-tetrad. Chembiochem 2012; 13:2219-24. [PMID: 22945376 DOI: 10.1002/cbic.201200481] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Indexed: 11/07/2022]
Abstract
Several anti-HIV aptamers adopt DNA quadruplex structures. Among these, "Hotoda's aptamer" (base sequence TGGGAG) was one of the first to be discovered. Although it has been the topic of some recent research, no detailed structural investigations have been reported. Here we report structural investigations on this aptamer and analogues with related sequences, by using UV, CD, and NMR spectroscopy as well as electrophoretic techniques. The addition of a 3'-end thymine has allowed us to obtain a single, investigable quadruplex structure. Data clearly point to the presence of an A-tetrad. Furthermore, the effects of the incorporation of an 8-methyl-2'-deoxyguanosine at the 5'-end of the G-run were investigated.
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Affiliation(s)
- Antonella Virgilio
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, I-80131 Napoli, Italy
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34
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Polyvalent nucleic acid aptamers and modulation of their activity: a focus on the thrombin binding aptamer. Pharmacol Ther 2012; 136:202-15. [PMID: 22850531 DOI: 10.1016/j.pharmthera.2012.07.011] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 07/16/2012] [Indexed: 01/29/2023]
Abstract
Nucleic acid-based aptamers can be selected from combinatorial libraries of synthetic oligonucleotides to bind, with affinity and specificity similar to antibodies, a wide range of biomedically relevant targets. Compared to protein therapeutics, aptamers exhibit significant advantages in terms of size, non-immunogenicity and wide synthetic accessibility. Various chemical modifications have been introduced in the natural oligonucleotide backbone of aptamers in order to increase their half-life, as well as their pharmacological properties. Very effective alternative approaches, devised in order to improve both the aptamer activity and stability, were based on the design of polyvalent aptamers, able to establish multivalent interactions with the target: thus, multiple copies of an aptamer can be assembled on the same molecular- or nanomaterial-based scaffold. In the present review, the thrombin binding aptamers (TBAs) are analyzed as a model system to study multiple-aptamer constructs aimed at improving their anticoagulation activity in terms of binding to the target and stability to enzymatic degradation. Indeed - even if the large number of chemically modified TBAs investigated in the last 20 years has led to encouraging results - a significant progress has been obtained only recently with bivalent or engineered dendritic TBA aptamers, or assemblies of TBAs on nanoparticles and DNA nanostructures. Furthermore, the modulation of the aptamers activity by means of tailored drug-active reversal agents, especially in the field of anticoagulant aptamers, as well as the reversibility of the TBA activity through the use of antidotes, such as porphyrins, complementary oligonucleotides or of external stimuli, are discussed.
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35
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N(3)-Protection of Thymidine with Boc for an Easy Synthetic Access to Sugar-Alkylated Nucleoside Analogs. Chem Biodivers 2012; 9:589-97. [DOI: 10.1002/cbdv.201100103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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36
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Chen W, Xu L, Cai L, Zheng B, Wang K, He J, Liu K. d(TGGGAG) with 5′-nucleobase-attached large hydrophobic groups as potent inhibitors for HIV-1 envelop proteins mediated cell–cell fusion. Bioorg Med Chem Lett 2011; 21:5762-4. [DOI: 10.1016/j.bmcl.2011.08.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 07/18/2011] [Accepted: 08/02/2011] [Indexed: 11/24/2022]
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37
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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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38
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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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39
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Tran PLT, Virgilio A, Esposito V, Citarella G, Mergny JL, Galeone A. Effects of 8-methylguanine on structure, stability and kinetics of formation of tetramolecular quadruplexes. Biochimie 2010; 93:399-408. [PMID: 21034790 DOI: 10.1016/j.biochi.2010.10.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 10/19/2010] [Indexed: 10/18/2022]
Abstract
Tetramolecular G-quadruplexes result from the association of four guanine-rich strands. Modification of the backbone strand or the guanine bases of the oligonucleotide may improve stability or introduce new functionalities. In this regard, the 8 position of a guanosine is particularly suitable for introduction of modifications since as it is positioned in the groove of the quadruplex structure. Modifications at this position should not interfere with structural assembly as would changes at Watson-Crick and Hoogsteen sites. In this study, we investigated the effect of an 8-methyl-2'-deoxyguanosine residue (M) on the structure and stability of tetramolecular parallel G-quadruplexes. In some cases, the presence of this residue resulted in the formation of unusual quadruplex structures containing all-syn tetrads. Furthermore, the modified nucleoside M at the 5'-end of the sequence accelerated quadruplex formation by 15-fold or more relative to the unmodified oligonucleotide, which makes this nucleobase an attractive replacement for guanine in the context of tetramolecular parallel quadruplexes.
