1
|
Yan VC, Pham CD, Ballato ES, Yang KL, Arthur K, Khadka S, Barekatain Y, Shrestha P, Tran T, Poral AH, Washington M, Raghavan S, Czako B, Pisaneschi F, Lin YH, Satani N, Hammoudi N, Ackroyd JJ, Georgiou DK, Millward SW, Muller FL. Prodrugs of a 1-Hydroxy-2-oxopiperidin-3-yl Phosphonate Enolase Inhibitor for the Treatment of ENO1-Deleted Cancers. J Med Chem 2022; 65:13813-13832. [PMID: 36251833 PMCID: PMC9620261 DOI: 10.1021/acs.jmedchem.2c01039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cancers harboring homozygous deletion of the glycolytic enzyme enolase 1 (ENO1) are selectively vulnerable to inhibition of the paralogous isoform, enolase 2 (ENO2). A previous work described the sustained tumor regression activities of a substrate-competitive phosphonate inhibitor of ENO2, 1-hydroxy-2-oxopiperidin-3-yl phosphonate (HEX) (5), and its bis-pivaloyoxymethyl prodrug, POMHEX (6), in an ENO1-deleted intracranial orthotopic xenograft model of glioblastoma [Nature Metabolism 2020, 2, 1423-1426]. Due to poor pharmacokinetics of bis-ester prodrugs, this study was undertaken to identify potential non-esterase prodrugs for further development. Whereas phosphonoamidate esters were efficiently bioactivated in ENO1-deleted glioma cells, McGuigan prodrugs were not. Other strategies, including cycloSal and lipid prodrugs of 5, exhibited low micromolar IC50 values in ENO1-deleted glioma cells and improved stability in human serum over 6. The activity of select prodrugs was also probed using the NCI-60 cell line screen, supporting its use to examine the relationship between prodrugs and cell line-dependent bioactivation.
Collapse
Affiliation(s)
- Victoria C. Yan
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States,. Twitter: @victoriacyanide
| | - Cong-Dat Pham
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Elliot S. Ballato
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Kristine L. Yang
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Kenisha Arthur
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Sunada Khadka
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States,Department
of Cancer Biology, University of Texas MD
Anderson Cancer Center, Houston, Texas 77054, United States
| | - Yasaman Barekatain
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States,Department
of Cancer Biology, University of Texas MD
Anderson Cancer Center, Houston, Texas 77054, United States
| | - Prakriti Shrestha
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Theresa Tran
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Anton H. Poral
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Mykia Washington
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Sudhir Raghavan
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Barbara Czako
- Institute
of Applied Cancer Science, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Federica Pisaneschi
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Yu-Hsi Lin
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Nikunj Satani
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Naima Hammoudi
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Jeffrey J. Ackroyd
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Dimitra K. Georgiou
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Steven W. Millward
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Florian L. Muller
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| |
Collapse
|
2
|
Asanuma H, Kamiya Y, Kashida H, Murayama K. Xeno nucleic acids (XNAs) having non-ribose scaffolds with unique supramolecular properties. Chem Commun (Camb) 2022; 58:3993-4004. [DOI: 10.1039/d1cc05868a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA and RNA have significance as a genetic materials, therapeutic potential, and supramolecular properties. Advances in nucleic acid chemistry have enabled large-scale synthesis of DNA and RNA oligonucleotides and oligomers...
Collapse
|
3
|
Knouse KW, Flood DT, Vantourout JC, Schmidt MA, Mcdonald IM, Eastgate MD, Baran PS. Nature Chose Phosphates and Chemists Should Too: How Emerging P(V) Methods Can Augment Existing Strategies. ACS CENTRAL SCIENCE 2021; 7:1473-1485. [PMID: 34584948 PMCID: PMC8461637 DOI: 10.1021/acscentsci.1c00487] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Indexed: 05/27/2023]
Abstract
Phosphate linkages govern life as we know it. Their unique properties provide the foundation for many natural systems from cell biology and biosynthesis to the backbone of nucleic acids. Phosphates are ideal natural moieties; existing as ionized species in a stable P(V)-oxidation state, they are endowed with high stability but exhibit enzymatically unlockable potential. Despite intense interest in phosphorus catalysis and condensation chemistry, organic chemistry has not fully embraced the potential of P(V) reagents. To be sure, within the world of chemical oligonucleotide synthesis, modern approaches utilize P(III) reagent systems to create phosphate linkages and their analogs. In this Outlook, we present recent studies from our laboratories suggesting that numerous exciting opportunities for P(V) chemistry exist at the nexus of organic synthesis and biochemistry. Applications to the synthesis of stereopure antisense oligonucleotides, cyclic dinucleotides, methylphosphonates, and phosphines are reviewed as well as chemoselective modification to peptides, proteins, and nucleic acids. Finally, an outlook into what may be possible in the future with P(V) chemistry is previewed, suggesting these examples represent just the tip of the iceberg.
