1
|
Gangopadhyay S, Das G, Gupta S, Ghosh A, Bagale SS, Roy PK, Mandal M, Harikrishna S, Sinha S, Gore KR. 4'- C-Acetamidomethyl-2'- O-methoxyethyl Nucleic Acid Modifications Improve Thermal Stability, Nuclease Resistance, Potency, and hAgo2 Binding of Small Interfering RNAs. J Org Chem 2024; 89:3747-3768. [PMID: 38394362 DOI: 10.1021/acs.joc.3c02506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
In this study, we designed the 4'-C-acetamidomethyl-2'-O-methoxyethyl (4'-C-ACM-2'-O-MOE) uridine and thymidine modifications, aiming to test them into small interfering RNAs. Thermal melting studies revealed that incorporating a single 4'-C-ACM-2'-O-MOE modification in the DNA duplex reduced thermal stability. In contrast, an increase in thermal stability was observed when the modification was introduced in DNA:RNA hybrid and in siRNAs. Thermal destabilization in DNA duplex was attributed to unfavorable entropy, which was mainly compensated by the enthalpy factor to some extent. A single 4'-C-ACM-2'-O-MOE thymidine modification at the penultimate position of the 3'-end of dT20 oligonucleotides in the presence of 3'-specific exonucleases, snake venom phosphodiesterase (SVPD), demonstrated significant stability as compared to monomer modifications including 2'-O-Me, 2'-O-MOE, and 2'-F. In gene silencing studies, we found that the 4'-C-ACM-2'-O-MOE uridine or thymidine modifications at the 3'-overhang in the passenger strand in combination with two 2'-F modifications exhibited superior RNAi activity. The results suggest that the dual modification is well tolerated at the 3'-end of the passenger strand, which reflects better siRNA stability and silencing activity. Interestingly, 4'-C-ACM-2'-O-MOE-modified siRNAs showed considerable gene silencing even after 96 h posttransfection; it showed that our modification could induce prolonged gene silencing due to improved metabolic stability. Molecular modeling studies revealed that the introduction of the 4'-C-ACM-2'-O-MOE modification at the 3'-end of the siRNA guide strand helps to anchor the strand within the PAZ domain of the hAgo2 protein. The overall results indicate that the 4'-C-ACM-2'-O-MOE uridine and thymidine modifications are promising modifications to improve the stability, potency, and hAgo2 binding of siRNAs.
Collapse
Affiliation(s)
- Sumit Gangopadhyay
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Gourav Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Shalini Gupta
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, Jadavpur 700032, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, Jadavpur 700032, India
| | | | - Pritam Kumar Roy
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Mahitosh Mandal
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - S Harikrishna
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, Jadavpur 700032, India
| | - Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| |
Collapse
|
2
|
Martín-Nieves V, Menéndez-Méndez LM, Fàbrega C, Fernández S, Sanghvi YS, Ferrero M, Eritja R. Synthesis of 2'- O-Methyl/2'- O-MOE-L-Nucleoside Derivatives and Their Applications: Preparation of G-Quadruplexes, Their Characterization, and Stability Studies. ACS OMEGA 2023; 8:44893-44904. [PMID: 38046329 PMCID: PMC10688165 DOI: 10.1021/acsomega.3c06231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 12/05/2023]
Abstract
Nucleosides and their analogues constitute an important family of molecules with potential antiviral and antiproliferative activity. The enantiomers of natural nucleosides, l-nucleoside derivatives, which have comparable biological activity but more favorable toxicological properties and greater metabolic stability than d-nucleosides, have emerged as a new class of therapeutic agents. Furthermore, l-nucleosides can be used as a building block to prepare l-oligonucleotides, which have identical physical properties in terms of solubility, hybridization kinetics, and duplex thermal stability as d-oligonucleotides but completely orthogonal in nature. Consequently, they are resistant to nuclease degradation, nontoxic, and immunologically passive, which are desirable properties for biomedical applications. Herein, we describe the synthesis of several 2'-O-methyl/2'-O-MOE-l-nucleoside pyrimidine derivatives and their incorporation into G-rich oligonucleotides. Finally, we evaluated the stability and resistance against nucleases of these new G-quadruplexes, demonstrating the potential of the l-nucleosides described in this work in providing enhanced nuclease resistance with a minimal impact in the nucleic acid structural properties.
Collapse
Affiliation(s)
- Virginia Martín-Nieves
- Departamento
de Química Orgánica e Inorgánica, Universidad de Oviedo, Oviedo (Asturias) 33006, Spain
| | - Luis Miguel Menéndez-Méndez
- Departamento
de Química Orgánica e Inorgánica, Universidad de Oviedo, Oviedo (Asturias) 33006, Spain
- Dpt.
Chemical & Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC, CSIC), Barcelona 08034, Spain
- CIBER-BBN
Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona 08034, Spain
| | - Carme Fàbrega
- Dpt.
Chemical & Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC, CSIC), Barcelona 08034, Spain
- CIBER-BBN
Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona 08034, Spain
| | - Susana Fernández
- Departamento
de Química Orgánica e Inorgánica, Universidad de Oviedo, Oviedo (Asturias) 33006, Spain
| | - Yogesh S. Sanghvi
- Rasayan
Inc., 2802 Crystal Ridge
Road, Encinitas, California 92024-6615, United
States
| | - Miguel Ferrero
- Departamento
de Química Orgánica e Inorgánica, Universidad de Oviedo, Oviedo (Asturias) 33006, Spain
| | - Ramon Eritja
- Dpt.
