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Hao W, Wu M, Tian X, Hu Z, Zhang H, Huang F, Li S, Chen YL. Preparation of bicyclo[1.1.1]pentane-derived nucleoside analogues. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 42:959-966. [PMID: 37270794 DOI: 10.1080/15257770.2023.2218446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/03/2023] [Accepted: 05/22/2023] [Indexed: 06/06/2023]
Abstract
Nucleoside analogues are prevalent in drug design and call for more diversified structures. Bicyclo[1.1.1]pentane (BCP) structure has recently found wide applications in drug discovery. However, incorporation of BCP fragment into nucleoside analogues is hitherto unknown. Thus, from readily available BCP-containing building blocks, six new compounds, including pyrimidine nucleoside analogues, purine nucleoside analogues, and C-nucleoside analogues were prepared in 1-4 steps, generally with good yields.
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Affiliation(s)
- Wanli Hao
- Anhui University, Hefei, P. R. China
| | | | - Xiaoran Tian
- Nature Pharmaceutical (Anhui) Co., Ltd, Anqing, P. R. China
| | - Zhigang Hu
- Nature Pharmaceutical (Anhui) Co., Ltd, Anqing, P. R. China
| | - Hui Zhang
- Anhui University, Hefei, P. R. China
| | | | - Shikuo Li
- Anhui University, Hefei, P. R. China
| | - Yue-Lei Chen
- Nature Pharmaceutical (Anhui) Co., Ltd, Anqing, P. R. China
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2
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Graczyk A, Radzikowska-Cieciura E, Kaczmarek R, Pawlowska R, Chworos A. Modified Nucleotides for Chemical and Enzymatic Synthesis of Therapeutic RNA. Curr Med Chem 2023; 30:1320-1347. [PMID: 36239720 DOI: 10.2174/0929867330666221014111403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022]
Abstract
In recent years, RNA has emerged as a medium with a broad spectrum of therapeutic potential, however, for years, a group of short RNA fragments was studied and considered therapeutic molecules. In nature, RNA plays both functions, with coding and non-coding potential. For RNA, like any other therapeutic, to be used clinically, certain barriers must be crossed. Among them, there are biocompatibility, relatively low toxicity, bioavailability, increased stability, target efficiency and low off-target effects. In the case of RNA, most of these obstacles can be overcome by incorporating modified nucleotides into its structure. This may be achieved by both, in vitro and in vivo biosynthetic methods, as well as chemical synthesis. Some advantages and disadvantages of each approach are summarized here. The wide range of nucleotide analogues has been tested for their utility as monomers for RNA synthesis. Many of them have been successfully implemented, and a lot of pre-clinical and clinical studies involving modified RNA have been carried out. Some of these medications have already been introduced into clinics. After the huge success of RNA-based vaccines that were introduced into widespread use in 2020, and the introduction to the market of some RNA-based drugs, RNA therapeutics containing modified nucleotides appear to be the future of medicine.
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Affiliation(s)
- Anna Graczyk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Renata Kaczmarek
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Roza Pawlowska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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3
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Manta S, Kollatos N. Unusual seven-membered ring sugars and nucleosides: synthesis and biological properties. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 42:407-425. [PMID: 36451584 DOI: 10.1080/15257770.2022.2151623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Methods of the synthesis and the investigation of the properties of unnatural seven-memebered cyclic sugars and nucleosides, are of high interest. Septanoses provide conformationally more flexible sugars and due to their similarity to natural carbohydrates they have interesting and potentially useful physical, chemical, and biological properties. Additionally, nucleosides with seven-membered sugar moiety are commonly found in natural products and biologically active molecules. Modification of such nucleosides hold great promise as therapeutic agents. The present review describes the chemical synthesis and biological properties of septanoses as well as nucleosides containing septanosyl moieties.