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Affiliation(s)
- Phong Lan Thao Tran
- INSERM U869, European Institute of Chemistry and Biology, Bordeaux University, 2 rue Robert Escarpit, Pessac, France
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40
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Oliviero G, Amato J, Borbone N, D'Errico S, Galeone A, Mayol L, Haider S, Olubiyi O, Hoorelbeke B, Balzarini J, Piccialli G. Tetra-end-linked oligonucleotides forming DNA G-quadruplexes: a new class of aptamers showing anti-HIV activity. Chem Commun (Camb) 2010; 46:8971-3. [PMID: 20972507 DOI: 10.1039/c0cc02866e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The biophysical and biological properties of unprecedented anti-HIV aptamers are presented. The most active aptamer (1L) shows a significant affinity to the HIV protein gp120.
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Affiliation(s)
- Giorgia Oliviero
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, I-80131 Napoli, Italy
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41
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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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42
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D'Onofrio J, Petraccone L, Martino L, Di Fabio G, Iadonisi A, Balzarini J, Giancola C, Montesarchio D. Synthesis, biophysical characterization, and anti-HIV activity of glyco-conjugated G-quadruplex-forming oligonucleotides. Bioconjug Chem 2008; 19:607-16. [PMID: 18254584 DOI: 10.1021/bc7003395] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Novel hybrid oligonucleotides carrying the G-quadruplex-forming d(5'TGGGAG3') sequence, conjugated with mono- or disaccharides at the 3' or 5'-end through phosphodiester bonds, have been synthesized as potential anti-HIV agents, via a fully automated, online phosphoramidite-based solid-phase strategy. CD-monitored thermal denaturation studies on the resulting quadruplexes indicated the insertion of a single monosaccharide at the 3'-end as the optimal modification, conferring improved stability to the quadruplex complex. In addition, the 3'-conjugation with glucose or mannose converted the anti-HIV inactive unmodified oligomer into active compounds. On the contrary, the 5'-tethering with these monosaccharides, as well as the conjugation, either at the 5' or 3'-end, with sucrose, were in all cases detrimental to quadruplex stability and did not improve the biological activity. On the basis of the assumption that the kinetically and thermodynamically favored formation of the quadruplex complex is a prerequisite for efficient antiviral activity, a novel bis-conjugated oligonucleotide was designed. This combined a mannose residue at the 3'-phosphate end with bulky aromatic tert-butyldiphenylsilyl (TBDPS) group at the 5'-end, previously shown to markedly favor the formation of quadruplex complexes. The 5',3'-bis-conjugated 6-mer, for which a detailed biophysical characterization has been carried out, resulted in 3-fold greater antiviral activity against HIV-1 than the sole 3'-glyco-conjugated oligonucleotide.
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Affiliation(s)
- Jennifer D'Onofrio
- Dipartimento di Chimica Organica e Biochimica and Dipartimento di Chimica Paolo Corradini, Università degli Studi di Napoli Federico II, Via Cintia 4, I-80126 Napoli, Italy
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