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Vázquez-Domínguez I, Garanto A, Collin RWJ. Molecular Therapies for Inherited Retinal Diseases-Current Standing, Opportunities and Challenges. Genes (Basel) 2019; 10:genes10090654. [PMID: 31466352 PMCID: PMC6770110 DOI: 10.3390/genes10090654] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/23/2019] [Accepted: 08/26/2019] [Indexed: 12/15/2022] Open
Abstract
Inherited retinal diseases (IRDs) are both genetically and clinically highly heterogeneous and have long been considered incurable. Following the successful development of a gene augmentation therapy for biallelic RPE65-associated IRD, this view has changed. As a result, many different therapeutic approaches are currently being developed, in particular a large variety of molecular therapies. These are depending on the severity of the retinal degeneration, knowledge of the pathophysiological mechanism underlying each subtype of IRD, and the therapeutic target molecule. DNA therapies include approaches such as gene augmentation therapy, genome editing and optogenetics. For some genetic subtypes of IRD, RNA therapies and compound therapies have also shown considerable therapeutic potential. In this review, we summarize the current state-of-the-art of various therapeutic approaches, including the pros and cons of each strategy, and outline the future challenges that lie ahead in the combat against IRDs.
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Affiliation(s)
- Irene Vázquez-Domínguez
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands
| | - Alejandro Garanto
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
| | - Rob W J Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
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Vejlegaard K, Wegeberg C, McKee V, Wengel J. Novel conformationally constrained 2'-C-methylribonucleosides: synthesis and incorporation into oligonucleotides. Org Biomol Chem 2019; 16:1312-1321. [PMID: 29392247 DOI: 10.1039/c7ob02663c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Synthesis of two novel conformationally constrained bicyclic ribonucleoside phosphoramidites bearing a 2'-C-methyl substituent has been accomplished. These phosphoramidites were used to incorporate the corresponding 2'-C-methyl nucleotides into oligonucleotides and to study their effects on duplex thermal stability. Whereas the C2'-O4'-linked LNA-type derivative induced severe destabilization of duplexes formed with complementary DNA and RNA, the C3'-O4'-linked derivative induced RNA-selective hybridization with increased affinity relative to that of the unmodified DNA-based probe.
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Affiliation(s)
- Kim Vejlegaard
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark. jwe@sdu
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Plashkevych O, Li Q, Chattopadhyaya J. How RNase HI (Escherichia coli) promoted site-selective hydrolysis works on RNA in duplex with carba-LNA and LNA substituted antisense strands in an antisense strategy context? MOLECULAR BIOSYSTEMS 2018; 13:921-938. [PMID: 28352859 DOI: 10.1039/c6mb00762g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A detailed kinetic study of 36 single modified AON-RNA heteroduplexes shows that substitution of a single native nucleotide in the antisense strand (AON) by locked nucleic acid (LNA) or by diastereomerically pure carba-LNA results in site-dependent modulation of RNase H promoted cleavage of complementary mRNA strands by 2 to 5 fold at 5'-GpN-3' cleavage sites, giving up to 70% of the RNA cleavage products. The experiments have been performed using RNase HI of Escherichia coli. The 2nd best cleavage site, being the 5'-ApN-3' sites, cleaves up to 23%, depending upon the substitution site in 36 isosequential complementary AONs. A comparison of the modified AON promoted RNA cleavage rates with that of the native AON shows that sequence-specificity is considerably enhanced as a result of modification. Clearly, relatively weaker 5'-purine (Pu)-pyrimidine (Py)-3' stacking in the complementary RNA strand is preferred (giving ∼90% of total cleavage products), which plays an important role in RNase H promoted RNA cleavage. A plausible mechanism of RNase H mediated cleavage of the RNA has been proposed to be two-fold, dictated by the balancing effect of the aromatic character of the purine aglycone: first, the locally formed 9-guanylate ion (pKa 9.3, ∼18-20% N1 ionized at pH 8) alters the adjoining sugar-phosphate backbone around the scissile phosphate, transforming its sugar N/S conformational equilibrium, to preferential S-type, causing preferential cleavage at 5'-GpN-3' sites around the center of 20 mer complementary mRNA. Second, the weaker nearest-neighbor strength of 5'-Pu-p-Py-3' stacking promotes preferential 5'-GpN-3' and 5'-ApN-3' cleavage, providing ∼90% of the total products, compared to ∼50% in that of the native one, because of the cLNA/LNA substituent effect on the neighboring 5'-Pu-p-Py-3' sites, providing both local steric flexibility and additional hydration. This facilitates both the water and water/Mg2+ ion availability at the cleavage site causing sequence-specific hydrolysis of the phosphodiester bond of scissile phosphate. The enhancement of the total rate of cleavage of the complementary mRNA strand by up to 25%, presented in this work, provides opportunities to engineer a single modification site in appropriately substituted AONs to design an effective antisense strategy based on the nucleolytic stability of the AON strand versus RNase H capability to cleave the complementary RNA strand.