Chemical & Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC, CSIC), Barcelona 08034, Spain
- CIBER-BBN
Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona 08034, Spain
| |
Collapse
|
3
|
Liczner C, Duke K, Juneau G, Egli M, Wilds CJ. Beyond ribose and phosphate: Selected nucleic acid modifications for structure-function investigations and therapeutic applications. Beilstein J Org Chem 2021; 17:908-931. [PMID: 33981365 PMCID: PMC8093555 DOI: 10.3762/bjoc.17.76] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Over the past 25 years, the acceleration of achievements in the development of oligonucleotide-based therapeutics has resulted in numerous new drugs making it to the market for the treatment of various diseases. Oligonucleotides with alterations to their scaffold, prepared with modified nucleosides and solid-phase synthesis, have yielded molecules with interesting biophysical properties that bind to their targets and are tolerated by the cellular machinery to elicit a therapeutic outcome. Structural techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chemically modified oligonucleotides that have been explored for gene silencing.
Collapse
Affiliation(s)
- Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Kieran Duke
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Gabrielle Juneau
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Martin Egli
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| |
Collapse
|
4
|
Szlenkier M, Boryski J. Application of Sugar-Base Anhydro Bridge for Modification of Nucleosides in the 2’- and/or 3’-Positions - Revisited. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190306155919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The nucleosides modified in the 2’- and/or 3’-position have been known for
years and include important, bioactive compounds such as zidovudine, cytarabine, didanosine,
puromycin, and fludarabine. This group consists of analogs with altered configuration,
2’,3’-dideoxy and 2’,3’-dideoxy-didehydro nucleosides, as well as derivatives with
additional substituents. These compounds are often targeted against viruses and tumors.
The sugar-base anhydro nucleosides have been known since the middle of the 20th century.
However, their application has not yet been fully explored and described. The number
of 2’,3’-dimodified derivatives, obtainable through sugar-base anhydrocyclic synthons,
could be vast, especially taking into consideration various combinations of S-alkyl,
S-aryl, O-alkyl, O-aryl, halogen, triazole, amine and azide substituents in both pyrimidine
and purine nucleosides. Furthermore, application of anhydrocyclic structures can be an efficient method of introducing
isotope labeled groups. The aim of this article is to provide an overview of the known methods of
functionalization of the 2’- and/or 3’-position of nucleosides, using anhydrocyclic structures, and also to present
a future outlook for this subject.
Collapse
Affiliation(s)
- Maurycy Szlenkier
- Department of Nucleoside and Nucleotide Chemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego str. 12/14, 61-704 Poznan, Poland
| | - Jerzy Boryski
- Department of Nucleoside and Nucleotide Chemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego str. 12/14, 61-704 Poznan, Poland
| |
Collapse
|
5
|
Benzaria S, Bardiot D, Bouisset T, Counor C, Rabeson C, Pierra C, Storer R, Loi AG, Cadeddu A, Mura M, Musiu C, Liuzzi M, Loddo R, Bergelson S, Bichko V, Bridges E, Cretton-Scott E, Mao J, Sommadossi JP, Seifer M, Standring D, Tausek M, Gosselin G, La Colla P. 2′-C-Methyl Branched Pyrimidine Ribonucleoside Analogues: Potent Inhibitors of RNA Virus Replication. ACTA ACUST UNITED AC 2016; 18:225-42. [PMID: 17907380 DOI: 10.1177/095632020701800406] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RNA viruses are the agents of numerous widespread and often severe diseases. Their unique RNA-dependent RNA polymerase (RDRP) is essential for replication and, thus, constitutes a valid target for the development of selective chemotherapeutic agents. In this regard, we have investigated sugar-modified ribonucleoside analogues as potential inhibitors of the RDRP. Title compounds retain ‘natural’ pyrimidine bases, but possess a β-methyl substituent at the 2′-position of the D- or L-ribose moiety. Evaluation against a broad range of RNA viruses, either single-stranded positive (ssRNA), single-stranded negative (ssRNA−) or double-stranded (dsRNA), revealed potent activities for D-2′- C-methyl-cytidine and -uridine against ssRNA+, and dsRNA viruses. None of the L-enantiomers were active. Moreover, the 5′-triphosphates of the active D-enantiomers were found to inhibit the bovine virus diarrhoea virus polymerase. Thus, the 2′-methyl branching of natural pyrimidine ribonucleosides transforms physiological molecules into potent, broad-spectrum antiviral agents that merit further development.
Collapse
Affiliation(s)
- Samira Benzaria
- Laboratoire Coopératif Idenix-CNRS-Université Montpellier II, Montpellier, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Kel'in AV, Zlatev I, Harp J, Jayaraman M, Bisbe A, O'Shea J, Taneja N, Manoharan RM, Khan S, Charisse K, Maier MA, Egli M, Rajeev KG, Manoharan M. Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides. J Org Chem 2016; 81:2261-79. [PMID: 26940174 DOI: 10.1021/acs.joc.5b02375] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Although judicious use of chemical modifications has contributed to the success of nucleic acid therapeutics, poor systemic stability remains a major hurdle. The introduction of functional groups around the phosphate backbone can enhance the nuclease resistance of oligonucleotides (ONs). Here, we report the synthesis of enantiomerically pure (R)- and (S)-5'-C-methyl (C5'-Me) substituted nucleosides and their incorporation into ONs. These modifications generally resulted in a decrease in thermal stability of oligonucleotide (ON) duplexes in a manner dependent on the stereoconfiguration at C5' with greater destabilization characteristic of (R)-epimers. Enhanced stability against snake venom phosphodiesterase resulted from modification of the 3'-end of an ON with either (R)- or (S)-C5'-Me nucleotides. The (S)-isomers with different 2'-substituents provided greater resistance against 3'-exonucleases than the corresponding (R)-isomers. Crystal structure analyses of RNA octamers with (R)- or (S)-5'-C-methyl-2'-deoxy-2'-fluorouridine [(R)- or (S)-C5'-Me-2'-FU, respectively] revealed that the stereochemical orientation of the C5'-Me and the steric effects that emanate from the alkyl substitution are the dominant determinants of thermal stability and are likely molecular origins of resistance against nucleases. X-ray and NMR structural analyses showed that the (S)-C5'-Me epimers are spatially and structurally more similar to their natural 5' nonmethylated counterparts than the corresponding (R)-epimers.
