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Ghezzo M, Grigoletto L, Rigo R, Herdewijn P, Groaz E, Sissi C. Modulation of the tetrameric I-motif folding of C-rich Tetrahymena telomeric sequences by hexitol nucleic acid (HNA) modifications. Biochimie 2023; 214:112-122. [PMID: 37558081 DOI: 10.1016/j.biochi.2023.08.003] [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: 04/24/2023] [Revised: 08/01/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
I-motifs are non-canonical DNA structures consisting of two parallel strands held together by hemiprotonated cytosine-cytosine+ base pairs, which intercalate to form a ordered column of stacked base pairs. This unique structure covers potential relevance in various fields, including gene regulation and biotechnological applications. A unique structural feature of I-motifs (iM), is the presence of sugar-sugar interactions through their extremely narrow minor grooves. Consistently, oligonucleotides containing pentose derivatives such as ribose, 2'-deoxyribose, arabinose, and 2'-deoxy-2'-fluoroarabinose highlighted a very different attitude to fold into iM. On the other hand, there is significant attention focused on exploring sugar-modifications that can increase nucleic acids resistance to nuclease degradation, a crucial requirement for therapeutic applications. An interesting example, not addressed in the iM field yet, is represented by hexitol nucleic acid (HNA), a metabolically stable six-membered ring analogue compatible with A-like double helix formation. Herein, we selected two DNA C-rich Tetrahymena telomeric sequences whose tetrameric iMs were already resolved by NMR and we investigated the iM folding of related HNA and RNA oligonucleotides by circular dichroism, differential scanning calorimetry and NMR. The comparison of their behaviours vs the DNA counterparts provided interesting insights into the influence of the sugar on iM folding. In particular, ribose and hexitol prevented iM formation. However, by clustering the hexitol-containing residues at the 3'-end, it was possible to modulate the distribution of the different topological species described for the DNA iMs. These data open new avenues for the exploitation of sugar modifications for I-motif characterization and applications.
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Affiliation(s)
- Michele Ghezzo
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5 35131, Padova, Italy
| | - Luca Grigoletto
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5 35131, Padova, Italy; KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000, Leuven, Belgium
| | - Riccardo Rigo
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5 35131, Padova, Italy
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000, Leuven, Belgium
| | - Elisabetta Groaz
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5 35131, Padova, Italy; KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000, Leuven, Belgium.
| | - Claudia Sissi
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5 35131, Padova, Italy.
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2
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Synthesis and antiviral properties of biomimetic iminosugar-based nucleosides. Eur J Med Chem 2022; 241:114618. [DOI: 10.1016/j.ejmech.2022.114618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/22/2022]
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3
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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4
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De Fenza M, Eremeeva E, Troisi R, Yang H, Esposito A, Sica F, Herdewijn P, D'Alonzo D, Guaragna A. Structure-Activity Relationship Study of a Potent α-Thrombin Binding Aptamer Incorporating Hexitol Nucleotides. Chemistry 2020; 26:9589-9597. [PMID: 32363791 DOI: 10.1002/chem.202001504] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/29/2020] [Indexed: 12/13/2022]
Abstract
The replacement of one or more nucleotide residues in the potent α-thrombin-binding aptamer NU172 with hexitol-based nucleotides has been devised to study the effect of these substitutions on the physicochemical and functional properties of the anticoagulant agent. The incorporation of single hexitol nucleotides at the T9 and G18 positions of NU172 substantially retained the physicochemical features of the parent oligonucleotide, as a result of the biomimetic properties of the hexitol backbone. Importantly, the NU172-TH 9 mutant exhibited a higher binding affinity toward human α-thrombin than the native aptamer and an improved stability even after 24 h in 90 % human serum, with a significant increase in the estimated half-life. The anticoagulant activity of the modified oligonucleotide was also found to be slightly preferable to NU172. Overall, these results confirm the potential of hexitol nucleotides as biomimetic agents, while laying the foundations for the development of NU172-inspired α-thrombin-binding aptamers.