Collapse
Affiliation(s)
- Kyle W. Knouse
- Elsie
Biotechnologies, 4955
Directors Place, San Diego, California 92121, United States
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dillon T. Flood
- Elsie
Biotechnologies, 4955
Directors Place, San Diego, California 92121, United States
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Julien C. Vantourout
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael A. Schmidt
- Chemical
and Synthetic Development, Bristol Myers
Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Ivar M. Mcdonald
- Small
Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Martin D. Eastgate
- Chemical
and Synthetic Development, Bristol Myers
Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Phil S. Baran
- Elsie
Biotechnologies, 4955
Directors Place, San Diego, California 92121, United States
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| |
Collapse
|
4
|
Stasińska AR, Putaj P, Chmielewski MK. Disulfide bridge as a linker in nucleic acids’ bioconjugation. Part I: An overview of synthetic strategies. Bioorg Chem 2019; 92:103223. [DOI: 10.1016/j.bioorg.2019.103223] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/26/2019] [Accepted: 08/26/2019] [Indexed: 12/23/2022]
|
5
|
|
6
|
Flamme M, McKenzie LK, Sarac I, Hollenstein M. Chemical methods for the modification of RNA. Methods 2019; 161:64-82. [PMID: 30905751 DOI: 10.1016/j.ymeth.2019.03.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
RNA is often considered as being the vector for the transmission of genetic information from DNA to the protein synthesis machinery. However, besides translation RNA participates in a broad variety of fundamental biological roles such as gene expression and regulation, protein synthesis, and even catalysis of chemical reactions. This variety of function combined with intricate three-dimensional structures and the discovery of over 100 chemical modifications in natural RNAs require chemical methods for the modification of RNAs in order to investigate their mechanism, location, and exact biological roles. In addition, numerous RNA-based tools such as ribozymes, aptamers, or therapeutic oligonucleotides require the presence of additional chemical functionalities to strengthen the nucleosidic backbone against degradation or enhance the desired catalytic or binding properties. Herein, the two main methods for the chemical modification of RNA are presented: solid-phase synthesis using phosphoramidite precursors and the enzymatic polymerization of nucleoside triphosphates. The different synthetic and biochemical steps required for each method are carefully described and recent examples of practical applications based on these two methods are discussed.
Collapse
Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Luke K McKenzie
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Ivo Sarac
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
| |
Collapse
|
7
|
Palumbo CM, Beal PA. Nucleoside analogs in the study of the epitranscriptome. Methods 2018; 156:46-52. [PMID: 30827466 DOI: 10.1016/j.ymeth.2018.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 09/27/2018] [Accepted: 10/13/2018] [Indexed: 01/15/2023] Open
Abstract
Over 150 unique RNA modifications are now known including several nonstandard nucleotides present in the body of messenger RNAs. These modifications can alter a transcript's function and are collectively referred to as the epitrancriptome. Chemically modified nucleoside analogs are poised to play an important role in the study of these epitranscriptomic marks. Introduced chemical features on nucleic acid strands provide unique structures or reactivity that can be used for downstream detection or quantification. Three methods are used in the field to synthesize RNA containing chemically modified nucleoside analogs. Nucleoside analogs can be introduced by metabolic labeling, via polymerases with modified nucleotide triphosphates or via phosphoramidite-based chemical synthesis. In this review, these methods for incorporation of nucleoside analogs will be discussed with specific recently published examples pertaining to the study of the epitranscriptome.