Collapse
Affiliation(s)
- Alexander V Kel'in
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Ivan Zlatev
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Joel Harp
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine , Nashville, Tennessee 37232, United States
| | - Muthusamy Jayaraman
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Anna Bisbe
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Jonathan O'Shea
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Nate Taneja
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Rajar M Manoharan
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Saeed Khan
- Department of Chemistry and Biochemistry, University of California , Los Angeles, California 90095, United States
| | - Klaus Charisse
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin A Maier
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin Egli
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine , Nashville, Tennessee 37232, United States
| | | | - Muthiah Manoharan
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| |
Collapse
|
7
|
Affiliation(s)
- Yonglian Zhang
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Spencer Knapp
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| |
Collapse
|
8
|
Saito Y, Hashimoto Y, Arai M, Tarashima N, Miyazawa T, Miki K, Takahashi M, Furukawa K, Yamazaki N, Matsuda A, Ishida T, Minakawa N. Chemistry, properties, and in vitro and in vivo applications of 2'-O-methoxyethyl-4'-thioRNA, a novel hybrid type of chemically modified RNA. Chembiochem 2014; 15:2535-40. [PMID: 25314258 DOI: 10.1002/cbic.201402398] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Indexed: 11/10/2022]
Abstract
We report the synthesis, properties, and in vitro and in vivo applications of 2'-O-methoxyethyl-4'-thioRNA (MOE-SRNA), a novel type of hybrid chemically modified RNA. In its hybridization with complementary RNA, MOE-SRNA showed a moderate improvement of Tm value (+3.4 °C relative to an RNA:RNA duplex). However, the results of a comprehensive comparison of the nuclease stability of MOE-SRNA relative to 2'-O-methoxyethylRNA (MOERNA), 2'-O-methyl-4'-thioRNA (Me-SRNA), 2'-O-methylRNA (MeRNA), 4'-thioRNA (SRNA), and natural RNA revealed that MOE-SRNA had the highest stability (t1/2 >48 h in human plasma). Because of the favorable properties of MOE-SRNA, we evaluated its in vitro and in vivo potencies as an anti-microRNA oligonucleotide against miR-21. Although the in vitro potency of MOE-SRNA was moderate, its in vivo potency was significant for the suppression of tumor growth (similar to that of MOERNA).
Collapse
Affiliation(s)
- Yota Saito
- Graduate School of Pharmaceutical Sciences, The University of Tokushima, 1-78-1 Shomachi, Tokushima 770-8505 (Japan)
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Meurillon M, Marton Z, Hospital A, Jordheim LP, Béjaud J, Lionne C, Dumontet C, Périgaud C, Chaloin L, Peyrottes S. Structure-activity relationships of β-hydroxyphosphonate nucleoside analogues as cytosolic 5'-nucleotidase II potential inhibitors: synthesis, in vitro evaluation and molecular modeling studies. Eur J Med Chem 2014; 77:18-37. [PMID: 24607586 DOI: 10.1016/j.ejmech.2014.02.055] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 01/10/2014] [Accepted: 02/22/2014] [Indexed: 12/11/2022]
Abstract
The cytosolic 5'-nucleotidase II (cN-II) has been proposed as an attractive molecular target for the development of novel drugs circumventing resistance to cytotoxic nucleoside analogues currently used for treating leukemia and other malignant hemopathies. In the present work, synthesis of β-hydroxyphosphonate nucleoside analogues incorporating modifications either on the sugar residue or the nucleobase, and their in vitro evaluation towards the purified enzyme were carried out in order to determine their potency towards the inhibition of cN-II. In addition to the biochemical investigations, molecular modeling studies revealed important structural features for binding affinities towards the target enzyme.
Collapse
Affiliation(s)
- Maïa Meurillon
- Institut des biomolécules Max Mousseron (IBMM), UMR 5247 CNRS - UM1 - UM2, Université Montpellier 2, cc1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Zsuzsanna Marton
- Centre d'études d'agents pathogènes et biotechnologies pour la santé (CPBS), UMR 5236 CNRS - UM1 - UM2, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Audrey Hospital
- Institut des biomolécules Max Mousseron (IBMM), UMR 5247 CNRS - UM1 - UM2, Université Montpellier 2, cc1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Lars Petter Jordheim
- Université de Lyon 1, INSERM U1052 CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, 69000 Lyon, France
| | - Jérôme Béjaud
- Institut des biomolécules Max Mousseron (IBMM), UMR 5247 CNRS - UM1 - UM2, Université Montpellier 2, cc1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Corinne Lionne
- Centre d'études d'agents pathogènes et biotechnologies pour la santé (CPBS), UMR 5236 CNRS - UM1 - UM2, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Charles Dumontet
- Université de Lyon 1, INSERM U1052 CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, 69000 Lyon, France
| | - Christian Périgaud
- Institut des biomolécules Max Mousseron (IBMM), UMR 5247 CNRS - UM1 - UM2, Université Montpellier 2, cc1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Laurent Chaloin
- Centre d'études d'agents pathogènes et biotechnologies pour la santé (CPBS), UMR 5236 CNRS - UM1 - UM2, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Suzanne Peyrottes
- Institut des biomolécules Max Mousseron (IBMM), UMR 5247 CNRS - UM1 - UM2, Université Montpellier 2, cc1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France.