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Affiliation(s)
- Maria De Fenza
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Elena Eremeeva
- Rega Institute for Medical Research, Herestraat 49-box 1041, 3000, Leuven, Belgium
| | - Romualdo Troisi
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Hui Yang
- Rega Institute for Medical Research, Herestraat 49-box 1041, 3000, Leuven, Belgium
| | - Anna Esposito
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Filomena Sica
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Piet Herdewijn
- Rega Institute for Medical Research, Herestraat 49-box 1041, 3000, Leuven, Belgium
| | - Daniele D'Alonzo
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Annalisa Guaragna
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
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5
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Esposito A, di Giovanni C, De Fenza M, Talarico G, Chino M, Palumbo G, Guaragna A, D'Alonzo D. A Stereoconvergent Tsuji-Trost Reaction in the Synthesis of Cyclohexenyl Nucleosides. Chemistry 2020; 26:2597-2601. [PMID: 31860145 DOI: 10.1002/chem.201905367] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/18/2019] [Indexed: 12/14/2022]
Abstract
A highly regio- and stereoselective route to d- and l-cyclohexenyl nucleosides has been devised, using the Tsuji-Trost reaction as the key step. Contrarily to the widely accepted mechanism (involving a net retention of configuration), the reaction proceeded in a highly stereoconvergent manner, providing cis nucleosides regardless of the relative configuration of the starting materials. DFT calculations confirmed the experimental data while suggesting the origin of the stereochemical reaction outcome.
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Affiliation(s)
- Anna Esposito
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Concetta di Giovanni
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Maria De Fenza
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Giovanni Talarico
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Marco Chino
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Giovanni Palumbo
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Annalisa Guaragna
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
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6
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De S, Jabgunde AM, Patil RS, De Jonghe S, Beigelman L, Herdewijn P. Synthesis of Protected Amino Hexitol Nucleosides as Building Blocks for Oligonucleotide Synthesis. J Org Chem 2018; 83:15155-15169. [PMID: 30525618 DOI: 10.1021/acs.joc.8b02444] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new synthesis protocol for the preparation of hitherto unknown 1',5'-anhydro-4'-amino-trityl/MMTr hexitol nucleosides has been developed. Key steps in the synthesis of the pyrimidine analogues (U and C) include the regioselective d- allo-hexitol oxirane and 2',4'-anhydronucleoside ring opening by uracil and azide, respectively. A different strategy using a regioselective epoxide ring opening of d- gulo-oxirane, followed by a SN2 type of azidation reaction, has been adopted for the purine analogues (A and G). These compounds can be easily converted to 6'-phosphoramidites for the solid-phase synthesis of N4' → P6' phosphoramidates of amino hexitol nucleic acids (AHNA).
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Affiliation(s)
- Swarup De
- KU Leuven , Rega Institute for Medical Research, Medicinal Chemistry , Herestraat 49 , Leuven 3000 , Belgium
| | - Amit M Jabgunde
- KU Leuven , Rega Institute for Medical Research, Medicinal Chemistry , Herestraat 49 , Leuven 3000 , Belgium
| | - Rahul S Patil
- KU Leuven , Rega Institute for Medical Research, Medicinal Chemistry , Herestraat 49 , Leuven 3000 , Belgium
| | - Steven De Jonghe
- KU Leuven , Rega Institute for Medical Research, Medicinal Chemistry , Herestraat 49 , Leuven 3000 , Belgium
| | - Leonid Beigelman
- Aligos Therapeutics , 1 Corporate Drive , South San Francisco , California 94080 , United States
| | - Piet Herdewijn
- KU Leuven , Rega Institute for Medical Research, Medicinal Chemistry , Herestraat 49 , Leuven 3000 , Belgium
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7
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D'Alonzo D, De Fenza M, Porto C, Iacono R, Huebecker M, Cobucci-Ponzano B, Priestman DA, Platt F, Parenti G, Moracci M, Palumbo G, Guaragna A. N-Butyl-l-deoxynojirimycin (l-NBDNJ): Synthesis of an Allosteric Enhancer of α-Glucosidase Activity for the Treatment of Pompe Disease. J Med Chem 2017; 60:9462-9469. [PMID: 29112434 DOI: 10.1021/acs.jmedchem.7b00646] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The highly stereocontrolled de novo synthesis of l-NBDNJ (the unnatural enantiomer of the iminosugar drug Miglustat) and a preliminary evaluation of its chaperoning potential are herein reported. l-NBDNJ is able to enhance lysosomal α-glucosidase levels in Pompe disease fibroblasts, either when administered singularly or when coincubated with the recombinant human α-glucosidase. In addition, differently from its d-enantiomer, l-NBDNJ does not act as a glycosidase inhibitor.