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Affiliation(s)
- Oleksandr Plashkevych
- Chemical Biology Program, Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 581, SE-751 23 Uppsala, Sweden.
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Kapoor R, Tripathi S, Singh SN, Keshari T, Yadav LDS. Visible light triggered regioselective ring expansion of N-tosylaziridines: An efficient approach to 2-nitroazetidines. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.08.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Plashkevych O, Upadhayaya RS, Chattopadhyaya J. Carbocyclic C-C Bond Formation: Intramolecular Radical Ring Closure to Yield Diastereomerically Pure (7'S-Me- or 7'R-Me-) Carba-LNA Nucleotide Analogs. ACTA ACUST UNITED AC 2017. [PMID: 28628208 DOI: 10.1002/cpnc.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In light of the impressive gene-silencing properties of carba-LNA modified oligo DNA and RNA, both in antisense RNA and siRNA approaches, which have been confirmed as proof-of-concept for biochemical applications in post-transcriptional gene silencing, we envision the true potential of carba-LNA modifications to be revealed soon. Herein we provide detailed protocols for synthesis of carba-LNA-A, -G, -5-Me C, and -T nucleosides on a medium/large scale (gram scale), as well as important guidelines for incorporation of these modified carba-LNAs into DNA or RNA oligonucleotides. Creation of a stereoselective C-C bond during the 5-exo radical intramolecular cyclization involves trapping of a C2' radical intermediate intramolecularly by the vicinal double bond of a C4'-tethered ─CH2 -CH═CH2 group. All diastereomers of substituted carba-LNAs are now available in pure form. The present procedure allows carba-LNA to be commercialized for medicinal or biotechnological purposes. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Ram Shankar Upadhayaya
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,Bioimics AB, Uppsala, Sweden
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6
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Mehra V, Lumb I, Anand A, Kumar V. Recent advances in synthetic facets of immensely reactive azetidines. RSC Adv 2017. [DOI: 10.1039/c7ra08884a] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Recent developments in synthetic strategies towards functionalized azetidines along with their versatility as heterocyclic synthons.
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Affiliation(s)
- Vishu Mehra
- Department of Chemistry
- Hindu College
- Amritsar-143005
- India
| | - Isha Lumb
- Department of Chemistry
- Baring Union Christian College
- Batala-143505
- India
| | - Amit Anand
- Department of Chemistry
- Khalsa College
- Amritsar-143005
- India
| | - Vipan Kumar
- Department of Chemistry
- Guru Nanak Dev University
- Amritsar-143005
- India
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Bornschein C, Lennox AJJ, Werkmeister S, Junge K, Beller M. A Mild and Selective Reduction of β-Lactams: Rh-Catalyzed Hydrosilylation towards Important Pharmacological Building Blocks. European J Org Chem 2015. [DOI: 10.1002/ejoc.201403655] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Lensen N, Marais J, Brigaud T. Straightforward synthesis of novel enantiopure α-trifluoromethylated azetidine 2-carboxylic acid and homoserines. Org Lett 2015; 17:342-5. [PMID: 25560883 DOI: 10.1021/ol503448w] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The straightforward syntheses of enantiopure (2R)-2-trifluoromethyl-2-carboxyazetidine and (R)- and (S)-trifluoromethylhomoserines are reported. The key step is a Strecker-type reaction on a common chiral CF3-containing bicyclic oxazolidine intermediate obtained by a condensation reaction of (R)-phenylglycinol and ethyl-4,4,4-trifluoroacetoacetate (ETFAA).