Collapse
Affiliation(s)
- Cody M Palumbo
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Peter A Beal
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA.
| |
Collapse
|
8
|
Schwenger A, Birchall N, Richert C. Solution-Phase Synthesis of Branched Oligonucleotides with up to 32 Nucleotides and the Reversible Formation of Materials. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700686] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Alexander Schwenger
- Institut für Organische Chemie; Universität Stuttgart; 70569 Stuttgart Germany
| | - Nicholas Birchall
- Institut für Organische Chemie; Universität Stuttgart; 70569 Stuttgart Germany
| | - Clemens Richert
- Institut für Organische Chemie; Universität Stuttgart; 70569 Stuttgart Germany
| |
Collapse
|
9
|
Abstract
Oligonucleotides carrying a variety of chemical modifications including conjugates are finding increasing applications in therapeutics, diagnostics, functional genomics, proteomics, and as research tools in chemical and molecular biology. The successful synthesis of oligonucleotides primarily depends on the use of appropriately protected nucleoside building blocks including the exocyclic amino groups of the nucleobases, the hydroxyl groups at the 2'-, 3'-, and 5'-positions of the sugar moieties, and the internucleotide phospho-linkage. This unit is a thoroughly revised update of the previously published version and describes the recent development of various protecting groups that facilitate reliable oligonucleotide synthesis. In addition, various protecting groups for the imide/lactam function of thymine/uracil and guanine, respectively, are described to prevent irreversible nucleobase modifications that may occur in the presence of reagents used in oligonucleotide synthesis. © 2017 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Geeta Meher
- Spring Bank Pharmaceuticals, Inc, Milford, Massachusetts
| | | | | |
Collapse
|
10
|
Zhang XH, Xu YZ. NMR studies on 4-thio-5-furan-modified and 4-thio-5-thiophene-modified nucleosides. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:887-892. [PMID: 27529164 DOI: 10.1002/mrc.4501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/03/2016] [Accepted: 08/12/2016] [Indexed: 06/06/2023]
Abstract
Systematic NMR characterization of 4-thio-5-furan-pyrimidine nucleosides or 4-thio-5-thiophene-pyrimidine nucleosides (ribonucleosides and 2'-deoxynucleosides) was performed. All proton and carbon signals of 4-thio-5-thiophene-ribouridine and related analogues were unambiguously assigned. The orientations of the base (4-thiouridine or its deoxy analogue) relative to the ring (furan or thiophene) are explored by a NMR approach and further supported by X-ray crystallographic studies. The procedures presented here would be applicable to other modified nucleosides and nucleotides. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Xiao-Hui Zhang
- College of Environment and Chemical Engineering, Dalian University, Dalian, 116622, China.
| | - Yao-Zhong Xu
- Department of Life, Health and Chemical Sciences, Open University, Walton Hall, Milton Keynes, MK7 6AA, UK.
| |
Collapse
|
11
|
Schott H, Häussler MP, Gowland P, Horber DH, Schwendener RA. Synthesis, and Some Properties of, Amphiphilic Dinucleoside Phosphate Derivatives of 3′-azido-2′,3′-dideoxythymidine (AZT). ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029400500606] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
N4-hexadecyl-5′-0-(4-monomethoxytrityl)-2′-deoxycytidine-3′-hydrogenphosphate was reacted with 3′-azido-2′,3′-dideoxythymidine (AZT) according to the hydrogenphosphate method to yield N4-hexadecyl-2′-deoxycytidylyl-(3′-5)-3′-azido-2′,3′-dideoxythymidine. N4-palmitoyl-5′-O-(4-monomethoxytrityl)-2′-deoxycytidine-3′-(2-chlorophenyl)-phosphate was condensed to AZT using the triester method to give N4-palmitoyl-2′-deoxycytidylyl-(3′-5′)-3,-azido-2′,3′-dideoxythymidine. Both dinucleosidephosphates have amphiphilic properties and represent a new class of AZT derivatives in which the polar AZT-5′-monophosphate is masked with lipophilic deoxycytidine residues of variable stability. The AZT derivatives are water soluble, by forming micelles, and as a result of their amphiphilic nature, they can be incorporated into the lipid membranes of liposomes. In contrast to the micellar drug preparations, the liposomal formulations were shown to exert no lytic activity on human erythrocytes. Both AZT derivatives have anti HIV-1 activity in vitro.
Collapse
Affiliation(s)
- H. Schott
- Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - M. P. Häussler
- Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - P. Gowland
- Division of Infectious Diseases, Department of Internal Medicine, University Hospital, CH-8091 Zürich, Switzerland
| | - D. H. Horber
- Division of Oncology, Department of Internal Medicine, University Hospital, CH-8091 Zürich, Switzerland
| | - R. A. Schwendener
- Division of Oncology, Department of Internal Medicine, University Hospital, CH-8091 Zürich, Switzerland
| |
Collapse
|
12
|
Bazin HG, Bess LS, Livesay MT, Mwakwari SC, Johnson DA. Phospholipidation of TLR7/8-active imidazoquinolines using a tandem phosphoramidite method. Tetrahedron Lett 2016; 57:2063-2066. [PMID: 32863446 PMCID: PMC7451945 DOI: 10.1016/j.tetlet.2016.03.091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A high-yielding and scalable phosphoramidite procedure was developed for the phospholipidation of TLR7/8-active imidazoquinolines. This method involves the reaction of a 1,2-diacyl- or dialkyl-sn-glycerol or 3-chlolesterylalkanol with 2-cyanoethyl N,N,N',N'-tetraisopropylphosphordiamidite in the presence of 1H-tetrazole followed by treatment of the resulting N,N'-diisopropylphosphoramidite lipid in situ with 1-imidazoquinolinylalkanols. The resulting phosphite can be purified or directly oxidized with t-butyl hydroperoxide. The cyanoethyl protecting group is then removed with triethylamine and the phospholipidated imidazoquinoline products isolated in good yield and purity by simple filtration.
Collapse
|
13
|
Matsuno Y, Shoji T, Kim S, Chiba K. Synthetic Method for Oligonucleotide Block by Using Alkyl-Chain-Soluble Support. Org Lett 2016; 18:800-3. [PMID: 26845521 DOI: 10.1021/acs.orglett.6b00077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A straightforward method for the synthesis of oligonucleotide blocks using a Cbz-type alkyl-chain-soluble support (Z-ACSS) attached to the 3'-OH group of 3'-terminal nucleosides was developed. The Z-ACSS allowed for the preparation of fully protected deoxyribo- and ribo-oligonucleotides without chromatographic purification and released dimer- to tetramer-size oligonucleotide blocks via hydrogenation using a Pd/C catalyst without significant loss or migration of protective groups such as 5'-end 4,4'-dimethoxtrityl, 2-cyanoethyl on internucleotide bonds, or 2'-TBS.
Collapse
Affiliation(s)
- Yuki Matsuno
- Laboratory of Bio-organic Chemistry, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Takao Shoji
- Laboratory of Bio-organic Chemistry, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Shokaku Kim
- Laboratory of Bio-organic Chemistry, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Kazuhiro Chiba
- Laboratory of Bio-organic Chemistry, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| |
Collapse
|
14
|
Christmann M, Hu J, Kitamura M, Stoltz B. Tetrahedron reports on organic chemistry. Tetrahedron 2015. [DOI: 10.1016/s0040-4020(15)00744-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
15
|
Rizzi V, Losito I, Ventrella A, Fini P, Agostiano A, Longobardi F, Cosma P. pH-related features and photostability of 4-thiothymidine in aqueous solution: an investigation by UV-visible, NMR and FTIR-ATR spectroscopies and by electrospray ionization mass spectrometry. RSC Adv 2014. [DOI: 10.1039/c4ra09747e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
16
|
Mensah E, Camasso N, Kaplan W, Nagorny P. Chiral Phosphoric Acid Directed Regioselective Acetalization of Carbohydrate-Derived 1,2-Diols. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304298] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
17
|
Mensah E, Camasso N, Kaplan W, Nagorny P. Chiral Phosphoric Acid Directed Regioselective Acetalization of Carbohydrate-Derived 1,2-Diols. Angew Chem Int Ed Engl 2013; 52:12932-6. [DOI: 10.1002/anie.201304298] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 07/29/2013] [Indexed: 01/21/2023]
|
18
|
Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2013. [DOI: 10.1016/s0040-4020(13)01252-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
19
|
Zhang X, Wang J, Xu YZ. Systematic assignment of NMR spectra of 5-substituted-4-thiopyrimidine nucleosides. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:523-529. [PMID: 23794140 DOI: 10.1002/mrc.3980] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 05/26/2013] [Accepted: 05/29/2013] [Indexed: 06/02/2023]
Abstract
Unambiguous characterization of 5-substituted-4-thiopyrimidine nucleosides (ribonucleosides and 2'-deoxynucleosides) was performed using NMR spectroscopy. Assignments of all proton and carbon signals of 5-bromo-4-thiouridine and related nucleosides were systematically carried out and firmly established by COSY and HMQC techniques. The NMR data of various 4-thiopyrimidine nucleosides are compared, and the key contributing factors discussed. The approach presented here is applicable to other modified nucleosides and nucleotides, as well as nucleobases.