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Affiliation(s)
- Daniele D'Alonzo
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II , via Cintia, 80126 Napoli, Italy
| | - Maria De Fenza
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II , via Cintia, 80126 Napoli, Italy
| | - Caterina Porto
- Department of Translational Medical Sciences, Section of Pediatrics, Università degli Studi di Napoli Federico II , Via S. Pansini 5, 80131 Napoli, Italy
| | - Roberta Iacono
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche , Via P. Castellino 111, 80131 Napoli, Italy
| | - Mylene Huebecker
- Department of Pharmacology, University of Oxford , Mansfield Road, Oxford OX1 3QT, U.K
| | - Beatrice Cobucci-Ponzano
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche , Via P. Castellino 111, 80131 Napoli, Italy
| | - David A Priestman
- Department of Pharmacology, University of Oxford , Mansfield Road, Oxford OX1 3QT, U.K
| | - Frances Platt
- Department of Pharmacology, University of Oxford , Mansfield Road, Oxford OX1 3QT, U.K
| | - Giancarlo Parenti
- Department of Translational Medical Sciences, Section of Pediatrics, Università degli Studi di Napoli Federico II , Via S. Pansini 5, 80131 Napoli, Italy.,Telethon Institute of Genetics and Medicine , Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Marco Moracci
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche , Via P. Castellino 111, 80131 Napoli, Italy.,Department of Biology, Università degli Studi di Napoli Federico II , via Cintia, 80126 Napoli, Italy
| | - Giovanni Palumbo
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II , via Cintia, 80126 Napoli, Italy
| | - Annalisa Guaragna
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II , via Cintia, 80126 Napoli, Italy
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8
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Carnero A, Pérez-Rentero S, Alagia A, Aviñó A, Sanghvi YS, Fernández S, Ferrero M, Eritja R. The impact of an extended nucleobase-2′-deoxyribose linker in the biophysical and biological properties of oligonucleotides. RSC Adv 2017. [DOI: 10.1039/c6ra26852h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The introduction of a novel thymine derivative at the 3′-end of the sense strand generates more potent and selective siRNAs.
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Affiliation(s)
- Alejandro Carnero
- Departamento de Química Orgánica e Inorgánica
- Instituto Universitario de Biotecnología de Asturias
- Universidad de Oviedo
- 33006-Oviedo
- Spain
| | - Sónia Pérez-Rentero
- Dpt. Chemical & Biomolecular Nanotechnology
- Institute for Advanced Chemistry of Catalonia (IQAC)
- CSIC
- 08034-Barcelona
- Spain
| | - Adele Alagia
- Dpt. Chemical & Biomolecular Nanotechnology
- Institute for Advanced Chemistry of Catalonia (IQAC)
- CSIC
- 08034-Barcelona
- Spain
| | - Anna Aviñó
- Dpt. Chemical & Biomolecular Nanotechnology
- Institute for Advanced Chemistry of Catalonia (IQAC)
- CSIC
- 08034-Barcelona
- Spain
| | | | - Susana Fernández
- Departamento de Química Orgánica e Inorgánica
- Instituto Universitario de Biotecnología de Asturias
- Universidad de Oviedo
- 33006-Oviedo
- Spain
| | - Miguel Ferrero
- Departamento de Química Orgánica e Inorgánica
- Instituto Universitario de Biotecnología de Asturias
- Universidad de Oviedo
- 33006-Oviedo
- Spain
| | - Ramon Eritja
- Dpt. Chemical & Biomolecular Nanotechnology
- Institute for Advanced Chemistry of Catalonia (IQAC)
- CSIC
- 08034-Barcelona
- Spain
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9
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Paolella C, D'Alonzo D, Schepers G, Van Aerschot A, Di Fabio G, Palumbo G, Herdewijn P, Guaragna A. Oligonucleotides containing a ribo-configured cyclohexanyl nucleoside: probing the role of sugar conformation in base pairing selectivity. Org Biomol Chem 2016; 13:10041-9. [PMID: 26293202 DOI: 10.1039/c5ob01449b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The synthesis and a preliminary evaluation of the pairing properties of ribo-cyclohexanyl nucleic acids (r-CNA) is herein reported. Incorporation of a single r-CNA nucleotide into natural duplexes did not enhance their stability, while a very high pairing selectivity for RNA was found. As deduced by comparative analysis of Tm and NMR data, a relationship between pairing selectivity and conformational preferences of the "sugar" moiety of r-CNA (and more generally of six-membered nucleic acids) was suggested.
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Affiliation(s)
- Concetta Paolella
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia, 80126 Napoli, Italy.