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Affiliation(s)
- Stella Manta
- Department of Biochemistry and Biotechnology, Laboratory of Bioorganic Chemistry, University of Thessaly, Larissa, Greece
| | - Nikolaos Kollatos
- Department of Biochemistry and Biotechnology, Laboratory of Bioorganic Chemistry, University of Thessaly, Larissa, Greece
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4
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Jana SK, Harikrishna S, Sudhakar S, El-Khoury R, Pradeepkumar PI, Damha MJ. Nucleoside Analogues with a Seven-Membered Sugar Ring: Synthesis and Structural Compatibility in DNA-RNA Hybrids. J Org Chem 2022; 87:2367-2379. [PMID: 35133166 DOI: 10.1021/acs.joc.1c02254] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein we describe results on the pairing properties of synthetic DNA and RNA oligonucleotides that contain nucleotide analogues with a 7-membered sugar ring (oxepane nucleotides). Specifically, we describe the stereoselective synthesis of a set of three oxepane thymine nucleosides (OxT), their conversion to phosphoramidite derivatives, and their use in solid-phase synthesis to yield chimeric OxT-DNA and OxT-RNA strands. The different regioisomeric OxT phosphoramidites allowed for positional variations of the phosphate bridge and assessment of duplex stability when the oxepane nucleotides were incorporated in dsDNA, dsRNA, and DNA-RNA hybrids. Little to no destabilization was observed when two of the three regioisomeric OxT units were incorporated in the DNA strand of DNA-RNA hybrids, a remarkable result considering the dramatically different structure of oxepanes in comparison to 2'-deoxynucleosides. Extensive molecular modeling and dynamics studies further revealed the various structural features responsible for the tolerance of both OxT modifications in DNA-RNA duplexes, such as base-base stacking and sugar-phosphate H-bond interactions. These studies suggest that oxepane nucleotide analogues may find applications in synthetic biology, where synthetic oligonucleotides can be used to create new tools for biotechnology and medicine.
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Affiliation(s)
- Sunit Kumar Jana
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - S Harikrishna
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Roberto El-Khoury
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Masad J Damha
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
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Ageely EA, Chilamkurthy R, Jana S, Abdullahu L, O'Reilly D, Jensik PJ, Damha MJ, Gagnon KT. Gene editing with CRISPR-Cas12a guides possessing ribose-modified pseudoknot handles. Nat Commun 2021; 12:6591. [PMID: 34782635 PMCID: PMC8593028 DOI: 10.1038/s41467-021-26989-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/01/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas12a is a leading technology for development of model organisms, therapeutics, and diagnostics. These applications could benefit from chemical modifications that stabilize or tune enzyme properties. Here we chemically modify ribonucleotides of the AsCas12a CRISPR RNA 5' handle, a pseudoknot structure that mediates binding to Cas12a. Gene editing in human cells required retention of several native RNA residues corresponding to predicted 2'-hydroxyl contacts. Replacing these RNA residues with a variety of ribose-modified nucleotides revealed 2'-hydroxyl sensitivity. Modified 5' pseudoknots with as little as six out of nineteen RNA residues, with phosphorothioate linkages at remaining RNA positions, yielded heavily modified pseudoknots with robust cell-based editing. High trans activity was usually preserved with cis activity. We show that the 5' pseudoknot can tolerate near complete modification when design is guided by structural and chemical compatibility. Rules for modification of the 5' pseudoknot should accelerate therapeutic development and be valuable for CRISPR-Cas12a diagnostics.
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Affiliation(s)
- Eman A Ageely
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL, USA
| | - Ramadevi Chilamkurthy
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, IL, USA
| | - Sunit Jana
- Department of Chemistry, McGill University, Montreal, Canada
| | | | - Daniel O'Reilly
- Department of Chemistry, McGill University, Montreal, Canada
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Philip J Jensik
- Department of Physiology, School of Medicine, Southern Illinois University, Carbondale, IL, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Canada.
| | - Keith T Gagnon
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL, USA.
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, IL, USA.
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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Phosphorus Pentachloride Promoted gem-Dichlorination of 2'- and 3'-Deoxynucleosides. Molecules 2018; 23:molecules23061457. [PMID: 29914115 PMCID: PMC6100136 DOI: 10.3390/molecules23061457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 11/16/2022] Open
Abstract
Halogen substitution at various positions of canonical nucleosides has generated a number of bioactive structural variants. Herein, the synthesis of two unique series of sugar modified nucleosides bearing a gem-dichloro group is presented. The synthetic plan entails the controlled addition of phosphorus pentachloride to suitably protected 2′- or 3′-ketodeoxynucleoside intermediates as the key step, facilitating the rapid construction of such functionalized molecules. Under the same reaction conditions, the highest chemoselectivity was observed for the formation of 2′,2′-dichloro-2′,3′-dideoxynucleosides, while a competing 2′,3′-elimination process occurred in the case of the 3′,3′-dichloro counterparts.
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Azzena U, Carraro M, Pisano L. Addressing Stereochemistry of Heterocyclic Compounds by DFT NMR Calculations. Chem Heterocycl Compd (N Y) 2018. [DOI: 10.1007/s10593-018-2279-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Vannam R, Peczuh MW. How to Homologate Your Sugar: Synthetic Approaches to Septanosyl Containing Carbohydrates. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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10
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Meyer AG, Smith JA, Hyland C, Williams CC, Bissember AC, Nicholls TP. Seven-Membered Rings. PROGRESS IN HETEROCYCLIC CHEMISTRY 2016. [DOI: 10.1016/b978-0-08-100755-6.00016-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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