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Affiliation(s)
- Nathalie Lensen
- Laboratoire de Chimie Biologique (LCB), EA 4505, Université de Cergy-Pontoise , 5 Mail, Gay-Lussac, Neuville sur Oise, 95000 Cergy-Pontoise Cedex, France
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9
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Barman J, Gurav D, Oommen OP, Varghese OP. 2′-N-Guanidino,4′-C-ethylene bridged thymidine (GENA-T) modified oligonucleotide exhibits triplex formation with excellent enzymatic stability. RSC Adv 2015. [DOI: 10.1039/c4ra14721a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We present the synthesis and characterization of 2′-N-guanidino,4′-C-ethylene bridged thymidine (GENA-T) modified oligo-DNA that forms a stable triplex (ΔTm +9.5 °C) with exceptional nuclease stability.
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Affiliation(s)
- Jharna Barman
- Agricultural and Ecological Research Unit
- Biological Science Division
- Indian Statistical Institute
- Kolkata 700108
- India
| | - Deepanjali Gurav
- Polymer Chemistry Division
- Department of Chemistry
- The Ångström Laboratory
- Uppsala University
- 751 21 Uppsala
| | - Oommen P. Oommen
- Polymer Chemistry Division
- Department of Chemistry
- The Ångström Laboratory
- Uppsala University
- 751 21 Uppsala
| | - Oommen P. Varghese
- Polymer Chemistry Division
- Department of Chemistry
- The Ångström Laboratory
- Uppsala University
- 751 21 Uppsala
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10
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Diastereoselective synthesis of 2,3-disubstituted 1-arylazetidines via NaBH4-promoted facile reduction of C-3 functionalized azetidin-2-ones. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.06.126] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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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]
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12
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Synthesis of piperidin-4-ones starting from 2-(2-bromo-1,1-dimethylethyl)azetidines and 2-(2-mesyloxyethyl)azetidines through a ring expansion–oxidation protocol. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.01.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Faigl F, Kovács E, Turczel G, Szöllősy Á, Mordini A, Balázs L, Holczbauer T, Czugler M. Novel stereoselective synthesis of 1,2,3-trisubstituted azetidines. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.tetasy.2012.10.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zhou C, Chattopadhyaya J. Intramolecular free-radical cyclization reactions on pentose sugars for the synthesis of carba-LNA and carba-ENA and the application of their modified oligonucleotides as potential RNA targeted therapeutics. Chem Rev 2012; 112:3808-32. [PMID: 22530946 DOI: 10.1021/cr100306q] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Chuanzheng Zhou
- Chemical Biology Program, Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Sweden
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Aralov AV, Klykov VN, Chakhmakhcheva OG, Efimov VA. [Monomers containing 2'-o-alkoxymethyl groups as synthons for the synthesis of oligoribonucleotides by the phosphotriester method]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012; 37:654-61. [PMID: 22332361 DOI: 10.1134/s1068162011050025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A general scheme for the synthesis of ribonucleotide monomers containing alkoxymethyl group in 2'-O-position for the solid-phase phosphotriester oligonucleotide synthesis using O-nucleophilic intramolecular catalysis has been developed. In particular, the monomers containing 2'-O-modifying 2-azidoethoxymethyl, propargyloxymethyl, or 3,4-cyclocarbonatebutoxymethyl groups has been prepared.