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10
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D'Alonzo D, Froeyen M, Schepers G, Di Fabio G, Van Aerschot A, Herdewijn P, Palumbo G, Guaragna A. 1',5'-Anhydro-L-ribo-hexitol Adenine Nucleic Acids (α-L-HNA-A): Synthesis and Chiral Selection Properties in the Mirror Image World. J Org Chem 2015; 80:5014-22. [PMID: 25853790 DOI: 10.1021/acs.joc.5b00406] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis and a preliminary investigation of the base pairing properties of (6' → 4')-linked 1',5'-anhydro-L-ribo-hexitol nucleic acids (α-L-HNA) have herein been reported through the study of a model oligoadenylate system in the mirror image world. Despite its considerable preorganization due to the rigidity of the "all equatorial" pyranyl sugar backbone, α-L-HNA represents a versatile informational biopolymer, in view of its capability to cross-communicate with natural and unnatural complements in both enantiomeric forms. This seems the result of an inherent flexibility of the oligonucleotide system, as witnessed by the singular formation of iso- and heterochiral associations composed of regular, enantiomorphic helical structures. The peculiar properties of α-L-HNA (and most generally of the α-HNA system) provide new elements in our understanding of the structural prerequisites ruling the stereoselectivity of the hybridization processes of nucleic acids.
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Affiliation(s)
- Daniele D'Alonzo
- †Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, 80126 Napoli, Italy
| | - Mathy Froeyen
- ‡Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Guy Schepers
- ‡Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Giovanni Di Fabio
- †Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, 80126 Napoli, Italy
| | - Arthur Van Aerschot
- ‡Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Piet Herdewijn
- ‡Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Giovanni Palumbo
- †Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, 80126 Napoli, Italy
| | - Annalisa Guaragna
- †Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, 80126 Napoli, Italy
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11
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Construction of an isonucleoside on a 2,6-dioxobicyclo[3.2.0]-heptane skeleton. Molecules 2015; 20:4623-34. [PMID: 25774493 PMCID: PMC6272333 DOI: 10.3390/molecules20034623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 12/05/2022] Open
Abstract
We have built a new isonucleoside derivative on a 2,6-dioxobicyclo[3.2.0]heptane skeleton as a potential anti-HIV agent. To synthesize the target compound, an acetal-protected dihydroxyacetone was first converted to a 2,3-epoxy-tetrahydrofuran derivative. Introduction of an azide group, followed by the formation of an oxetane ring, gave a pseudosugar derivative with a 2,6-dioxobicyclo[3.2.0]heptane skeleton. The desired isonucleoside was obtained by constructing a purine base moiety on the scaffold, followed by amination.
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12
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Venkatesham A, Kachare D, Schepers G, Rozenski J, Froeyen M, Van Aerschot A. Hybridisation potential of 1',3'-Di-O-methylaltropyranoside nucleic acids. Molecules 2015; 20:4020-41. [PMID: 25741897 PMCID: PMC6272658 DOI: 10.3390/molecules20034020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 02/16/2015] [Accepted: 02/24/2015] [Indexed: 01/16/2023] Open
Abstract
In further study of our series of six-membered ring-containing nucleic acids, different 1',3'-di-O-methyl altropyranoside nucleoside analogs (DMANA) were synthesized comprising all four base moieties, adenine, cytosine, uracil and guanine. Following assembly into oligonucleotides (ONs), their affinity for natural oligonucleotides was evaluated by thermal denaturation of the respective duplexes. Data were compared with results obtained previously for both anhydrohexitol (HNAs) and 3'-O-methylated altrohexitol modified ONs (MANAs). We hereby demonstrate that ONs modified with DMANA monomers, unlike some of our previously described analogues with constrained 6-membered hexitol rings, did not improve thermodynamic stability of dsRNA complexes, most probably in view of an energetic penalty when forced in the required 1C4 pairing conformation. Overall, a single incorporation was more or less tolerated or even positive for the adenine congener, but incorporation of a second modification afforded a slight destabilization (except for A), while a fully modified sequence displayed a thermal stability of -0.3 °C per modification. The selectivity of pairing remained very high, and the new modification upon incorporation into a DNA strand, strongly destabilized the corresponding DNA duplexes. Unfortunately, this new modification does not bring any advantage to be further evaluated for antisense or siRNA applications.
