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Wahab A, Cheng G, Su H, Yang L, Gao Z, Yu B. Furan ring opening reaction for the synthesis of 2,5-dicarbonyl-3-ene-phosphates. Org Biomol Chem 2023; 21:7219-7223. [PMID: 37642497 DOI: 10.1039/d3ob00933e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Furan ring opening reactions are essential in organic synthesis, enabling the incorporation of diverse functional groups and the construction of complex molecular structures. A highly efficient and practical method for synthesizing 2,5-dicarbonyl-3-ene-phosphates from readily available biomass furan and dialkyl phosphonates is reported. The reaction, catalyzed by FeCl3, demonstrated wide substrate scope and high synthetic efficiency. Gram-scale synthesis was achieved, and a one-pot reaction provided a quick access route to the desired compounds. Additionally, a successful Diels-Alder reaction highlighted the versatility of the methodology.
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Affiliation(s)
- Abdul Wahab
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Guanghai Cheng
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Hang Su
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Lihua Yang
- Oil & Gas Technology Research Institute, Changqing Oilfield Branch Company, Petrochina, Xi'an, 710018, China.
- National Engineering Laboratory for Low-permeability Oil & Gas Exploration and Development, Xi'an, 710018, China
| | - Ziwei Gao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Binxun Yu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
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Liu X, Pei J, Gao Z, Gao H. Synthesis of ortho-Phosphated (Hetero)Arylamines through Cascade Atherton-Todd Reaction/[3,3]-Rearrangement from Arylhydroxylamines and Dialkyl Phosphites. Org Lett 2022; 24:7690-7695. [PMID: 36222849 DOI: 10.1021/acs.orglett.2c03269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A practical and facile strategy for the synthesis of ortho-phosphated (hetero)arylamines from readily available arylhydroxylamines and dialkyl phosphites via cascade Atherton-Todd reaction/[3,3]-rearrangement was developed. This method is amenable to various arylhydroxylamines such as phenylhydroxylamines, naphthylhydroxylamines, and pyridylhydroxylamines, has mild reaction conditions, is oxidant-free, and has good functional-group compatibility and excellent regioselectivity.
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Affiliation(s)
- Xiao Liu
- School of Chemistry and Chemical Engineering, Shandong University, 27 South Shanda Road, Ji'nan 250100, Shandong, China
| | - Jingtai Pei
- School of Chemistry and Chemical Engineering, Shandong University, 27 South Shanda Road, Ji'nan 250100, Shandong, China
| | - Zhiwei Gao
- School of Chemistry and Chemical Engineering, Shandong University, 27 South Shanda Road, Ji'nan 250100, Shandong, China
| | - Hongyin Gao
- School of Chemistry and Chemical Engineering, Shandong University, 27 South Shanda Road, Ji'nan 250100, Shandong, China
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3
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Clavé G, Reverte M, Vasseur JJ, Smietana M. Modified internucleoside linkages for nuclease-resistant oligonucleotides. RSC Chem Biol 2021; 2:94-150. [PMID: 34458777 PMCID: PMC8341215 DOI: 10.1039/d0cb00136h] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.
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Affiliation(s)
| | - Maeva Reverte
- IBMM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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4
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Catalyst- and additive-free cascade phosphorylation/cyclization of propargylic alcohols and R2P(O)OH. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2020.152761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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5
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Electrochemical Phosphorylation of Organic Molecules. CHEM REC 2020; 20:1530-1552. [DOI: 10.1002/tcr.202000096] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/12/2020] [Accepted: 09/14/2020] [Indexed: 02/04/2023]
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6
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Duschmalé J, Hansen HF, Duschmalé M, Koller E, Albaek N, Møller MR, Jensen K, Koch T, Wengel J, Bleicher K. In vitro and in vivo properties of therapeutic oligonucleotides containing non-chiral 3' and 5' thiophosphate linkages. Nucleic Acids Res 2020; 48:63-74. [PMID: 31754711 PMCID: PMC6943131 DOI: 10.1093/nar/gkz1099] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 10/28/2019] [Accepted: 11/07/2019] [Indexed: 11/12/2022] Open
Abstract
The introduction of non-bridging phosphorothioate (PS) linkages in oligonucleotides has been instrumental for the development of RNA therapeutics and antisense oligonucleotides. This modification offers significantly increased metabolic stability as well as improved pharmacokinetic properties. However, due to the chiral nature of the phosphorothioate, every PS group doubles the amount of possible stereoisomers. Thus PS oligonucleotides are generally obtained as an inseparable mixture of a multitude of diastereoisomeric compounds. Herein, we describe the introduction of non-chiral 3′ thiophosphate linkages into antisense oligonucleotides and report their in vitro as well as in vivo activity. The obtained results are carefully investigated for the individual parameters contributing to antisense activity of 3′ and 5′ thiophosphate modified oligonucleotides (target binding, RNase H recruitment, nuclease stability). We conclude that nuclease stability is the major challenge for this approach. These results highlight the importance of selecting meaningful in vitro experiments particularly when examining hitherto unexplored chemical modifications.
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Affiliation(s)
- Jörg Duschmalé
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
- To whom correspondence should be addressed. Tel: +41 61 68 86081; Fax: +41 61 68 88714;
| | - Henrik Frydenlund Hansen
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Martina Duschmalé
- Pharmaceutical Sciences, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Erich Koller
- Pharmaceutical Sciences, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Nanna Albaek
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Marianne Ravn Møller
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Klaus Jensen
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Troels Koch
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Konrad Bleicher
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
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7
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Horiba M, Yamaguchi T, Obika S. Synthesis and Properties of Oligonucleotides Having Ethynylphosphonate Linkages. J Org Chem 2020; 85:1794-1801. [PMID: 31867976 DOI: 10.1021/acs.joc.9b01318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ethynylphosphonate (EP)-linked thymidine dimers were synthesized via a palladium-catalyzed cross-coupling reaction and successfully incorporated into oligonucleotides. The oligonucleotides containing EP linkages appropriately formed a duplex with their complementary single-stranded RNA (ssRNA) and single-stranded DNA. The oligonucleotides containing both the EP linkages and 2'-O,4'-C-methylene-bridged nucleic acid/locked nucleic acid exhibited strong duplex-forming ability toward the complementary ssRNA. The EP-modified oligonucleotides exhibited higher exonuclease resistances than their natural counterparts. Moreover, one EP modification to a gapmer-type antisense oligonucleotide resulted in a switch of the cleavage site in the target ssRNA. Therefore, the EP modification can be applied for controlling the cleavage site in the RNase H-dependent mechanism.
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Affiliation(s)
- Masahiko Horiba
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan
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8
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Thorpe C, Epple S, