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Falanga AP, Terracciano M, Oliviero G, Roviello GN, Borbone N. Exploring the Relationship between G-Quadruplex Nucleic Acids and Plants: From Plant G-Quadruplex Function to Phytochemical G4 Ligands with Pharmaceutic Potential. Pharmaceutics 2022; 14:2377. [PMID: 36365194 PMCID: PMC9698481 DOI: 10.3390/pharmaceutics14112377] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/19/2022] [Accepted: 11/01/2022] [Indexed: 10/31/2023] Open
Abstract
G-quadruplex (G4) oligonucleotides are higher-order DNA and RNA secondary structures of enormous relevance due to their implication in several biological processes and pathological states in different organisms. Strategies aiming at modulating human G4 structures and their interrelated functions are first-line approaches in modern research aiming at finding new potential anticancer treatments or G4-based aptamers for various biomedical and biotechnological applications. Plants offer a cornucopia of phytocompounds that, in many cases, are effective in binding and modulating the thermal stability of G4s and, on the other hand, contain almost unexplored G4 motifs in their genome that could inspire new biotechnological strategies. Herein, we describe some G4 structures found in plants, summarizing the existing knowledge of their functions and biological role. Moreover, we review some of the most promising G4 ligands isolated from vegetal sources and report on the known relationships between such phytochemicals and G4-mediated biological processes that make them potential leads in the pharmaceutical sector.
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Affiliation(s)
- Andrea P. Falanga
- 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
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Giovanni N. Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Area di Ricerca site and Headquarters, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
- Institute of Applied Sciences and Intelligent Systems, Italian National Council of Research (ISASI-CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
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2
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Greco F, Falanga AP, Terracciano M, D’Ambrosio C, Piccialli G, Oliviero G, Roviello GN, Borbone N. CD, UV, and In Silico Insights on the Effect of 1,3-Bis(1'-uracilyl)-2-propanone on Serum Albumin Structure. Biomolecules 2022; 12:1071. [PMID: 36008965 PMCID: PMC9405946 DOI: 10.3390/biom12081071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 07/29/2022] [Indexed: 02/04/2023] Open
Abstract
1,3-diaryl-2-propanone derivatives are synthetic compounds used as building blocks for the realization not only of antimicrobial drugs but also of new nanomaterials thanks to their ability to self-assemble in solution and interact with nucleopeptides. However, their ability to interact with proteins is a scarcely investigated theme considering the therapeutic importance that 1,3-diaryl-2-propanones could have in the modulation of protein-driven processes. Within this scope, we investigated the protein binding ability of 1,3-bis(1'-uracilyl)-2-propanone, which was previously synthesized in our laboratory utilizing a Dakin-West reaction and herein indicated as U2O, using bovine serum albumin (BSA) as the model protein. Through circular dichroism (CD) and UV spectroscopy, we demonstrated that the compound, but not the similar thymine derivative T2O, was able to alter the secondary structure of the serum albumin leading to significant consequences in terms of BSA structure with respect to the unbound protein (Δβ-turn + Δβ-sheet = +23.6%, Δα = -16.7%) as revealed in our CD binding studies. Moreover, molecular docking studies suggested that U2O is preferentially housed in the domain IIIB of the protein, and its affinity for the albumin is higher than that of the reference ligand HA 14-1 (HDOCK score (top 1-3 poses): -157.11 ± 1.38 (U2O); -129.80 ± 6.92 (HA 14-1); binding energy: -7.6 kcal/mol (U2O); -5.9 kcal/mol (HA 14-1)) and T2O (HDOCK score (top 1-3 poses): -149.93 ± 2.35; binding energy: -7.0 kcal/mol). Overall, the above findings suggest the ability of 1,3-bis(1'-uracilyl)-2-propanone to bind serum albumins and the observed reduction of the α-helix structure with the concomitant increase in the β-structure are consistent with a partial protein destabilization due to the interaction with U2O.
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Affiliation(s)
- Francesca Greco
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy; (F.G.); (A.P.F.); (M.T.); (C.D.); (G.P.); (N.B.)
| | - Andrea Patrizia Falanga
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy; (F.G.); (A.P.F.); (M.T.); (C.D.); (G.P.); (N.B.)
| | - Monica Terracciano
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy; (F.G.); (A.P.F.); (M.T.); (C.D.); (G.P.); (N.B.)
- Institute of Applied Sciences and Intelligent Systems “Eduardo Caianiello”, Italian National Council of Research (ISASI-CNR), Via Pietro Castellino 111, 80131 Naples, Italy
| | - Carlotta D’Ambrosio
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy; (F.G.); (A.P.F.); (M.T.); (C.D.); (G.P.); (N.B.)
| | - Gennaro Piccialli
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy; (F.G.); (A.P.F.); (M.T.); (C.D.); (G.P.); (N.B.)
- ISBE-IT, University of Naples Federico II, Corso Umberto I, 80138 Naples, Italy;
| | - Giorgia Oliviero
- ISBE-IT, University of Naples Federico II, Corso Umberto I, 80138 Naples, Italy;
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Giovanni Nicola Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Area di Ricerca Site and Headquarters, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy; (F.G.); (A.P.F.); (M.T.); (C.D.); (G.P.); (N.B.)