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Affiliation(s)
- Akkaladevi Venkatesham
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Dhuldeo Kachare
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Guy Schepers
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Mathy Froeyen
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Arthur Van Aerschot
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
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13
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Guaragna A, Dell’Isola A, D’Errico S, Palumbo G, D’Alonzo D. Beyond Achmatowicz reaction: DDQ-mediated chemo- and stereoconvergent domino-one pot cyclization/rearrangement of bis-thioenol ether-containing chiral building blocks. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.10.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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14
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Migawa MT, Prakash TP, Vasquez G, Seth PP, Swayze EE. Synthesis and biophysical properties of constrained D-altritol nucleic acids (cANA). Org Lett 2013; 15:4316-9. [PMID: 23937264 DOI: 10.1021/ol401730d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The first synthesis of constrained altritol nucleic acids (cANA) containing antisense oligonucleotides (ASOs) was carried out to ascertain how conformationally restricting the D-altritol backbone-containing ASO (Me-ANA) would affect their ability to form duplexes with RNA. It was found that the thermal stability was reduced (cANA/RNA -1.1 °C/modification) compared to DNA/RNA, suggesting the constrained system results in a small destabilizing perturbation in the duplex structure.
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Affiliation(s)
- Michael T Migawa
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, USA.
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15
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D'Alonzo D, Amato J, Schepers G, Froeyen M, Van Aerschot A, Herdewijn P, Guaragna A. Enantiomeric Selection Properties of β-homoDNA: Enhanced Pairing for Heterochiral Complexes. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301659] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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D'Alonzo D, Amato J, Schepers G, Froeyen M, Van Aerschot A, Herdewijn P, Guaragna A. Enantiomeric selection properties of β-homoDNA: enhanced pairing for heterochiral complexes. Angew Chem Int Ed Engl 2013; 52:6662-5. [PMID: 23670912 DOI: 10.1002/anie.201301659] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Daniele D'Alonzo
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Via Cintia 21, 80126 Napoli, Italy.
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Paolella C, D'Alonzo D, Palumbo G, Guaragna A. Sulfur-assisted domino access to bicyclic dihydrofurans: case study and early synthetic applications. Org Biomol Chem 2013; 11:7825-9. [DOI: 10.1039/c3ob41324a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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18
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D’Errico S, Oliviero G, Borbone N, Amato J, D’Alonzo D, Piccialli V, Mayol L, Piccialli G. A facile synthesis of 5'-fluoro-5'-deoxyacadesine (5'-F-AICAR): a novel non-phosphorylable AICAR analogue. Molecules 2012; 17:13036-44. [PMID: 23124472 PMCID: PMC6268913 DOI: 10.3390/molecules171113036] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 10/31/2012] [Accepted: 10/31/2012] [Indexed: 11/17/2022] Open
Abstract
The substitution of a hydroxyl group by a fluorine atom in a potential drug is an efficient reaction that can, in principle, improve its pharmacological properties. Herein, the synthesis of the novel compound 5'-fluoro-5'-deoxyacadesine (5'-F-AICAR), a strict analogue of AICAR that cannot be 5'-phosphorylated to ZMP by cellular kinases, is reported.
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Affiliation(s)
- Stefano D’Errico
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Giorgia Oliviero
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Jussara Amato
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Daniele D’Alonzo
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Via Cintia 21, 80126, Napoli, Italy
| | - Vincenzo Piccialli
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Via Cintia 21, 80126, Napoli, Italy
| | - Luciano Mayol
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Gennaro Piccialli
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
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19
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Chatelain G, Schepers G, Rozenski J, Van Aerschot A. Hybridization potential of oligonucleotides comprising 3'-O-methylated altritol nucleosides. Mol Divers 2012; 16:825-37. [PMID: 23054535 DOI: 10.1007/s11030-012-9402-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 09/25/2012] [Indexed: 10/27/2022]
Abstract
A series of 3'-O-methylated-d-altrohexitol nucleoside analogs (MANA) was synthesized comprising all four base moieties, adenine, cytosine, uracil, and guanine. These monomers were incorporated into oligonucleotides (ONs) by automated solid phase synthesis and the thermal and thermodynamic stability of all new modified constructs were evaluated. Data were compared with results obtained for both anhydrohexitol (HNAs) and 3'-O-altrohexitol-modified ONs (ANAs). We hereby demonstrate that ONs modified with MANA monomers have an improved thermal and thermodynamic stability compared to RNA, ANA, or HNA containing ONs of which the extent depends on the number of incorporated moieties and their position in the sequence. Thermodynamic analysis afforded comparable or even improved results in comparison with the incorporation of locked nucleic acids. While the specificity of these new synthons is slightly lower compared to mismatches within RNA double strands, it is similar to the discrimination potential of other hexitol modifications (HNA and ANA) which already proved their biologic interest, highlighting the potential of MANA constructs in antisense and in siRNA applications.