| |
Collapse
|
10
|
Mathis G, Bourg S, Aci-Sèche S, Truffert JC, Asseline U. Synthesis and properties of 2'-O-neopentyl modified oligonucleotides. Org Biomol Chem 2013; 11:1345-57. [PMID: 23318410 DOI: 10.1039/c2ob26871j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
2'-O-Neopentyldeoxyuridine (Un) was synthesized and incorporated into a series of oligodeoxyribonucleotides. Single and triple incorporations in various arrangements were performed. The Watson and Crick pairing properties with complementary DNA and RNA were investigated by UV melting curves, CD spectroscopy, and molecular dynamic simulations. The results were compared to those obtained with DNA-DNA and DNA-RNA duplexes involving dU at the same positions. Oligonucleotides containing Un clearly demonstrated their ability to form duplexes with both complementary DNA and RNA but with higher stabilities for the DNA-RNA duplexes similar to the one of the parent DNA-RNA duplex. Investigations into the thermodynamic properties of these 17-base-pair duplexes revealed ΔG values (37 °C) that are in line with the measured T(m) values for both the DNA-DNA and DNA-RNA duplexes. CD spectroscopic structural investigations indicated that the conformations of the DNA-DNA and DNA-RNA duplexes involving Un are similar to those of the dT-rA and dU-rA containing duplexes. Only small changes in intensities and weak blue shifts were observed when three Uns were incorporated into the duplexes. The results of the molecular dynamic simulations showed, for the six duplexes involving the modified nucleoside Un, calculated curvatures similar to those of the corresponding unmodified duplexes without base-pair disruption. The neopentyl group is able to be accommodated in the minor grooves of both the DNA-DNA and RNA-DNA duplexes. However, molecular dynamic simulations indicated that the Uns adopt a C2'-exo sugar pucker conformation close to an A-helix type without perturbing the C2'-endo sugar pucker conformations of their 2'-deoxynucleoside neighbours. These results confirm the potential of 2'-O-neopentyldeoxyuridine as a nucleoside surrogate for oligonucleotide based therapeutic strategies.
Collapse
Affiliation(s)
- Gérald Mathis
- Centre de Biophysique Moléculaire UPR 4301 CNRS, Conventionnée avec l'Université d'Orléans, Rue Charles Sadron, 45071 Orléans Cedex 02, France
| | | | | | | | | |
Collapse
|
11
|
Kotikam V, Kumar VA. Synthesis and properties of 2′-O-[R- and S-(2-amino-3-methoxy)propyl] (R-AMP and S-AMP) nucleic acids. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.05.104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
12
|
Masaki Y, Miyasaka R, Ohkubo A, Seio K, Sekine M. Linear relationship between deformability and thermal stability of 2'-O-modified RNA hetero duplexes. J Phys Chem B 2010; 114:2517-24. [PMID: 20108976 PMCID: PMC2825091 DOI: 10.1021/jp909851j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We describe the relationship between the experimentally determined melting temperatures of 2′-O-modified-RNA/RNA duplexes and their deformability estimated from molecular dynamics simulations. To clarify this relationship, we synthesized several fully modified oligoribonucleotides such as 2′-O-cyanoethyl RNAs and 2′-O-methoxyethyl RNAs and compared the actual melting temperatures of the duplexes with their calculated deformabilities. An increase of the melting temperatures by 2′-O-modifications was found to correlate strongly with an increase of the helical elastic constants in U14/A14, (CU)7/(AG)7, and (GACU)3/(AGUC)3 sequences. Linear regression analyses could be used to estimate the melting temperature with an accuracy of ±2.0 °C in our model case. Although the strong correlation was observed in the same base sequence, the linear regression functions were different from each base sequence. Our results indicated the possibility of predicting the thermal stability of 2′-O-modified duplexes at the computer-aided molecular design stage.
Collapse
Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan
| | | | | | | | | |
Collapse
|
13
|
Hansen JB, Fisker N, Westergaard M, Kjaerulff LS, Hansen HF, Thrue CA, Rosenbohm C, Wissenbach M, Orum H, Koch T. SPC3042: a proapoptotic survivin inhibitor. Mol Cancer Ther 2008; 7:2736-45. [PMID: 18790754 DOI: 10.1158/1535-7163.mct-08-0161] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The ability to regulate the cellular homeostasis of a higher organism through tight control of apoptosis and cell division is crucial for life. Dysregulation of these mechanisms is often associated with cancerous phenotypes in cells. Optimal cancer therapy is a fine balance between effective cancer cell killing and at the same time minimizing, or avoiding, damage to the surrounding healthy tissue. To obtain this, it is necessary to identify and inhibit molecular targets on which the cancer cells are strongly dependent. Survivin represents such a target, and it has been published previously that peptide vaccines, the small-molecule YM155, and the antisense molecule LY2181308/ISIS23722, via different mechanisms, have been used as survivin inhibitors. In this article, a new potent antisense inhibitor of survivin, SPC3042, is presented, and the properties of SPC3042 are compared with the previously published antisense drug, LY2181308/ISIS23722. SPC3042 is a 16-mer locked nucleic acid (LNA) oligonucleotide and designed as a fully phosphorothiolated gapmer containing 7 LNA nucleotides in the flanks. The LNA nucleotides in SPC3042 provide nuclease stability and higher potency for survivin mRNA inhibition compared with earlier generations of antisense reagents. It is shown that the down-regulation of survivin with SPC3042 leads to cell cycle arrest, pronounced cellular apoptosis, and down-regulation of Bcl-2. It is also shown that SPC3042 is a sensitizer of prostate cancer cells to Taxol treatment in vitro and in vivo.