Collapse
Affiliation(s)
- Xiaohui Zhang
- College of Environment and Chemical Engineering, Dalian University, Dalian 116622, China.
| | | | | |
Collapse
|
20
|
Aralov AV, Chakhmakhchieva OG. [Protection of 2'-hydroxyls in the chemical synthesis of oligoribonucleotides]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013; 39:3-25. [PMID: 23844504 DOI: 10.1134/s1068162013010020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The review is devoted to the chemical synthesis of oligoribonucleotides and the protecting groups used. In particular the existent methods of blocking 2'-OH function in nucleotide monomers for the RNA synthesis are discussed in detail.
Collapse
|
21
|
van der Heden van Noort GJ, van Delft P, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Filippov DV. Fully automated sequential solid phase approach towards viral RNA-nucleopeptides. Chem Commun (Camb) 2012; 48:8093-5. [PMID: 22781550 DOI: 10.1039/c2cc33477a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The synthesis of two ribonucleoprotein fragments of unprecedented complexity is reported. These hybrid biomolecules are prepared combining the use of an automated solid phase peptide and oligonucleotide synthesizer on a single solid support.
Collapse
|
22
|
Madsen AS, Wengel J. Oligonucleotides with 1,4-dioxane-based nucleotide monomers. J Org Chem 2012; 77:3878-86. [PMID: 22439826 DOI: 10.1021/jo300222q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An epimeric mixture of H-phosphonates 5R and 5S has been synthesized in three steps from known secouridine 1. Separation of the epimers has been accomplished by RP-HPLC, allowing full characterization and incorporation of monomers X and Y into 9-mer oligonucleotides using H-phosphonates building blocks 5R and 5S, respectively. A single incorporation of either monomer X or monomer Y in the central position of a DNA 9-mer results in decreased thermal affinity toward both DNA and RNA complements (ΔT(m) = -3.5 °C/-3.5 °C for monomer X and ΔT(m) = -11.0 °C/-6.5 °C for monomer Y). CD measurements do not reveal major rearrangements of the duplexes formed, but molecular modeling suggests that local rearrangement of the sugar phosphate backbone and decreased base interactions with neighboring bases might be the origin of the decreased stability of duplexes.
Collapse
Affiliation(s)
- Andreas S Madsen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | | |
Collapse
|
23
|
Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2011. [DOI: 10.1016/s0040-4020(11)00770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
24
|
Oh JM, Park DH, Choy JH. Integrated bio-inorganic hybrid systems for nano-forensics. Chem Soc Rev 2010; 40:583-95. [PMID: 21152667 DOI: 10.1039/c0cs00051e] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This tutorial review describes a new class of data processing system that applies information theory at the molecular level. We also summarize the recent multidisciplinary advances in biotechnology and nanotechnology that have facilitated the development of reliable nano-level code systems. After a brief introduction of information theory, we present possible ways to adapt this concept to the molecular world. This review explains the requirements and solutions for each step necessary to apply a nano code system to real products. Finally, we introduce a designed nano code system for agricultural products as one example of the many possible applications for nano codes.