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Plashkevych O, Chattopadhyaya J. Molecular structure of the core-modified siRNA duplexes containing diastereomeric pair of [C6'(R)-OH]- versus [C6'(S)-OH]-carba-LNAs suggests a model for RNAi action. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2012; 30:815-25. [PMID: 22060548 DOI: 10.1080/15257770.2011.586956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Molecular structures of native and a pair of modified small interfering RNA-RNA duplexes containing carbocyclic [6 '-(R)-OH/7 '-(S)-methyl]- and [6 '-(S)-OH/7 '-(S)-methyl]-carba-LNA-thymine nucleotides, which are two diastereomeric analogs of the native T nucleotide, incorporated at position 13 in the antisense (AS) strand of siRNA, have been simulated using molecular mechanics/dynamics techniques. The main aim of the project has been to find a plausible structural explanation of why modification of siRNA at T(13) position by the [6 '(R)-O-(p-Toluoyl)-7 '(S)-methyl]-carba-LNA-Thymine [IC(50) of 3.32 ± 0.17 nM] is ca 24 times more active as an RNA silencing agent against the target HIV-1 TAR RNA than the [6 '(S)-O-(p-Toluoyl)-7 '(S)-methyl]-counterpart [IC(50) of 79.8 ± 17 nM] [1]. The simulations reveal that introduction of both C6 '(R)-OH and C6 '(S)-OH stereoisomers does not lead even to local perturbation of the siRNA-RNA duplex structures compared to the native, and the only significant difference between 6 '(S)- and 6 '(R)-diastereomers found is the exposure of the 6 '-OH group of the 6 '(R)-diastereoisomer toward the edge of the duplex while the 6 '-hydroxyl group of the 6 '(S)-diastereoisomer is somewhat buried in the minor groove of the duplex. This rules out a hypothesis about any possible local distortion by the nature of chemical modification of the siRNA-target the RNA duplex, which might have influenced the formation of the effective RNA silencing complex (RISC) and puts some weight on the hypothesis about the 6 '-hydroxy group being directly involved with most probably Ago protein, since it is known from exhaustive X-ray studies [2, 3] that the core residues are indeed involved with hydrogen bonding with the internucleotidyl phosphates. Further systematic investigation is in progress to map the position-dependent functional and nonfunctional interactions of the modified [6 '(R or S)-O-(p-Toluoyl)-7 '(S)-methyl]-carba-LNA-T with the Ago2 protein of the RISC.
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Affiliation(s)
- Oleksandr Plashkevych
- Department of Cell and Molecular Biology, Program of Chemical Biology, Biomedical Center, Uppsala University, Uppsala, Sweden.
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Liboska R, Snášel J, Barvík I, Buděšínský M, Pohl R, Točík Z, Páv O, Rejman D, Novák P, Rosenberg I. 4'-Alkoxy oligodeoxynucleotides: a novel class of RNA mimics. Org Biomol Chem 2011; 9:8261-7. [PMID: 22051918 DOI: 10.1039/c1ob06148h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
4'-Alkoxy-oligothymidylates were prepared as model compounds to study the influence of a C4'-alkoxy group on hybridisation. The phosphodiester homooligomers (15 units long) containing either a 4'-methoxy or 4'-(2-methoxyethoxy) group were found to display increased hybridisation with both dA(15) and rA(15) complementary counterparts compared to the natural oligothymidylate. In addition, we found their hybridisation behaviour to be similar to that of the regioisomeric 2'-O-methyl-oligothymidylate. The formed complexes (duplexes and triplexes) were studied using UV spectroscopy and polyacrylamide gel electrophoresis (PAGE). Structural background of the hybridization behaviour was examined using NMR and MDS. The favourable hybridisation properties of the 4'-alkoxyoligothymidylates indicated that 4'-alkoxy modified nucleotides are promising compounds for the assembly of chimeric oligonucleotides with tunable properties.