Collapse
Affiliation(s)
- Jens Bo Hansen
- Research Division, Santaris Pharma A/S, Boege alle 3, Hoersholm 2970 Denmark.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Brennan L, Peng G, Srinivasan N, Fox KR, Brown T. 2'-o-dimethylaminoethoxyuridine and 5-dimethylaminopropargyl deoxyuridine for at base pair recognition in triple helices. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1283-6. [PMID: 18066769 DOI: 10.1080/15257770701530525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The nucleoside analogues 2'-O-dimethylaminoethoxy uridine and 5-dimethylaminopropargyl deoxyuridine have been synthesised and incorporated into oligonucleotides. Their triplex-stabilising properties have been determined in fluorescence melting experiments.
Collapse
Affiliation(s)
- Lavinia Brennan
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom.
| | | | | | | | | |
Collapse
|
15
|
Milton S, Strömberg R. Evaluation of lactam protection for synthesis of 2'-O-alkylated uridines. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1491-3. [PMID: 18066812 DOI: 10.1080/15257770701542868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Two different classes of protection for the uridine lactam function have been evaluated. These are benzoyl protections and different acetal functions. In particular the triisopropylsiloxymethyl protection is a most promising lactam protecting group for use in synthesis of 2'-O-alkyl-uridines.
Collapse
Affiliation(s)
- Stefan Milton
- Department of Biosciences and Nutrition, Karolinska Institutet, NOVUM, S-14157 Huddinge, Sweden
| | | |
Collapse
|
16
|
Sivets GG. Synthesis study of 2'-O-(2-methoxyethyl)-purine derivatives. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1237-40. [PMID: 18066759 DOI: 10.1080/15257770701528180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Alkylation of adenosine and 2-aminoadenosine was studied in dimethylsulfoxide with application of 1-methanesulfonyloxy-2-methoxyethane as an alkylating agent and t-BuOK, KOH and NaH as bases under mild heating. Using new reaction conditions, the improved synthesis of 2'-O-MOE-purine derivatives is described.
Collapse
Affiliation(s)
- Grigorii G Sivets
- Institute of Bioorganic Chemistry, National Academy of Sciences, Minsk, Acad. Kuprevicha 5/2, Belarus.
| |
Collapse
|
17
|
Saneyoshi H, Okamoto I, Masaki Y, Ohkubo A, Seio K, Sekine M. Facile synthesis of 2′-O-cyanoethyluridine by ring-opening reaction of 2,2′-anhydrouridine with cyanoethyl trimethylsilyl ether in the presence of BF3·Et2O. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.09.105] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
18
|
Zatsepin TS, Romanova EA, Oretskaya TS. Synthesis of 2'-O-alkylnucleosides. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc2002v071n06abeh000714] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
19
|
Saneyoshi H, Seio K, Sekine M. A general method for the synthesis of 2'-O-cyanoethylated oligoribonucleotides having promising hybridization affinity for DNA and RNA and enhanced nuclease resistance. J Org Chem 2006; 70:10453-60. [PMID: 16323857 DOI: 10.1021/jo051741r] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] An effective method for the synthesis of 2'-O-cyanoethylated oligoribonucleotides as a new class of 2'-O-modified RNAs was developed. The reaction of appropriately protected ribonucleoside derivatives with acrylonitrile in t-BuOH in the presence of Cs2CO3 gave 2'-O-cyanoethylated ribonucleoside derivatives in excellent yields, which were converted by a successive selective deprotection/protection strategy to 2'-O-cyanoethylated 5'-O-dimethoxytritylribonucleoside 3'-phosphoramidite derivatives in high yields. Fully 2'-O-cyanoethylated oligoribonucleotides, (Uce)12 and (GceAceCceUce)3, were successfully synthesized in the phosphoramidite approach by use of the phosphoramidite building blocks. It was also found that oligoribonucleotides having a 2'-O-cyanoethylated ribonucleoside (Uce, Cce, Ace, or Gce) could be obtained by the selective removal of the TBDMS group from fully protected oligoribonucleotide intermediates without loss of the cyanoethyl group by use of NEt3 x 3HF as a desilylating reagent. The detailed T(m) experiments revealed that oligoribonucleotides containing 2'-O-cyanoethylated ribonucleosides have higher hybridization affinity for both DNA and RNA than the corresponding unmodified and 2'-O-methylated oligoribonucleotides. In addition, introduction of a cyanoethyl group into the 2'-position of RNA resulted in significant increase of nuclease resistance toward snake venom and bovine spleen phosphodiesterases compared with that of the methyl group.
Collapse
Affiliation(s)
- Hisao Saneyoshi
- Department of Life Science, Tokyo Institute of Technology, Division of Collaborative Research for Bioscience and Biotechnology, Japan
| | | | | |
Collapse
|
20
|
|
21
|
Pierra C, Amador A, Badaroux E, Storer R, Gosselin G. Synthesis of 2'-C-Methylcytidine and 2'-C-Methyluridine Derivatives Modified in the 3'-Position as Potential Antiviral Agents. ACTA ACUST UNITED AC 2006. [DOI: 10.1135/cccc20060991] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
As part of our anti-hepatitis C program, we recently discovered 2'-C-methylcytidine (1) and 2'-C-methyluridine (2), which are potent inhibitors in cell culture of several viruses (bovine viral diarrhea virus (BVDV), yellow fever virus (YFV)) closely related to HCV. In order to characterize structure-activity relationships, we introduced some structural and functional modifications into the 3'-position of 2'-C-methylcytidine and 2'-C-methyluridine. All these hitherto unknown compounds thus synthesized were tested for the activity against a wide range of viruses and found to be inactive.