Collapse
Affiliation(s)
- Jae-Min Oh
- Department of Chemistry and Medical Chemistry, College of Science and Technology, Yonsei University, Wonju, Gangwondo, Korea
| | | | | |
Collapse
|
25
|
Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2010. [DOI: 10.1016/s0040-4020(10)01735-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
26
|
van der Marel GA, Marugg JE, de Vroom E, Wille G, Tromp M, van Boeckel CAA, van Boom JH. Phosphotriester synthesis of DNA fragments on cellulose and polystyrene solid supports. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19821010702] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
27
|
den Hartog JAJ, van Boom JH. 4-Nitrophenyl 4-morpholinylphosphonochloridate: A convenient reagent for the synthesis of ribonucleoside mono-, di- and tri-phosphates. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19811000709] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
28
|
de Vroom E, Dreef CE, van den Elst H, van der Marel GA, van Boom JH. Preparation of internucleotide phosphate analogues via the corresponding H-phosphonate diester. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19881071004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
29
|
van Boeckel CAA, Visser GM, Hermans JPG, van Boom JH. Synthesis of a teichoic acid fragment of Bacillus subtilis
using a modified phosphotriester approach. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19831021208] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
30
|
Hermans JPG, Poot L, van der Marel GA, Hoogerhout P, Kloosterman M, van Boom JH, van Boeckel CAA, Evenberg D, Poolman JT. Synthesis of fragments of the capsular polysaccharide of Haemophilus influenzae type b: Part I. Preparation of suitably protected 1-O-β-D-ribofuranosyl-D-ribitol building blocks. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19871060905] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
31
|
de Rooij JFM, Wille-Hazeleger G, van Deursen PH, Serdijn J, van Boom JH. Synthesis of complementary DNA fragments via phosphotriester intermediates. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19790981105] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
32
|
Beld A, Claesen CAA, Roersma ES, Schippers WJM, Keizer LM, Tesser GI. Bis[2-(methylsulfonyl)ethyl] phosphochloridate, a new phosphorylating agent. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19841030604] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
33
|
van der Marel GA, Wille G, van Boom JH. Solid-phase synthesis of the RNA fragment: rAAGAAGAAGAAGA. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19821010703] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
34
|
Verdegaal CHM, Jansse PL, de Rooij JFM, Veeneman G, van Boom JH. A convenient synthesis of 2′-O
-acetal-N
2
-acyl derivatives of riboguanosine. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19811000507] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
35
|
Sund C, Rousse B, Puri N, Viswanadham G, Agback P, Sandström A, Glemarec C, Yamakage SI, Chattopadhyaya J. The Synthesis of Lariat-RNAs and their Conformational Analysis by NMR Spectroscopy: The Study of their Unique Self-Cleavage Reaction Modelling Some Catalytic RNAs (Ribozymes). ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bscb.19941030910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
36
|
Beaucage SL, Reese CB. Recent advances in the chemical synthesis of RNA. ACTA ACUST UNITED AC 2009; Chapter 2:Unit 2.16 1-31. [PMID: 19746354 DOI: 10.1002/0471142700.nc0216s38] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
As a consequence largely of recent developments in RNA interference (RNAi) research, the availability of rapid and efficient methods for the chemical synthesis of RNA sequences has become a matter of considerable urgency. This unit is concerned mainly with work that has been carried out, especially in the past decade, on the design of new and improved methods of RNA synthesis. The main criteria for the choice of protecting groups for the 2'-hydroxy functions of the ribonucleoside building blocks, which is arguably the most crucial strategic decision to be made, are discussed. A number of new ether-, acetal-, orthoester-, and ester-based 2'-protecting groups are described and their application, mainly in phosphoramidite-based solid-phase synthesis, is discussed in some detail. Brief consideration is also given to solution-phase RNA synthesis, which may well prove to be of great importance if a systemic drug is developed and multikilogram quantities of synthetic RNA sequences are required.
Collapse
|
37
|
Laba VI, Sviridova AV, Nesterov VN. Structural study of 2,4,6-triisopropylbenzenesulfonyl chloride. CRYSTALLOGR REP+ 2009. [DOI: 10.1134/s1063774509010088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
38
|
Abstract
A wide variety of p-tolyl thioriboside donors are examined for O-ribosylations of primary and secondary alcohols. p-Tolylsulfenyl trifluoromethanesulfonate (p-TolSOTf) is very effective in promoting O-ribosylations with p-tolyl thioriboside; all reactions are completed within 1-15 min to provide the desired products in good yield with reliable alpha/beta selectivity. A wide range of functional groups are tolerated under these conditions. The described O-ribosylation conditions are very useful for the generation of ribosaminouridine library molecules in solution or on polymer support.
Collapse
Affiliation(s)
- Michio Kurosu
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, 1682 Campus Delivery, Fort Collins, Colorado 80523-1682, USA.
| | | |
Collapse
|
39
|
Peyrottes S, Périgaud C. Chemistry of bisSATE mononucleotide prodrugs. ACTA ACUST UNITED AC 2008; Chapter 15:Unit 15.3. [PMID: 18428973 DOI: 10.1002/0471142700.nc1503s29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
On the basis of AZT as a nucleosidic model, the protocols herein describe the synthesis of various bis(S-acyl-2-thioethyl) phosphotriester derivatives. These compounds, bearing transient phosphate-protecting groups, were designed to liberate the corresponding 5'-mononucleotide inside the cell through an esterase-mediated activation process. Two synthetic approaches are presented using either phosphoramidite intermediates or esterification of a nucleoside 5'-monophosphate.