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Affiliation(s)
- Radek Liboska
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v. v. i., Flemingovo 2, 166 10 Prague 6, Czech Republic
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Mollet K, Catak S, Waroquier M, Van Speybroeck V, D’hooghe M, De Kimpe N. Stereoselective Synthesis of cis-3,4-Disubstituted Piperidines through Ring Transformation of 2-(2-Mesyloxyethyl)azetidines. J Org Chem 2011; 76:8364-75. [DOI: 10.1021/jo201556t] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Karen Mollet
- Department of Sustainable Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Saron Catak
- Center for Molecular Modeling, Ghent University (Member of QCMM-Alliance Ghent-Brussels), Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Michel Waroquier
- Center for Molecular Modeling, Ghent University (Member of QCMM-Alliance Ghent-Brussels), Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Veronique Van Speybroeck
- Center for Molecular Modeling, Ghent University (Member of QCMM-Alliance Ghent-Brussels), Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Matthias D’hooghe
- Department of Sustainable Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Norbert De Kimpe
- Department of Sustainable Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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Pradhan TK, Krishnan KS, Vasse JL, Szymoniak J. Access to Enantiomerically Enriched cis-2,3-Disubstituted Azetidines via Diastereoselective Hydrozirconation. Org Lett 2011; 13:1793-5. [DOI: 10.1021/ol200323r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Tarun K. Pradhan
- Institut de Chimie Moléculaire de Reims, CNRS (UMR 6229) and Université de Reims, 51687 Reims Cedex 2, France
| | - K. Syam Krishnan
- Institut de Chimie Moléculaire de Reims, CNRS (UMR 6229) and Université de Reims, 51687 Reims Cedex 2, France
| | - Jean-Luc Vasse
- Institut de Chimie Moléculaire de Reims, CNRS (UMR 6229) and Université de Reims, 51687 Reims Cedex 2, France
| | - Jan Szymoniak
- Institut de Chimie Moléculaire de Reims, CNRS (UMR 6229) and Université de Reims, 51687 Reims Cedex 2, France
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Krishna Reddy VVRM, Udaykiran D, Chintamani U, Mahesh Reddy E, Kameswararao C, Madhusudhan G. Development of an Optimized Process for the Preparation of 1-Benzylazetidin-3-ol: An Industrially Important Intermediate for Substituted Azetidine. Org Process Res Dev 2011. [DOI: 10.1021/op100247m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- V. V. R. M. Krishna Reddy
- Research and Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India
| | - D. Udaykiran
- Research and Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India
| | - U.S. Chintamani
- Research and Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India
| | - E. Mahesh Reddy
- Research and Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India
| | - Ch. Kameswararao
- Analytical Research and Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India
| | - G. Madhusudhan
- Research and Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India
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Dutta S, Bhaduri N, Rastogi N, Chandel SG, Vandavasi JK, Upadhayaya RS, Chattopadhyaya J. Carba-LNA modified siRNAs targeting HIV-1 TAR region downregulate HIV-1 replication successfully with enhanced potency. MEDCHEMCOMM 2011. [DOI: 10.1039/c0md00225a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Rai A, Yadav LDS. Strategic applications of Baylis–Hillman adducts to general syntheses of 3-nitroazetidines. Org Biomol Chem 2011; 9:8058-61. [DOI: 10.1039/c1ob06274c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Zhou C, Chattopadhyaya J. Why Carba-LNA-modified oligonucleotides show considerably improved 3'-exonuclease stability compared to that of the LNA modified or the native counterparts: A Michaelis-Menten kinetic analysis. J Org Chem 2010; 75:2341-9. [PMID: 20225808 DOI: 10.1021/jo100170g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In this study, 12 different native or LNA, carba-LNA-modified dinucleoside phosphates were designed as simple chemical models to study how carba-LNA modifications improve the 3'-exonuclease (SVPDE in this study) resistance of internucleotidic phosphate compared to those exhibited by LNA-modified and the native counterparts. Michaelis-Menten kinetic studies for dimers 3 - 7, in which the LNA or carba-LNA modifications are located at the 5'-end, showed that (i) increased 3'-exonuclease resistance of (5')[LNA-T](p)T (3) compared to the native (5')T(p)T (1) was mainly attributed to steric hindrance imposed by the LNA modification that retards the nuclease binding (K(M)) and (ii) digestion of (5')[carba-LNA-dT](p)T (4) and (5')[LNA-T](p)T (3), however, exhibit similar K(M)s, whereas the former shows a 100x decrease in K(cat) and is hence more stable than the latter. By studying the correlation between log k(cat) and pK(a) of the departing 3'(or 6')-OHs for 3-7, we found the pK(a) of 3'-OH of carba-LNA-T was 1.4 pK(a) units higher than that of LNA-T, and this relatively less acidic character of the 3'-OH in the former leads to the 100x decrease in the catalytic efficiency for the digestion of (5')[carba-LNA-T](p)T (4). In contrast, Michaelis-Menten kinetic studies for dimers 9-12, with the LNA or carba-LNA modifications at the 3'-end, showed that the digestion of (5')T(p)[LNA-T] (9) exhibited similar K(M) but k(cat) decreased around 40 times compared to that of the native (5')T(p)T (1). Similar k(cat) values have been observed for digestion of (5')T(p)[carba-LNA-T] (10) and (5')T(p)[LNA-T] (9). The higher stability of carba-LNA modified dimer 10 compared with LNA modified dimer 9 comes solely from the increased K(M).