Collapse
|
22
|
Pierra C, Benzaria S, Amador A, Moussa A, Mathieu S, Storer R, Gosselin G. Nm 283, an efficient prodrug of the potent anti-HCV agent 2'-C-methylcytidine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:767-70. [PMID: 16248033 DOI: 10.1081/ncn-200060112] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In order to improve the oral bioavailability of 2-C-methylcytidine, a potent anti-HCV agent, the corresponding 3'-O-L-valinyl ester derivative (NM 283) has been synthesized Based on its ease of synthesis and its physicochemical properties, NM 283 has emerged as a promising antiviral drug for treatment of chronic HCV infection.
Collapse
Affiliation(s)
- C Pierra
- Laboratoire Coopératif Idenix-CNRS, Université Montpellier II, Montpellier Cedex 5, France
| | | | | | | | | | | | | |
Collapse
|
23
|
Honcharenko D, Varghese OP, Plashkevych O, Barman J, Chattopadhyaya J. Synthesis and Structure of Novel Conformationally Constrained 1‘,2‘-Azetidine-Fused Bicyclic Pyrimidine Nucleosides: Their Incorporation into Oligo-DNAs and Thermal Stability of the Heteroduplexes. J Org Chem 2005; 71:299-314. [PMID: 16388649 DOI: 10.1021/jo052115x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
[structures: see text] The synthesis of novel 1',2'-aminomethylene bridged (6-aza-2-oxabicyclo[3.2.0]heptane) "azetidine" pyrimidine nucleosides and their transformations to the corresponding phosphoramidite building blocks (20, 39, and 42) for automated solid-phase oligonucleotide synthesis is reported. The novel bicyclonucleoside "azetidine" monomers were synthesized by two different strategies starting from the known sugar intermediate 6-O-benzyl-1,2:3,4-bis-O-isopropylidene-D-psicofuranose. Conformational analysis performed by molecular modeling (ab initio and MD simulations) and NMR showed that the azetidine-fused furanose sugar is locked in a North-East conformation with pseudorotational phase angle (P) in the range of 44.5-53.8 degrees and sugar puckering amplitude (phi(m)) of 29.3-32.6 degrees for the azetidine-modified T, U, C, and 5-Me-C nucleosides. Thermal denaturation studies of azetidine-modified oligo-DNA/RNA heteroduplexes show that the azetidine-fused nucleosides display improved binding affinities when compared to that of previously synthesized North-East sugar constrained oxetane fused analogues.
Collapse
Affiliation(s)
- Dmytro Honcharenko
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, Uppsala University, SE-75123 Uppsala, Sweden
| | | | | | | | | |
Collapse
|
24
|
Lönnberg T, Korhonen J. Hydrolysis of 2',3'-O-methyleneadenosin-5'-yl bis-5'-O-methyluridin-3'-yl phosphate: the 2'-hydroxy group stabilizes the phosphorane intermediate, not the departing 3'-oxyanion, by hydrogen bonding. J Am Chem Soc 2005; 127:7752-8. [PMID: 15913365 DOI: 10.1021/ja050325l] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrolytic reactions of 2',3'-O-methyleneadenosin-5'-yl bis-5'-O-methyluridin-3'-yl phosphate (1a) have been followed by RP HPLC over a wide pH range to elucidate the role of the 2'-OH group as an intermolecular hydrogen bond donor facilitating the cleavage of 1a. At pH < 2, where the decomposition of 1 is first-order in hydronium-ion concentration, the P-O5' and P-O3' bonds are cleaved equally rapidly. Over a relatively wide range from pH 2 to 4, the hydrolysis is pH-independent and the P-O5' bond is cleaved 1.6 times as rapidly as the P-O3' bond. At pH 6, the reaction becomes first-order in hydroxide-ion concentration and cleavage of the P-O3' bond starts to predominate, accounting for 89% of the overall hydrolysis in 10 mmol L(-)(1) aqueous sodium hydroxide. Under alkaline conditions, the 2'-OH group facilitates the cleavage of 1 by a factor of 27 compared to the 2'-OMe counterpart, the influence on the P-O3' and P-O5' bond cleavage being equal. Accordingly, the 2'-hydroxy group stabilizes the phosphorane intermediate, not the departing 3'-oxyanion, by hydrogen bonding.
Collapse
Affiliation(s)
- Tuomas Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
| | | |
Collapse
|
25
|
Radi M, Mugnaini C, Petricci E, Corelli F, Botta M. Synthesis of reactive cytidine derivatives as building blocks for cross-linking oligonucleotides. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.04.083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
26
|
Oka N, Sanghvi YS, Theodorakis EA. 3,3(')-Oxybis(dimethoxytrityl chloride) (O-DMTCl): synthesis and applications of a novel bifunctional protecting group. Bioorg Med Chem Lett 2005; 14:3241-4. [PMID: 15149683 DOI: 10.1016/j.bmcl.2004.03.097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2004] [Accepted: 03/29/2004] [Indexed: 11/24/2022]
Abstract
3,3(')- Oxybis(dimethoxytrityl chloride) (O-DMTCl) was synthesized as a novel, acid-labile bifunctional protecting reagent. The reactions of O-DMTCl with base-protected ribonucleosides afforded unexpectedly 2('),5(')-cyclic protected ribonucleosides in addition to the expected 3('),5(')-cyclic protected ribonucleosides in good yields.