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Affiliation(s)
- G Chatelain
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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20
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D'Alonzo D, Guaragna A, Palumbo G. Exploring the role of chirality in nucleic acid recognition. Chem Biodivers 2012; 8:373-413. [PMID: 21404424 DOI: 10.1002/cbdv.201000303] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The study of the base-pairing properties of nucleic acids with sugar moieties in the backbone belonging to the L-series (β-L-DNA, β-L-RNA, and their analogs) are reviewed. The major structural factors underlying the formation of stable heterochiral complexes obtained by incorporation of modified nucleotides into natural duplexes, or by hybridization between homochiral strands of opposite sense of chirality are highlighted. In addition, the perspective use of L-nucleic acids as candidates for various therapeutic applications, or as tools for both synthetic biology and etiology-oriented investigations on the structure and stereochemistry of natural nucleic acids is discussed.
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Affiliation(s)
- Daniele D'Alonzo
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, via Cinthia, 4, I-80126 Napoli.
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21
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Singh J, Kaur H, Kaushik A, Peer S. A Review of Antisense Therapeutic Interventions for Molecular Biological Targets in Various Diseases. INT J PHARMACOL 2011. [DOI: 10.3923/ijp.2011.294.315] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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22
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Paolella C, D’Alonzo D, Guaragna A, Cermola F, Palumbo G. Synthesis of 2,3-dihydro-1,4-dithiinyl nucleosides via Pummerer-type glycosidation. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.09.060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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D’Alonzo D, Guaragna A, Van Aerschot A, Herdewijn P, Palumbo G. Toward l-Homo-DNA: Stereoselective de Novo Synthesis of β-l-erythro-Hexopyranosyl Nucleosides. J Org Chem 2010; 75:6402-10. [DOI: 10.1021/jo100691y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniele D’Alonzo
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, via Cinthia 4, I-80126 Napoli, Italy
| | - Annalisa Guaragna
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, via Cinthia 4, I-80126 Napoli, Italy
| | - Arthur Van Aerschot
- Katholieke Universiteit Leuven, Rega Institute for Medical Research, Minderbroederstraat 10, B-3000 Leuven, Belgium
| | - Piet Herdewijn
- Katholieke Universiteit Leuven, Rega Institute for Medical Research, Minderbroederstraat 10, B-3000 Leuven, Belgium
| | - Giovanni Palumbo
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, via Cinthia 4, I-80126 Napoli, Italy
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24
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Yoshimura Y, Asami K, Imamichi T, Okuda T, Shiraki K, Takahata H. Design and Synthesis of Isonucleosides Constructed on a 2-Oxa-6-thiabicyclo[3.2.0]heptane Scaffold. J Org Chem 2010; 75:4161-71. [DOI: 10.1021/jo100556u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yuichi Yoshimura
- Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan
| | - Kazuhiro Asami
- Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan
| | - Tomozumi Imamichi
- Laboratory of Human Retrovirology, Applied and Development Research Program, National Institute of Allergy and Infectious Diseases at Frederick, Science Applications International Corporation-Frederick, Inc. Frederick, Maryland 21702
| | - Tomoko Okuda
- Department of Virology, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Kimiyasu Shiraki
- Department of Virology, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Hiroki Takahata
- Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan
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25
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Guaragna A, D’Alonzo D, Paolella C, Napolitano C, Palumbo G. Highly Stereoselective de Novo Synthesis of l-Hexoses. J Org Chem 2010; 75:3558-68. [DOI: 10.1021/jo100077k] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Annalisa Guaragna
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II-Complesso Universitario Monte Sant'Angelo, via Cinthia, 4 I-80126 Napoli, Italy
| | - Daniele D’Alonzo
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II-Complesso Universitario Monte Sant'Angelo, via Cinthia, 4 I-80126 Napoli, Italy
| | - Concetta Paolella
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II-Complesso Universitario Monte Sant'Angelo, via Cinthia, 4 I-80126 Napoli, Italy
| | - Carmela Napolitano
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
| | - Giovanni Palumbo
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II-Complesso Universitario Monte Sant'Angelo, via Cinthia, 4 I-80126 Napoli, Italy
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