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Affiliation(s)
- Chuanzheng Zhou
- Bioorganic Chemistry Program, Department of Cell and Molecular Biology, Box 581, Biomedical Centre, Uppsala University, SE-751 23 Uppsala, Sweden
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Reddy VVRMK, Babu KK, Ganesh A, Srinivasulu P, Madhusudhan G, Mukkanti K. Improved Process for the Preparation of 1-Benzhydrylazetidin-3-ol: Development of an Efficient Synthesis and Identification of Process-related Impurities and/or Intermediates. Org Process Res Dev 2010. [DOI: 10.1021/op100100y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- V. V. R. M. Krishna Reddy
- Research & Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India, Analytical Research & Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India, and Centre for pharmaceutical sciences, Institute of Science and Technology, Jawaharlal Nehru Technological University, Kukatpally, Hyderabad, Andhra Pradesh 500072, India
| | - K. Kishore Babu
- Research & Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India, Analytical Research & Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India, and Centre for pharmaceutical sciences, Institute of Science and Technology, Jawaharlal Nehru Technological University, Kukatpally, Hyderabad, Andhra Pradesh 500072, India
| | - A. Ganesh
- Research & Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India, Analytical Research & Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India, and Centre for pharmaceutical sciences, Institute of Science and Technology, Jawaharlal Nehru Technological University, Kukatpally, Hyderabad, Andhra Pradesh 500072, India
| | - P. Srinivasulu
- Research & Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India, Analytical Research & Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India, and Centre for pharmaceutical sciences, Institute of Science and Technology, Jawaharlal Nehru Technological University, Kukatpally, Hyderabad, Andhra Pradesh 500072, India
| | - G. Madhusudhan
- Research & Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India, Analytical Research & Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India, and Centre for pharmaceutical sciences, Institute of Science and Technology, Jawaharlal Nehru Technological University, Kukatpally, Hyderabad, Andhra Pradesh 500072, India
| | - K. Mukkanti
- Research & Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India, Analytical Research & Development, Inogent Laboratories Private Limited, (A GVK BIO Company), 28A, IDA, Nacharam, Hyderabad, Andhra Pradesh 500076, India, and Centre for pharmaceutical sciences, Institute of Science and Technology, Jawaharlal Nehru Technological University, Kukatpally, Hyderabad, Andhra Pradesh 500072, India
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25
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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
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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.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan
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26
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Medjahdi M, González-Gómez JC, Foubelo F, Yus M. Stereoselective synthesis of azetidines and pyrrolidines from N-tert-butylsulfonyl(2-aminoalkyl)oxiranes. J Org Chem 2009; 74:7859-65. [PMID: 19764731 DOI: 10.1021/jo9016666] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Base-induced cyclization of enantiopure (2-aminoalkyl)oxiranes allowed the stereospecific formation of pyrrolidin-3-ols and/or 2-(hydroxymethyl)azetidines, depending on the reaction conditions. The oxidation of 2-(hydroxymethyl)azetidines led to azetidine-2-carboxylic acids in high yields.