- Institute of Applied Sciences and Intelligent Systems “Eduardo Caianiello”, Italian National Council of Research (ISASI-CNR), Via Pietro Castellino 111, 80131 Naples, Italy
- ISBE-IT, University of Naples Federico II, Corso Umberto I, 80138 Naples, Italy;
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Scognamiglio PL, Vicidomini C, Fontanella F, De Stefano C, Palumbo R, Roviello GN. Protein Binding of Benzofuran Derivatives: A CD Spectroscopic and In Silico Comparative Study of the Effects of 4-Nitrophenyl Functionalized Benzofurans and Benzodifurans on BSA Protein Structure. Biomolecules 2022; 12:biom12020262. [PMID: 35204762 PMCID: PMC8961527 DOI: 10.3390/biom12020262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 02/06/2023] Open
Abstract
Benzofuran derivatives are synthetic compounds that are finding an increasing interest in the scientific community not only as building blocks for the realization of new materials, but also as potential drugs thanks to their ability to interact with nucleic acids, interfere with the amyloid peptide aggregation and cancer cell cycle. However, their ability to interact with proteins is a theme still in need of investigation for the therapeutic importance that benzofurans could have in the modulation of protein-driven processes and for the possibility of making use of serum albumins as benzofurans delivery systems. To this scope, we investigated the protein binding ability of two 4-nitrophenyl-functionalized benzofurans previously synthesized in our laboratory and herein indicated as BF1 and BDF1, which differed for the number of furan rings (a single moiety in BF1, two in BDF1), using bovine serum albumin (BSA) as a model protein. By circular dichroism (CD) spectroscopy we demonstrated the ability of the two heteroaromatic compounds to alter the secondary structure of the serum albumin leading to different consequences in terms of BSA thermal stability with respect to the unbound protein (ΔTm > 3 °C for BF1, −0.8 °C for BDF1 with respect to unbound BSA, in PBS buffer, pH 7.5) as revealed in our CD melting studies. Moreover, a molecular docking study allowed us to compare the possible ligand binding modes of the mono and difuranic derivatives showing that while BF1 is preferentially housed in the interior of protein structure, BDF1 is predicted to bind the albumin surface with a lower affinity than BF1. Interestingly, the different affinity for the protein target predicted computationally was confirmed also experimentally by fluorescence spectroscopy (kD = 142.4 ± 64.6 nM for BDF1 vs. 28.4 ± 10.1 nM for BF1). Overall, the above findings suggest the ability of benzofurans to bind serum albumins that could act as their carriers in drug delivery applications.
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Affiliation(s)
| | - Caterina Vicidomini
- Istituto di Biostrutture e Bioimmagini IBB-CNR, via Tommaso De Amicis 95, I-80145 Naples, Italy; (C.V.); (R.P.)
| | - Francesco Fontanella
- Department of Electrical and Information Engineering (DIEI), University of Cassino and Southern Lazio, 03043 Cassino (FR), Italy; (F.F.); (C.D.S.)
| | - Claudio De Stefano
- Department of Electrical and Information Engineering (DIEI), University of Cassino and Southern Lazio, 03043 Cassino (FR), Italy; (F.F.); (C.D.S.)
| | - Rosanna Palumbo
- Istituto di Biostrutture e Bioimmagini IBB-CNR, via Tommaso De Amicis 95, I-80145 Naples, Italy; (C.V.); (R.P.)
| | - Giovanni N. Roviello
- Istituto di Biostrutture e Bioimmagini IBB-CNR, via Tommaso De Amicis 95, I-80145 Naples, Italy; (C.V.); (R.P.)
- Correspondence: ; Tel.: +39-3491928417
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Smirnov I, Kolganova N, Troisi R, Sica F, Timofeev E. Expanding the recognition interface of the thrombin-binding aptamer HD1 through modification of residues T3 and T12. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:863-871. [PMID: 33614235 PMCID: PMC7868722 DOI: 10.1016/j.omtn.2021.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/08/2021] [Indexed: 01/11/2023]
Abstract
Post-SELEX modification of DNA aptamers is an established strategy to improve their affinity or inhibitory characteristics. In this study, we examined the possibility of increasing the recognition interface between the thrombin-binding aptamer HD1 (TBA) and thrombin by adding a chemically modified side chain to selected nucleotide residues. A panel of 22 TBA variants with N3-modified residues T3 and T12 was prepared by a two-step modification procedure. Aptamers were characterized by a combination of biophysical and biochemical methods. We identified mutants with enhanced affinity and improved anticoagulant activity. The crystal structures of thrombin complexes with three selected modified variants revealed that the modified pyrimidine base invariably allocates in proximity to thrombin residues Tyr76 and Ile82 due to the directing role of the unmodified TT loop. The modifications induced an increase in the contact areas between thrombin and the modified TBAs. Comparative analysis of the structural, biochemical, and biophysical data suggests that the non-equivalent binding modes of the mutants with thrombin in the T3- and T12-modified series account for the observed systematic differences in their affinity characteristics. In this study, we show that extending the recognition surface between the protein and modified aptamers is a promising approach that may improve characteristics of aptamer ligands.
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Affiliation(s)
- Igor Smirnov
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | - Natalia Kolganova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Edward Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Bao HL, Ishizuka T, Yamashita A, Furukoji E, Asada Y, Xu Y. Improving Thermodynamic Stability and Anticoagulant Activity of a Thrombin Binding Aptamer by Incorporation of 8-trifluoromethyl-2'-deoxyguanosine. J Med Chem 2020; 64:711-718. [PMID: 33289557 DOI: 10.1021/acs.jmedchem.0c01711] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In this study, we incorporated 8-trifluoromethyl-2'-deoxyguanosine (FG) into a thrombin binding aptamer (TBA). Circular dichroism, nuclear magnetic resonance (NMR), electrophoresis, and prothrombin time (PT) assay were performed to investigate the structure, thermodynamic stability, biological stability, and anticoagulant activity of the FG-modified TBA sequences. We found that the replacement of FG into TBA sequences led to a remarkable improvement in the melting temperature up to 30 °C compared with the native sequence. The trifluoromethyl group allowed us to investigate the TBA G-quadruplex structure by 19F NMR spectroscopy. Furthermore, PT assays showed that the modified sequences can significantly improve the anticoagulant activity in comparison with the native TBA. Finally, we demonstrated that the trifluoromethyl-modified TBA sequence could function as an anticoagulant reagent in live rats. Our results strongly suggested that FG is a powerful nucleoside derivative to increase the thermodynamic stability and anticoagulant activity of TBA.
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Affiliation(s)
- Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Atsushi Yamashita
- Department of Pathology, Division of Pathophysiology, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Eiji Furukoji
- Department of Radiology, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yujiro Asada
- Department of Pathology, Division of Pathophysiology, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
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6
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Imperatore C, Varriale A, Rivieccio E, Pennacchio A, Staiano M, D’Auria S, Casertano M, Altucci C, Valadan M, Singh M, Menna M, Varra M. Spectroscopic Properties of Two 5'-(4-Dimethylamino)Azobenzene Conjugated G-Quadruplex Forming Oligonucleotides. Int J Mol Sci 2020; 21:ijms21197103. [PMID: 32993097 PMCID: PMC7582650 DOI: 10.3390/ijms21197103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/10/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
The synthesis of two 5′-end (4-dimethylamino)azobenzene conjugated G-quadruplex forming aptamers, the thrombin binding aptamer (TBA) and the HIV-1 integrase aptamer (T30695), was performed. Their structural behavior was investigated by means of UV, CD, fluorescence spectroscopy, and gel electrophoresis techniques in K+-containing buffers and water-ethanol blends. Particularly, we observed that the presence of the 5′-(4-dimethylamino)azobenzene moiety leads TBA to form multimers instead of the typical monomolecular chair-like G-quadruplex and almost hampers T30695 G-quadruplex monomers to dimerize. Fluorescence studies evidenced that both the conjugated G-quadruplexes possess unique fluorescence features when excited at wavelengths corresponding to the UV absorption of the conjugated moiety. Furthermore, a preliminary investigation of the trans-cis conversion of the dye incorporated at the 5′-end of TBA and T30695 showed that, unlike the free dye, in K+-containing water-ethanol-triethylamine blend the trans-to-cis conversion was almost undetectable by means of a standard UV spectrophotometer.
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Affiliation(s)
- Concetta Imperatore
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Antonio Varriale
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Elisa Rivieccio
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Angela Pennacchio
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Maria Staiano
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Sabato D’Auria
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Marcello Casertano
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Carlo Altucci
- Department of Physics “Ettore Pancini”, University of Naples Federico II, Via Cinthia, 21—Building 6, 80126 Naples, Italy; (C.A.); (M.V.); (M.S.)
| | - Mohammadhassan Valadan
- Department of Physics “Ettore Pancini”, University of Naples Federico II, Via Cinthia, 21—Building 6, 80126 Naples, Italy; (C.A.); (M.V.); (M.S.)
| | - Manjot Singh
- Department of Physics “Ettore Pancini”, University of Naples Federico II, Via Cinthia, 21—Building 6, 80126 Naples, Italy; (C.A.); (M.V.); (M.S.)
| | - Marialuisa Menna
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Michela Varra
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
- Correspondence: ; Tel.: +39-081-678540
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7
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Riccardi C, Napolitano E, Platella C, Musumeci D, Montesarchio D. G-quadruplex-based aptamers targeting human thrombin: Discovery, chemical modifications and antithrombotic effects. Pharmacol Ther 2020; 217:107649. [PMID: 32777331 DOI: 10.1016/j.pharmthera.2020.107649] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
First studies on thrombin-inhibiting DNA aptamers were reported in 1992, and since then a large number of anticoagulant aptamers has been discovered. TBA - also named HD1, a 15-mer G-quadruplex (G4)-forming oligonucleotide - is the best characterized thrombin binding aptamer, able to specifically recognize the protein exosite I, thus inhibiting the conversion of soluble fibrinogen into insoluble fibrin strands. Unmodified nucleic acid-based aptamers, in general, and TBA in particular, exhibit limited pharmacokinetic properties and are rapidly degraded in vivo by nucleases. In order to improve the biological performance of aptamers, a widely investigated strategy is the introduction of chemical modifications in their backbone at the level of the nucleobases, sugar moieties or phosphodiester linkages. Besides TBA, also other thrombin binding aptamers, able to adopt a well-defined G4 structure, e.g. mixed duplex/quadruplex sequences, as well as homo- and hetero-bivalent constructs, have been identified and optimized. Considering the growing need of new efficient anticoagulant agents associated with the strong therapeutic potential of these thrombin inhibitors, the research on thrombin binding aptamers is still a very hot and intriguing field. Herein, we comprehensively described the state-of-the-art knowledge on the DNA-based aptamers targeting thrombin, especially focusing on the optimized analogues obtained by chemically modifying the oligonucleotide backbone, and their biological performances in therapeutic applications.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Department of Advanced Medical and Surgical Sciences, 2(nd) 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.
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; 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.
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Porous Silicon-Based Aptasensors: The Next Generation of Label-Free Devices for Health Monitoring. Molecules 2019; 24:molecules24122216. [PMID: 31200538 PMCID: PMC6630495 DOI: 10.3390/molecules24122216] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/04/2019] [Accepted: 06/12/2019] [Indexed: 12/12/2022] Open
Abstract
Aptamers are artificial nucleic acid ligands identified and obtained from combinatorial libraries of synthetic nucleic acids through the in vitro process SELEX (systematic evolution of ligands by exponential enrichment). Aptamers are able to bind an ample range of non-nucleic acid targets with great specificity and affinity. Devices based on aptamers as bio-recognition elements open up a new generation of biosensors called aptasensors. This review focuses on some recent achievements in the design of advanced label-free optical aptasensors using porous silicon (PSi) as a transducer surface for the detection of pathogenic microorganisms and diagnostic molecules with high sensitivity, reliability and low limit of detection (LoD).
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9
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Chai Z, Guo L, Jin H, Li Y, Du S, Shi Y, Wang C, Shi W, He J. TBA loop mapping with 3'-inverted-deoxythymidine for fine-tuning of the binding affinity for α-thrombin. Org Biomol Chem 2019; 17:2403-2412. [PMID: 30735210 DOI: 10.1039/c9ob00053d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
TBA is a 15-mer DNA aptamer for human α-thrombin, and its three T-rich loops are involved in the binding interactions with thrombin differently. In order to clarify their specific spatial locations in the binding interactions and search for more favourable positions, here a systematic investigation of all the loop residues was conducted with 3'-inverted thymidine (iT), by which both unnatural 3'-3'- and 5'-5'-linkages for each incorporation were introduced in the tertiary structure. The changes in Tm values and CD spectra revealed that motifs T3T12 and T4T13 are structurally distinct. Longer anti-clotting time was obtained for the T3 and T12 modifications, respectively, while T4 and T13 were completely intolerant with such changes, in terms of stability and binding to thrombin. In particular, the increased affinity bindings and longer anti-clotting time were obtained with the replacement on the central loop T7G8T9, which were closely related to the existence of a monovalent ion, K+ or Na+, consistently with the supposed binding site of these ions in TBA. It is worthwhile to note that both the subtle variations of the loop residues induced by iT and the monovalent ions determined the interacting residues of TBA and the binding strength rather than the thermal stability of the TBA structure.
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Affiliation(s)
- Zhilong Chai
- School of Pharmaceutical Sciences, Guizhou University, Guizhou 550025, China
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10
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Marzano M, Falanga AP, D'Errico S, Pinto B, Roviello GN, Piccialli G, Oliviero G, Borbone N. New G-Quadruplex-Forming Oligodeoxynucleotides Incorporating a Bifunctional Double-Ended Linker (DEL): Effects of DEL Size and ODNs Orientation on the Topology, Stability, and Molecularity of DEL-G-Quadruplexes. Molecules 2019; 24:molecules24030654. [PMID: 30759875 PMCID: PMC6384581 DOI: 10.3390/molecules24030654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 01/13/2023] Open
Abstract
G-quadruplexes (G4s) are unusual secondary structures of DNA occurring in guanosine-rich oligodeoxynucleotide (ODN) strands that are extensively studied for their relevance to the biological processes in which they are involved. In this study, we report the synthesis of a new kind of G4-forming molecule named double-ended-linker ODN (DEL-ODN), in which two TG₄T strands are attached to the two ends of symmetric, non-nucleotide linkers. Four DEL-ODNs differing for the incorporation of either a short or long linker and the directionality of the TG₄T strands were synthesized, and their ability to form G4 structures and/or multimeric species was investigated by PAGE, HPLC⁻size-exclusion chromatography (HPLC⁻SEC), circular dichroism (CD), and NMR studies in comparison with the previously reported monomeric tetra-ended-linker (TEL) analogues and with the corresponding tetramolecular species (TG₄T)₄. The structural characterization of DEL-ODNs confirmed the formation of stable, bimolecular DEL-G4s for all DEL-ODNs, as well as of additional DEL-G4 multimers with higher molecular weights, thus suggesting a way towards the obtainment of thermally stable DNA nanostructures based on reticulated DEL-G4s.
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Affiliation(s)
- Maria Marzano
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Andrea Patrizia Falanga
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Brunella Pinto
- Dipartimento di Chimica, Università degli Studi di Milano, via Camillo Golgi 19, 20133 Milano, Italy.
| | | | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Giorgia Oliviero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, via Sergio Pansini 5, 80131 Napoli, Italy.
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
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11
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Mo M, Kong D, Ji H, Lin D, Tang X, Yang Z, He Y, Wu L. Reversible Photocontrol of Thrombin Activity by Replacing Loops of Thrombin Binding Aptamer using Azobenzene Derivatives. Bioconjug Chem 2019; 30:231-241. [PMID: 30582682 DOI: 10.1021/acs.bioconjchem.8b00848] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The photoisomerization of azobenzenes provides a general means for the photocontrol of many important biomolecular structures and organismal functions. For temporal and spatial control activity of thrombin binding aptamer (TBA) by light, azobenzene derivatives were carefully selected as light-triggered molecular switches to replace TT loops and the TGT loop of TBA to reversibly control enzyme activity. These molecules interconverted between the trans and cis states under alternate UV and visible light irradiation, which consequently triggered reversible formation of G-quadruplex morphology. In addition, we investigated the impact of three azobenzene derivatives on stability, thrombin binding ability, and anticoagulant properties. The result showed that 4,4'-bis(hydroxymethyl)azobenzene at the TGT loop position significantly photoregulated affinity to thrombin and blood clotting in human plasma, which provided a successful strategy to control blood clotting in human plasma and a further evidence for design of TBA analogues with pivotal positions of modifications.
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Affiliation(s)
- Mengwu Mo
- School of Chemical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Dejia Kong
- School of Chemical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Heming Ji
- School of Chemical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Dao Lin
- School of Chemical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| | - Yujian He
- School of Chemical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Li Wu
- School of Chemical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
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12
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Rivieccio E, Tartaglione L, Esposito V, Dell'Aversano C, Koneru PC, Scuotto M, Virgilio A, Mayol L, Kvaratskhelia M, Varra M. Structural studies and biological evaluation of T30695 variants modified with single chiral glycerol-T reveal the importance of LEDGF/p75 for the aptamer anti-HIV-integrase activities. Biochim Biophys Acta Gen Subj 2018; 1863:351-361. [PMID: 30414444 DOI: 10.1016/j.bbagen.2018.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 10/18/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022]
Abstract
Some G-quadruplex (GQ) forming aptamers, such as T30695, exhibit particularly promising properties among the potential anti-HIV drugs. T30695 G-quadruplex binds to HIV-1 integrase (IN) and inhibits its activity during 3'-end processing at nanomolar concentrations. Herein we report a study concerning six T30695-GQ variants, in which the R or S chiral glycerol T, singly replaced the thymine residues at the T30695 G-quadruplex loops. CD melting, EMSA and HMRS experiments provided information about the thermal stability and the stoichiometry of T30695-GQ variants, whereas CD and 1H NMR studies were performed to evaluate the effects of the modifications on T30695-GQ topology. Furthermore, LEDGF/p75 dependent and independent integration assays were carried out to evaluate how T loop modifications impact T30695-GQ biological activities. The obtained results showed that LEDGF/p75 adversely affects the potencies of T30695 and its variants. The IN inhibitory activities of the modified aptamers also depended on the position and on the chirality (R or S) of glycerol T loop in the GQ, mostly regardless of the G-quadruplex stabilities. In view of our and literature data, we suggest that the allosteric modulation of IN tetramer conformations by LEDGF/p75 alters the interactions between the aptamers and the enzyme. Therefore, the new T30695 variants could be suitable tools in studies aimed to clarify the HIV-1 IN tetramers allostery and its role in the integration activity.
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Affiliation(s)
- Elisa Rivieccio
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Luciana Tartaglione
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Veronica Esposito
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Carmela Dell'Aversano
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - P C Koneru
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 500 West 12th Ave., Columbus, OH 43210, USA; Division of Infectious Diseases, University of Colorado School of Medicine, 12700 E. 19th Avenue, Aurora, CO 80045, USA
| | - Maria Scuotto
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Antonella Virgilio
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Luciano Mayol
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 500 West 12th Ave., Columbus, OH 43210, USA; Division of Infectious Diseases, University of Colorado School of Medicine, 12700 E. 19th Avenue, Aurora, CO 80045, USA.
| | - Michela Varra
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Naples, Italy.
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13
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Dolot R, Lam CH, Sierant M, Zhao Q, Liu FW, Nawrot B, Egli M, Yang X. Crystal structures of thrombin in complex with chemically modified thrombin DNA aptamers reveal the origins of enhanced affinity. Nucleic Acids Res 2018; 46:4819-4830. [PMID: 29684204 PMCID: PMC5961234 DOI: 10.1093/nar/gky268] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/26/2018] [Accepted: 04/15/2018] [Indexed: 01/11/2023] Open
Abstract
Thrombin-binding aptamer (TBA) is a DNA 15-mer of sequence 5'-GGT TGG TGT GGT TGG-3' that folds into a G-quadruplex structure linked by two T-T loops located on one side and a T-G-T loop on the other. These loops are critical for post-SELEX modification to improve TBA target affinity. With this goal in mind we synthesized a T analog, 5-(indolyl-3-acetyl-3-amino-1-propenyl)-2'-deoxyuridine (W) to substitute one T or a pair of Ts. Subsequently, the affinity for each analog was determined by biolayer interferometry. An aptamer with W at position 4 exhibited about 3-fold increased binding affinity, and replacing both T4 and T12 with W afforded an almost 10-fold enhancement compared to native TBA. To better understand the role of the substituent's aromatic moiety, an aptamer with 5-(methyl-3-acetyl-3-amino-1-propenyl)-2'-deoxyuridine (K; W without the indole moiety) in place of T4 was also synthesized. This K4 aptamer was found to improve affinity 7-fold relative to native TBA. Crystal structures of aptamers with T4 replaced by either W or K bound to thrombin provide insight into the origins of the increased affinities. Our work demonstrates that facile chemical modification of a simple DNA aptamer can be used to significantly improve its binding affinity for a well-established pharmacological target protein.
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Affiliation(s)
- Rafal Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90–363 Lodz, Sienkiewicza 112, Poland
| | - Curtis H Lam
- AM Biotechnologies, LLC, 12521 Gulf Freeway, Houston, TX 77034, USA
| | - Malgorzata Sierant
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90–363 Lodz, Sienkiewicza 112, Poland
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Feng-Wu Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou 450001, Henan, China
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90–363 Lodz, Sienkiewicza 112, Poland
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Xianbin Yang
- AM Biotechnologies, LLC, 12521 Gulf Freeway, Houston, TX 77034, USA
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14
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Awachat R, Wagh AA, Aher M, Fernandes M, Kumar VA. Favorable 2'-substitution in the loop region of a thrombin-binding DNA aptamer. Bioorg Med Chem Lett 2018; 28:1765-1768. [PMID: 29678465 DOI: 10.1016/j.bmcl.2018.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/06/2018] [Accepted: 04/11/2018] [Indexed: 11/19/2022]
Abstract
Simple 2'-OMe-chemical modification in the loop region of the 15mer G-rich DNA sequence GGTTGGTGTGGTTGG is reported. The G-quadruplex structure of this thrombin-binding aptamer (TBA), is stabilized by single modifications (T → 2'-OMe-U), depending on the position of the modification. The structural stability also renders significantly increased inhibition of thrombin-induced fibrin polymerization, a process closely associated with blood-clotting.
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Affiliation(s)
- Ragini Awachat
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Homi Bhabha Road, Pashan, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-NCL Campus, Pune 411008, India
| | - Atish A Wagh
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Homi Bhabha Road, Pashan, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-NCL Campus, Pune 411008, India
| | - Manisha Aher
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Homi Bhabha Road, Pashan, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-NCL Campus, Pune 411008, India
| | - Moneesha Fernandes
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Homi Bhabha Road, Pashan, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-NCL Campus, Pune 411008, India.
| | - Vaijayanti A Kumar
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Homi Bhabha Road, Pashan, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-NCL Campus, Pune 411008, India.
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15
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Virgilio A, Amato T, Petraccone L, Filosa R, Varra M, Mayol L, Esposito V, Galeone A. Improved thrombin binding aptamer analogues containing inversion of polarity sites: structural effects of extra-residues at the ends. Org Biomol Chem 2018; 14:7707-14. [PMID: 27461474 DOI: 10.1039/c6ob00931j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In this paper, we report the investigations, based on NMR, molecular modelling, CD measurements and electrophoresis, of thrombin binding aptamer (TBA) analogues containing an extra-residue at the 3'-end or at both the ends of the original TBA sequence, linked through 3'-3' or 5'-5' phosphodiester bonds. The data indicate that most of the modified aptamers investigated adopt chair-like G-quadruplex structures very similar to that of the TBA and that stacking interactions occur between the 3'-3' or 5'-5' extra residues and the deoxyguanosines of the upper G-tetrad. A comparison of the thermodynamic data of TBA-A and TBA-T containing a 3'-3' extra residue and their canonical versions clearly indicates that the 3'-3' phosphodiester bond is fundamental in endowing the modified aptamers with remarkably higher thermal stabilities than the original TBA.
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Affiliation(s)
- A Virgilio
- Department of Pharmacy, University of Naples Federico II, via D. Montesano, 49, 80131 Naples, Italy.
| | - T Amato
- Department of Pharmacy, University of Naples Federico II, via D. Montesano, 49, 80131 Naples, Italy.
| | - L Petraccone
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, I-80126 Naples, Italy
| | - R Filosa
- Department of Experimental Medicine, Second University of Naples, via Costantinopoli 16, 80138 Naples, Italy
| | - M Varra
- Department of Pharmacy, University of Naples Federico II, via D. Montesano, 49, 80131 Naples, Italy.
| | - L Mayol
- Department of Pharmacy, University of Naples Federico II, via D. Montesano, 49, 80131 Naples, Italy.
| | - V Esposito
- Department of Pharmacy, University of Naples Federico II, via D. Montesano, 49, 80131 Naples, Italy.
| | - A Galeone
- Department of Pharmacy, University of Naples Federico II, via D. Montesano, 49, 80131 Naples, Italy.
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16
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The "Janus face" of the thrombin binding aptamer: Investigating the anticoagulant and antiproliferative properties through straightforward chemical modifications. Bioorg Chem 2017; 76:202-209. [PMID: 29190476 DOI: 10.1016/j.bioorg.2017.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/31/2017] [Accepted: 11/15/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND The thrombin binding aptamer (TBA) is endowed with both anticoagulant and antiproliferative activities. Its chemico-physical and/or biological properties can be tuned by the site-specific replacement of selected residues. METHODS Four oligodeoxynucleotides (ODNs) based on the TBA sequence (5'-GGTTGGTGTGGTTGG-3') and containing 2'-deoxyuridine (U) or 5-bromo-2'-deoxyuridine (B) residues at positions 4 or 13 have been investigated by NMR and CD techniques. Furthermore, their anticoagulant (PT assay) and antiproliferative properties (MTT assay) have been tested and compared with two further ODNs containing 5-hydroxymethyl-2'-deoxyuridine (H) residues in the same positions, previously investigated. RESULTS The CD and NMR data suggest that all the investigated ODNs are able to form G-quadruplexes strictly resembling that of TBA. The introduction of B residues in positions 4 or 13 increases the melting temperature of the modified aptamers by 7 °C. The replacement of thymidines with U in the same positions results in an enhanced anticoagulant activity compared to TBA, also at low ODN concentration. Although all ODNs show antiproliferative properties, only TBA derivatives containing H in the positions 4 and 13 lose the anticoagulant activity and remarkably preserve the antiproliferative one. CONCLUSIONS All ODNs have shown antiproliferative activities against two cancer cell lines but only those with U and B are endowed with anticoagulant activities similar or improved compared to TBA. GENERAL SIGNIFICANCE The appropriate site-specific replacement of the residues in the TT loops of TBA with commercially available thymine analogues is a useful strategy either to improve the anticoagulant activity or to preserve the antiproliferative properties by quenching the anticoagulant ones.
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17
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Sagi J. In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids? J Nucleic Acids 2017; 2017:1641845. [PMID: 29181193 PMCID: PMC5664352 DOI: 10.1155/2017/1641845] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/15/2017] [Indexed: 01/03/2023] Open
Abstract
Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.
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Affiliation(s)
- Janos Sagi
- Rimstone Laboratory, RLI, Carlsbad, CA 92010, USA
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18
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Fan X, Sun L, Li K, Yang X, Cai B, Zhang Y, Zhu Y, Ma Y, Guan Z, Wu Y, Zhang L, Yang Z. The Bioactivity of D-/L-Isonucleoside- and 2'-Deoxyinosine-Incorporated Aptamer AS1411s Including DNA Replication/MicroRNA Expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 9:218-229. [PMID: 29246300 PMCID: PMC5651494 DOI: 10.1016/j.omtn.2017.09.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/28/2017] [Accepted: 09/28/2017] [Indexed: 12/20/2022]
Abstract
In this study, chemical modification of 2'-deoxyinosine (2'-dI) and D-/L-isothymidine (D-/L-isoT) was performed on AS1411. They could promote the nucleotide-protein interaction by changing the local conformation. Twenty modified sequences were obtained, FCL-I and FCL-II showed the most noticeable activity improvement. They stabilized the G-quadruplex, remained highly resistant to serum degradation and specificity for nucleolin, further inhibited tumor cell growth, exhibited a stronger ability to influence the different phases of the tumor cell cycle, induced S-phase arrest, promoted the inhibition of DNA replication, and suppressed the unwound function of a large T antigen as powerful as AS1411. The microarray analysis and TaqMan PCR results showed that FCL-II can upregulate the expression of four breast-cancer-related, lowly expressed miRNAs and downregulate the expression of three breast-cancer-related, highly expressed miRNAs (>2.5-fold). FCL-II resulted in enhanced treatment effects greater than AS1411 in animal experiments (p < 0.01). The computational results further proved that FCL-II exhibits more structural advantages than AS1411 for binding to the target protein nucleolin, indicating its great potential in antitumor therapy.
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Affiliation(s)
- Xinmeng Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Lidan Sun
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University Medical College, Yichang 443002, PR China
| | - Kunfeng Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Xiantao Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Baobin Cai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Yanfen Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Yuejie Zhu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Yuan Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Zhu Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Yun Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China.
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Feng M, Ruan Z, Shang J, Xiao L, Tong A, Xiang Y. Photocaged G-Quadruplex DNAzyme and Aptamer by Post-Synthetic Modification on Phosphodiester Backbone. Bioconjug Chem 2016; 28:549-555. [PMID: 27931100 DOI: 10.1021/acs.bioconjchem.6b00646] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
G-quadruplex-containing DNAzymes and aptamers are widely applied in many research fields because of their high stability and prominent activities versus the protein counterparts. In this work, G-quadruplex DNAs were equipped with photolabile groups to construct photocaged DNAzymes and aptamers. We incorporated TEEP-OH (thioether-enol phosphate, phenol substituted) into phosphodiester backbone of G-quadruplex DNA by a facile post-synthetic method to achieve efficient photocaging of their activities. Upon light irradiation, the peroxidase-mimicking activity of the caged G-quadruplex DNAzyme was activated, through the transformation of TEEP-OH into a native DNA phosphodiester without any artificial scar. Similarly, the caged G-quadruplex thrombin-binding aptamer also showed light-induced activation of thrombin inhibition activity. This method could serve as a general strategy to prepare photocaged G-quadruplex DNA with other activities for noninvasive control of their functions.
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Affiliation(s)
- Mengli Feng
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University , Beijing 100084, China
| | - Zhiyuan Ruan
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University , Beijing 100084, China
| | - Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University , Beijing 100084, China
| | - Lu Xiao
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University , Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University , Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University , Beijing 100084, China
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20
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Fan X, Sun L, Wu Y, Zhang L, Yang Z. Bioactivity of 2'-deoxyinosine-incorporated aptamer AS1411. Sci Rep 2016; 6:25799. [PMID: 27194215 PMCID: PMC4872150 DOI: 10.1038/srep25799] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/18/2016] [Indexed: 11/09/2022] Open
Abstract
Aptamers can be chemically modified to enhance nuclease resistance and increase target affinity. In this study, we performed chemical modification of 2'-deoxyinosine in AS1411, an anti-proliferative G-rich oligodeoxynucleotide aptamer, which binds selectively to the nucleolin protein. Its function was augmented when 2'-deoxyinosine was incorporated at positions 12, 13, 15, and 24 of AS1411, respectively. In addition, double incorporation of 2'-deoxyinosine at positions 12 and 24 (FAN-1224dI), 13 and 24 (FAN-1324dI), and 15 and 24 (FAN-1524dI) promoted G-quartet formation, as well as inhibition of DNA replication and tumor cell growth, and induced S-phase cell cycle arrest. In further animal experiments, FAN-1224dI, FAN-1324dI and FAN-1524dI resulted in enhanced treatment effects than AS1411 alone. These results suggested that the position and number of modification substituents in AS1411 are critical parameters to improve the diagnostic and therapeutic function of the aptamer. Structural investigations of the FAN-1524dI/nucleolin complex structure, using molecular dynamics simulation, revealed the critical interactions involving nucleolin and 2'-dI incorporated AS1411 compared with AS1411 alone. These findings augment understanding of the role of 2'-deoxyinosine moieties in interactive binding processes.
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Affiliation(s)
- Xinmeng Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Lidan Sun
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University Medical College, Yichang, 443002 China
| | - Yun Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
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21
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Gouda AS, Amine MS, Pedersen EB. Synthesis of New DNA G-Quadruplex Constructs with Anthraquinone Insertions and Their Anticoagulant Activity. Helv Chim Acta 2016. [DOI: 10.1002/hlca.201500207] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Torabi R, Bagherzadeh K, Ghourchian H, Amanlou M. An investigation on the interaction modes of a single-strand DNA aptamer and RBP4 protein: a molecular dynamic simulations approach. Org Biomol Chem 2016; 14:8141-53. [DOI: 10.1039/c6ob01094f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Monitoring and evaluating structural and functional alternations in RBP4 induced by its specific aptamer binding to design new aptamers for diagnostic and therapeutic purposes with reduced insulin resistance.
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Affiliation(s)
- Raheleh Torabi
- Laboratory of Microanalysis
- Institute of Biochemistry & Biophysics
- University of Tehran
- Tehran
- Iran
| | - Kowsar Bagherzadeh
- Razi Drug Research Center
- Iran University of Medical Sciences
- Tehran
- Iran
- Department of Medicinal Chemistry
| | - Hedayatollah Ghourchian
- Laboratory of Microanalysis
- Institute of Biochemistry & Biophysics
- University of Tehran
- Tehran
- Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry
- Faculty of Pharmacy and Drug Design and Development Research Center
- Tehran University of Medical Sciences
- Tehran
- Iran
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23
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Terracciano M, De Stefano L, Borbone N, Politi J, Oliviero G, Nici F, Casalino M, Piccialli G, Dardano P, Varra M, Rea I. Solid phase synthesis of a thrombin binding aptamer on macroporous silica for label free optical quantification of thrombin. RSC Adv 2016. [DOI: 10.1039/c6ra18401d] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Human α-thrombin (TB) is a serine protease with a crucial role in coagulation and hemostasis.
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Affiliation(s)
- Monica Terracciano
- Institute for Microelectronics and Microsystems
- National Council of Research
- Naples
- Italy
| | - Luca De Stefano
- Institute for Microelectronics and Microsystems
- National Council of Research
- Naples
- Italy
| | - Nicola Borbone
- Department of Pharmacy
- University of Naples Federico II
- Naples
- Italy
| | - Jane Politi
- Institute for Microelectronics and Microsystems
- National Council of Research
- Naples
- Italy
| | - Giorgia Oliviero
- Department of Pharmacy
- University of Naples Federico II
- Naples
- Italy
| | - Fabrizia Nici
- Department of Pharmacy
- University of Naples Federico II
- Naples
- Italy
| | - Maurizio Casalino
- Institute for Microelectronics and Microsystems
- National Council of Research
- Naples
- Italy
| | | | - Principia Dardano
- Institute for Microelectronics and Microsystems
- National Council of Research
- Naples
- Italy
| | - Michela Varra
- Department of Pharmacy
- University of Naples Federico II
- Naples
- Italy
| | - Ilaria Rea
- Institute for Microelectronics and Microsystems
- National Council of Research
- Naples
- Italy
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24
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Virgilio A, Petraccone L, Vellecco V, Bucci M, Varra M, Irace C, Santamaria R, Pepe A, Mayol L, Esposito V, Galeone A. Site-specific replacement of the thymine methyl group by fluorine in thrombin binding aptamer significantly improves structural stability and anticoagulant activity. Nucleic Acids Res 2015; 43:10602-11. [PMID: 26582916 PMCID: PMC4678827 DOI: 10.1093/nar/gkv1224] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/29/2015] [Indexed: 12/20/2022] Open
Abstract
Here we report investigations, based on circular dichroism, nuclear magnetic resonance spectroscopy, molecular modelling, differential scanning calorimetry and prothrombin time assay, on analogues of the thrombin binding aptamer (TBA) in which individual thymidines were replaced by 5-fluoro-2′-deoxyuridine residues. The whole of the data clearly indicate that all derivatives are able to fold in a G-quadruplex structure very similar to the ‘chair-like’ conformation typical of the TBA. However, only ODNs TBA-F4 and TBA-F13 have shown a remarkable improvement both in the melting temperature (ΔTm ≈ +10) and in the anticoagulant activity in comparison with the original TBA. These findings are unusual, particularly considering previously reported studies in which modifications of T4 and T13 residues in TBA sequence have clearly proven to be always detrimental for the structural stability and biological activity of the aptamer. Our results strongly suggest the possibility to enhance TBA properties through tiny straightforward modifications.