Collapse
Affiliation(s)
- Natsuhisa Oka
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | | | | |
Collapse
|
27
|
Lönnberg T, Kiiski J, Mikkola S. Hydrolytic stability of 2′,3′-O-methyleneadenos-5′-yl 2′,5′-di-O-methylurid-3′-yl 5′-O-methylurid-3′(2′)-yl phosphate: implications to feasibility of existence of phosphate-branched RNA under physiological conditions. Org Biomol Chem 2005; 3:1089-96. [PMID: 15750653 DOI: 10.1039/b500054h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrolytic reactions of 2',3'-O-methyleneadenos-5'-yl 2',5'-di-O-methylurid-3'-yl 5'-O-methylurid-3'(2')-yl phosphate (1a,b) have been followed by RP-HPLC over a wide pH range to evaluate the feasibility of occurrence of phosphate-branched RNA under physiological conditions. At pH <2, where the decomposition of is first order in [H3O+], the P-O5' bond is cleaved 1.5 times as rapidly as the P-O3' bond. Under these conditions, the reaction probably proceeds by an attack of the 2'-OH on the phosphotriester monocation. Over a relatively wide range from pH 2 to 5, the hydrolysis is pH-independent, referring to rapid initial deprotonation of the attacking 2'-OH followed by general acid catalyzed departure of the leaving nucleoside. The P-O5' bond is cleaved 3 times as rapidly as the P-O3' bond. At pH 6, the reaction becomes first order in [HO-], consistent with an attack of the 2'-oxyanion on neutral phosphate. The product distribution is gradually inversed: in 10 mmol L(-1) aqueous sodium hydroxide, cleavage of the P-O3' bond is favored over P-O5' by a factor of 7.3. The results of the present study suggest that the half-life for the cleavage of under physiological conditions is only 100 s. Even at pH 2, where is most stable, the half-life for its cleavage is less than one hour and the isomerization between and is even more rapid than cleavage. The mechanisms of the partial reactions are discussed.
Collapse
Affiliation(s)
- Tuomas Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
| | | | | |
Collapse
|
28
|
Jeannot F, Gosselin G, Mathé C. Synthesis and studies of 3'-C-trifluoromethyl-beta-D-ribonucleosides bearing the five naturally occurring nucleic acid bases. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2004; 22:2195-202. [PMID: 14714766 DOI: 10.1081/ncn-120026874] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
3'-C-Trifloromethyl-beta-D-ribonucleoside derivatives bearing the five naturally occurring nucleic acid bases have been synthesized. All these derivatives were prepared by glycosylation reactions of purine and pyrimidine bases with a suitable peracylated 3-C-trifluoromethyl ribofuranose precursor. After deprotection, the resulting title nucleoside analogues were tested for their inhibitory properties against the replication of HIV, HBV and several RNA viruses. However, none of these compounds showed significant antiviral activity.
Collapse
Affiliation(s)
- Frédéric Jeannot
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, UMR 5625 CNRS-Université Montpellier II, Montpellier, France
| | | | | |
Collapse
|
29
|
Colacino E, Sindona G, Gosselin G, Mathé C. Synthesis and biological evaluation of some 5-nitro- and 5-amino derivatives of 2'-deoxycytidine, 2',3'-dideoxyuridine, and 2',3'-dideoxycytidine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2004; 22:2013-26. [PMID: 14680024 DOI: 10.1081/ncn-120026403] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In this article, we describe the synthesis of 5-nitro-1-(2-deoxy-alpha-D-erythro-pentofuranosyl)cytosine (4alpha), 5-nitro-1-(2-deoxy-beta-D-erythro-pentofuranosyl)cytosine (4beta), 5-amino-1-(2-deoxy-alpha-D-erythro-pentofuranosyl)cytosine (5alpha), 5-nitro-1-(2-deoxy-beta-D-erythro-pentofuranosyl)cytosine (5beta), 5-nitro-1-(2,3-dideoxy-beta-D-ribofuranosyl)uracil (6beta), 5-amino-1-(2,3-dideoxy-alpha,beta-D-ribofuranosyl)uracil (7), 5-nitro-1-(2,3-dideoxy-alpha,beta-D-ribofuranosyl)cytosine (8) and 5-amino-1-(2,3-dideoxy-beta-D-ribofuranosyl)cytosine (9beta). The prepared compounds were tested for their activity against HIV and HBV viruses, but they did not show significant activity.
Collapse
Affiliation(s)
- Evelina Colacino
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, UMR 5625 CNRS, Université Montpellier II, Montpellier, France
| | | | | | | |
Collapse
|
30
|
Okamoto I, Shohda KI, Seio K, Sekine M. A new route to 2'-O-alkyl-2-thiouridine derivatives via 4-O-protection of the uracil base and hybridization properties of oligonucleotides incorporating these modified nucleoside derivatives. J Org Chem 2004; 68:9971-82. [PMID: 14682690 DOI: 10.1021/jo035246b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oligonucleotides containing 2-thiouridine (s2U) in place of uridine form stable RNA duplexes with complementary RNAs. Particularly, this modified nucleoside has proved to recognize highly selectively adenosine, the genuine partner, without formation of a mismatched base pair with the guanosine counterpart. In this paper, we describe new methods for the synthesis of 2-thiouridine and various 2'-O-alkyl-2-thiouridine derivatives. Oligoribonucleotides having these modified nucleoside derivatives were synthesized, and their hybridization and structural properties were studied in detail by the 1H NMR analysis of these modified nucleosides and Tm experiments of RNA duplexes with their complementary RNA strands.