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Affiliation(s)
- Mohamed Medjahdi
- Departamento de Química Orgánica, Facultad de Ciencias and Instituto de Síntesis Orgánica, Universidad de Alicante, Apdo. 99, 03080 Alicante, Spain
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Brandi A, Cicchi S, Cordero FM. Novel Syntheses of Azetidines and Azetidinones. Chem Rev 2008; 108:3988-4035. [DOI: 10.1021/cr800325e] [Citation(s) in RCA: 395] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alberto Brandi
- Dipartimento di Chimica Organica “Ugo Schiff”, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi - HeteroBioLab, Università degli Studi di Firenze, via della Lastruccia 13, 50019 Sesto F.no (FI), Italy
| | - Stefano Cicchi
- Dipartimento di Chimica Organica “Ugo Schiff”, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi - HeteroBioLab, Università degli Studi di Firenze, via della Lastruccia 13, 50019 Sesto F.no (FI), Italy
| | - Franca M. Cordero
- Dipartimento di Chimica Organica “Ugo Schiff”, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi - HeteroBioLab, Università degli Studi di Firenze, via della Lastruccia 13, 50019 Sesto F.no (FI), Italy
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28
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Honcharenko D, Zhou C, Chattopadhyaya J. Modulation of pyrene fluorescence in DNA probes depends upon the nature of the conformationally restricted nucleotide. J Org Chem 2008; 73:2829-42. [PMID: 18331060 DOI: 10.1021/jo702747w] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The DNA probes (ODNs) containing a 2'-N-(pyren-1-yl)-group on the conformationally locked nucleosides [2'-N-(pyren-1-yl)carbonyl-azetidine thymidine, Aze-pyr (X), and 2'-N-(pyren-1-yl)carbonyl-aza-ENA thymidine, Aza-ENA-pyr (Y)], show that they can bind to complementary RNA more strongly than to the DNA. The Aze-pyr (X) containing ODNs with the complementary DNA and RNA duplexes showed an increase in the fluorescence intensity (measured at lambda em approximately 376 nm) depending upon the nearest neighbor at the 3'-end to X [dA ( approximately 12-20-fold) > dG ( approximately 9-20-fold) > dT ( approximately 2.5-20-fold) > dC ( approximately 6-13-fold)]. They give high fluorescence quantum yields (Phi F = 0.13-0.89) as compared to those of the single-stranded ODNs. The Aza-ENA-pyr (Y)-modified ODNs, on the other hand, showed an enhancement of the fluorescence intensity only with the complementary DNA (1.4-3.9-fold, Phi F = 0.16-0.47); a very small increase in fluorescence is also observed with the complementary RNA (1.1-1.7-fold, Phi F = 0.17-0.22), depending both upon the site of the Y modification introduced as well as on the chemical nature of the nucleobase adjacent to the modification site into the ODN. The fluorescence properties, thermal denaturation experiments, absorption, and circular dichroism (CD) studies with the X- and Y-modified ODNs in the form of matched homo- and heteroduplexes consistently suggested (i) that the orientation of the pyrene moiety is outside the helix of the nucleic acid duplexes containing a dT-d/rA base pair at the 3'-end of the modification site for both X and Y types of modifications, and (ii) that the microenvironment around the pyrene moiety in the ODN/DNA and ODN/RNA duplexes is dictated by the chemical nature of the conformational constraint in the sugar moiety, as well as by the nature of neighboring nucleobases. The pyrene fluorescence emission in both X and Y types of the conformationally restricted nucleotides is found to be sensitive to a mismatched base present in the target RNA: (i) The X-modified ODN showed a decrease ( approximately 37-fold) in the fluorescence intensity (measured at lambda em approximately 376 nm) upon duplex formation with RNA containing a G nucleobase mismatch (dT-rG pair instead of dT-rA) opposite to the modification site. (ii) In contrast, the Y-modified ODN in the heteroduplex resulted in a approximately 3-fold increase in the fluorescence intensity upon dT-rG mismatch, instead of matched dT-rA pair, in the RNA strand. Our data corroborate that the pyrene moiety is intercalated in the X-modified mismatched ODN/RNA (G mismatch) heteroduplex as compared to that of the Y-modified ODN/RNA (G mismatch) heteroduplex, in which it is located outside the helix.
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Affiliation(s)
- Dmytro Honcharenko
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, Uppsala University, SE-75123 Uppsala, Sweden
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