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Affiliation(s)
- Antonella Virgilio
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Luigi Petraccone
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II,via Cintia, I-80126 Napoli, Italy
| | - Valentina Vellecco
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Mariarosaria Bucci
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Michela Varra
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Carlo Irace
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Rita Santamaria
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Antonietta Pepe
- Dipartimento di Scienze, Università degli Studi della Basilicata, Viale dell'Ateneo Lucano 10, I-85100 Potenza, Italy
| | - Luciano Mayol
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Veronica Esposito
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Aldo Galeone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
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25
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Scuotto M, Rivieccio E, Varone A, Corda D, Bucci M, Vellecco V, Cirino G, Virgilio A, Esposito V, Galeone A, Borbone N, Varra M, Mayol L. Site specific replacements of a single loop nucleoside with a dibenzyl linker may switch the activity of TBA from anticoagulant to antiproliferative. Nucleic Acids Res 2015; 43:7702-16. [PMID: 26250112 PMCID: PMC4652776 DOI: 10.1093/nar/gkv789] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/23/2015] [Indexed: 12/20/2022] Open
Abstract
Many antiproliferative G-quadruplexes (G4s) arise from the folding of GT-rich strands. Among these, the Thrombin Binding Aptamer (TBA), as a rare example, adopts a monomolecular well-defined G4 structure. Nevertheless, the potential anticancer properties of TBA are severely hampered by its anticoagulant action and, consequently, no related studies have appeared so far in the literature. We wish to report here that suitable chemical modifications in the TBA sequence can preserve its antiproliferative over anticoagulant activity. Particularly, we replaced one residue of the TT or TGT loops with a dibenzyl linker to develop seven new quadruplex-forming TBA based sequences (TBA-bs), which were studied for their structural (CD, CD melting, 1D NMR) and biological (fibrinogen, PT and MTT assays) properties. The three-dimensional structures of the TBA-bs modified at T13 (TBA-bs13) or T12 (TBA-bs12), the former endowed with selective antiproliferative activity, and the latter acting as potently as TBA in both coagulation and MTT assays, were further studied by 2D NMR restrained molecular mechanics. The comparative structural analyses indicated that neither the stability, nor the topology of the G4s, but the different localization of the two benzene rings of the linker was responsible for the loss of the antithrombin activity for TBA-bs13.
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Affiliation(s)
- Maria Scuotto
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Elisa Rivieccio
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Alessia Varone
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Daniela Corda
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Mariarosaria Bucci
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Valentina Vellecco
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Giuseppe Cirino
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Antonella Virgilio
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Veronica Esposito
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Aldo Galeone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Michela Varra
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Luciano Mayol
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
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26
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Cai B, Yang X, Sun L, Fan X, Li L, Jin H, Wu Y, Guan Z, Zhang L, Zhang L, Yang Z. Stability and bioactivity of thrombin binding aptamers modified with D-/L-isothymidine in the loop regions. Org Biomol Chem 2015; 12:8866-76. [PMID: 25264858 DOI: 10.1039/c4ob01525h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thrombin binding aptamer (TBA) is a 15-mer single-strand DNA that was identified by SELEX screening technology. It adopts a chair-type antiparallel G-quadruplex and can specifically interact with thrombin, thus inhibiting blood coagulation. Isonucleoside (isoNA) is a type of nucleoside isomer in which the base is shifted to 2′-positions of the glycosyl group, endowed with the ability to modulate local conformation of nucleotides, and L-isoNA could alter the conformation more due to the inversion of glycosyl configuration. Incorporation of L-isothymidine (L-isoT) at T3, T9, T12 positions and D-isoT at the T7 position in TBA's loop regions promoted the formation of G-quadruplex, resulting in enhanced affinity with thrombin and an increased anticoagulant effect. Computer simulation indicated that TBA-12L showed the strongest binding with thrombin, which was consistent with experimental results. The bioactivity of double isoNA incorporated TBA with D-IsoT at T7 and L-IsoT at T12 was comparable to that of TBA-12L, suggesting that the T12 of TBA was very important in interaction with thrombin. Our study also suggested that TBA might interact with two thrombin molecules through the TT loops (T3T4, T12T13) and TGT loop, but the second bonding did not show additional biological effects.
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Affiliation(s)
- Baobin Cai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China.
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27
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Kononevich YM, Bobkova LS, Smolski AS, Demchenko AM. Synthesis and Antioxidant Activity of 7-Thio Derivatives of 6,7-Dihydro-1H-cyclopenta[d]pyrimidine-2,4(3H,5H)-dione. Sci Pharm 2015; 83:41-8. [PMID: 26839800 PMCID: PMC4729228 DOI: 10.3797/scipharm.1406-09] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/29/2014] [Indexed: 11/22/2022] Open
Abstract
New 7-thio derivatives of 6,7-dihydro-1H-cyclopenta[d]pyrimidine-2,4(3H,5H)-dione have been synthesized by the reaction of 3-cyclohexyl-7-thio-6,7-dihydro-1H-cyclopenta[d]pyrimidine-2,4(3H,5H)-dione with alkylhalogenides. The synthesized compounds were tested for antioxidant activity on the model of Fe(2+)-dependent oxidation of adrenaline in vitro. It was found that the antiradical activity of 7-thio derivatives of 6,7-dihydro-1H-cyclopenta[d]pyrimidine-2,4(3H,5H)-dione significantly depends on the structure of the substituent which is part of the thioether fragment of the base molecule.
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Affiliation(s)
- Yuriy M Kononevich
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991, Moscow, Russian Federation
| | - Ludmila S Bobkova
- Institute of Pharmacology and Toxicology, National Academy of Medical Science of Ukraine, Ezhena Pot'je str. 14, 03680, Kyiv, Ukraine
| | - Alexander S Smolski
- T. G. Shevchenko Chernihiv National Pedagogical University, Het'mana Polubotka str. 53, 14013, Chernihiv, Ukraine
| | - Anatoly M Demchenko
- Institute of Pharmacology and Toxicology, National Academy of Medical Science of Ukraine, Ezhena Pot'je str. 14, 03680, Kyiv, Ukraine
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