Collapse
|
40
|
Tetrahedron reports on organic chemistry. Tetrahedron 2008. [DOI: 10.1016/s0040-4020(08)00897-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
41
|
Abstract
Protecting groups for the imide/lactam function of thymine/uracil and guanine, respectively, prevent irreversible nucleobase modifications that may occur in the presence of alkylating or condensing reagents that are commonly used in nucleoside protection and oligonucleotide synthesis. This unit reviews these protecting groups, and also identifies protecting groups for the exocyclic amino function of cytosine, adenine, and guanine. The unit also explores recent trends in nucleobase protection that permit reliable oligonucleotide synthesis and removal of N-protecting groups under very mild conditions.
Collapse
Affiliation(s)
- R P Iyer
- OriGenix Technologies, Laval, Quebec, Canada
| |
Collapse
|
42
|
Abstract
The main purpose of this article is to discuss 2'-protection in the context of effective oligoribonucleotide synthesis. Emphasis is placed on the 2'-protecting groups of choice in the synthesis of oligo-and polyribonucleotides, and the requirements that a protective group must satisfy to become the 2'-hydroxyl-protecting group of choice. Finally, the unit discusses the issue of 2'-O-acyl and 2'-O-silyl group migration to the 3'-hydroxy function of ribonucleosides during protection, along with the consequences of the conditions used for their removal on the stability of internucleotide linkages.
Collapse
|
43
|
Seliger H. Protection of 5'-hydroxy functions of nucleosides. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2008; Chapter 2:Unit 2.3. [PMID: 18428836 DOI: 10.1002/0471142700.nc0203s00] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The 5-hydroxy group is the primary hydroxy group of nucleosides. It is mandatory to protect 5-hydroxyls in all methods of oligonucleotide synthesis that require nucleoside synthons. This unit discusses a wide variety of acid-labile and base-labile protecting groups, as well as enzymatic methods for 5-protection and deprotection.
Collapse
|
44
|
Tetrahedron reports on organic chemistry. Tetrahedron 2007. [DOI: 10.1016/s0040-4020(07)01371-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
45
|
Reese CB, Rao MV, Serafinowska HT, Thompson EA, Yu PS. Studies in the Solid Phase Synthesis of Oligo- and Poly-Ribonucleotides. ACTA ACUST UNITED AC 2007. [DOI: 10.1080/07328319108046437] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Colin B. Reese
- a Department of Chemistry , King's College London , Strand, London , WC2R 2LS , England
| | - M. Vaman Rao
- a Department of Chemistry , King's College London , Strand, London , WC2R 2LS , England
| | | | - Elizabeth A. Thompson
- a Department of Chemistry , King's College London , Strand, London , WC2R 2LS , England
| | - Pak Sang Yu
- a Department of Chemistry , King's College London , Strand, London , WC2R 2LS , England
| |
Collapse
|
46
|
Tetrahedron reports on organic chemistry. Tetrahedron 2007. [DOI: 10.1016/s0040-4020(07)00834-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
47
|
Celewicz L, Mayer M, Shetlar MD. The Photochemistry of Thymidylyl-(3′-5′)-5-methyl-2′-deoxycytidine in Aqueous Solution¶. Photochem Photobiol 2007. [DOI: 10.1111/j.1751-1097.2005.tb00201.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
48
|
Tetrahedron reports on organic chemistry. Tetrahedron 2007. [DOI: 10.1016/s0040-4020(07)00205-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
49
|
Lackey JG, Sabatino D, Damha MJ. Solid-phase synthesis and on-column deprotection of RNA from 2'- (and 3'-) O-levulinated (Lv) ribonucleoside monomers. Org Lett 2007; 9:789-92. [PMID: 17279762 DOI: 10.1021/ol0629521] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
[reaction: see text] The solid-phase synthesis of oligoribonucleotides derived from ribonucleosides esterified at the 2'- (or 3'-) position with the levulinyl (Lv) group is described. The oligomers can be released from the solid support as 2'-O-Lv ester derivatives or fully deprotected while still attached to the solid support.
Collapse
Affiliation(s)
- Jeremy G Lackey
- Department of Chemistry, McGill University, Montreal, QC, Canada
| | | | | |
Collapse
|
50
|
Anderson DJ, Reischer RJ, Taylor AJ, Wechter WJ. Preparation and Characterization of Oligonucleotides of D- and L-2’ Deoxyuridine. ACTA ACUST UNITED AC 2007. [DOI: 10.1080/07328318408081285] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|