Collapse
Affiliation(s)
- Itaru Okamoto
- Department of Life Science and Frontier Collaborative Research Center, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | | | | | | |
Collapse
|
31
|
Lönnberg T, Mikkola S. Hydrolysis of 2‘,3‘-O-methyleneadenos-5‘-yl Bis(2‘,5‘-di-O-methylurid-3‘-yl) Phosphate, a Sugar O-Alkylated Trinucleoside 3‘,3‘,5‘-Monophosphate: Implications for the Mechanism of Large Ribozymes. J Org Chem 2004; 69:802-10. [PMID: 14750807 DOI: 10.1021/jo035094k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrolytic reactions of 2',3'-O-methyleneadenos-5'-yl bis(2',5'-di-O-methylurid-3'-yl) phosphate (1), a sugar O-alkylated trinucleoside 3',3',5'-monophosphate, have been followed by RP HPLC over a wide pH range. Under neutral and mildly acidic conditions, the only reaction observed was a pH-independent cleavage of the O-C5' bond of the 5'-linked nucleoside. Under more alkaline conditions nucleophilic attack by hydroxide ion starts to compete. The reaction is first order in [OH(-)] and becomes predominant at pH 10. Each of the 3'-linked nucleosides is displaced 2.9 times as readily as the 5'-linked one. To determine the beta(lg) value for the hydroxide ion catalyzed hydrolysis of 1, two diesters (2a,b) having 2',3'-O-methyleneadenosine (7) and 2',5'-di-O-methyluridine (4) as leaving groups were hydrolyzed under alkaline conditions. Since the beta(lg) value for this reaction is known, DeltapK(a) between 4 and 7 could be calculated. The beta(lg) for the hydrolysis of 1 was estimated to be -0.5 with use of this information. The mechanisms of the partial reactions and the role of leaving group properties in ribozyme reactions of large ribozymes are discussed.
Collapse
Affiliation(s)
- Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland.
| | | |
Collapse
|
32
|
Ozaki H, Nakajima K, Tatsui K, Izumi C, Kuwahara M, Sawai H. Convenient synthesis of oligodeoxyribonucleotides bearing arabinofuranosyl pyrimidine derivatives and its duplex formation with complementary DNA. Bioorg Med Chem Lett 2003; 13:2441-3. [PMID: 12852939 DOI: 10.1016/s0960-894x(03)00500-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The oligodeoxyribonucleotides bearing 2,2'-anhydro-beta-D-arabinofuranosyluracil derivatives were synthesized and the modified residue was converted to beta-D-arabinofuranosyluracil derivatives or beta-D-arabinofuranosylisocytosine derivatives by post-synthetic modification method. The melting profiles of their ODNs with complementary DNA were studied.
Collapse
Affiliation(s)
- Hiroaki Ozaki
- Department of Chemistry, Faculty of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan.
| | | | | | | | | | | |
Collapse
|
33
|
Jeannot F, Gosselin G, Mathé C. Synthesis and antiviral evaluation of 2'-deoxy-2'-C-trifiuoromethyl beta-D-ribonucleoside analogues bearing the five naturally occurring nucleic acid bases. Org Biomol Chem 2003; 1:2096-102. [PMID: 12945900 DOI: 10.1039/b303093h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
2'-Deoxy-2'-C-trifluoromethyl-beta-D-ribonucleoside derivatives bearing the five naturally occurring acid bases have been synthesized. All these derivatives were prepared by glycosylation reactions of purine and pyrimidine bases with a suitable peracylated 2-deoxy-2-C-trifluoromethyl sugar precursor to afford anomeric mixtures of protected nucleosides. After separation and deprotection, the resulting beta-nucleoside analogues were tested for their activity against HIV, HBV and several RNA viruses. However, none of these compounds showed significant antiviral activity nor cytotoxicity.
Collapse
Affiliation(s)
- Frédéric Jeannot
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, UMR 5625 CNRS-Université Montpellier II, case courrier 008, Place Eugene Bataillon, 34095 Montpellier Cedex 5, France
| | | | | |
Collapse
|
34
|
Martin P. Ein neuer Zugang zu 2′-O-(2-Methoxyethyl)ribonucleosiden ausgehend vonD-Glucose. Helv Chim Acta 2003. [DOI: 10.1002/hlca.200390013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
35
|
Botta M, Piero Stasi L, Mugnaini C, Alcaro S, Corelli F. Synthesis and Conformational Studies of 3'-(2'-Aminoborane-2'-deoxyuridyl)-5'-thymidilyl Hydrogen Phosphate to be Used in the Construction of Oligonucleotide Sequences. HETEROCYCLES 2003. [DOI: 10.3987/com-03-s56] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
36
|
Wen K, Chow S, Sanghvi YS, Theodorakis EA. Synthesis of 2'-O-methoxyethylguanosine using a novel silicon-based protecting group. J Org Chem 2002; 67:7887-9. [PMID: 12398522 DOI: 10.1021/jo025970e] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A short and efficient synthesis of 2'-O-methoxyethylguanosine (8) is described. Central to this strategy is the development of a novel silicon-based protecting group (MDPSCl(2), 2) used to protect the 3',5'-hydroxyl groups of the ribose. Silylation of guanosine with 2 proceeded with excellent regioselectivity and in 79% yield. Alkylation of the 2'-hydroxyl group of 6 proceeded with methoxyethyl bromide and NaHMDS and afforded compound 7 in 85% yield, without any noticeable cleavage of the silyl protecting group and without the need to protect the guanine base moiety. Finally, deprotection of 7 was achieved using TBAF and produced 8 in 97% yield.
Collapse
Affiliation(s)
- Ke Wen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla 92093-0358, USA
| | | | | | | |
Collapse
|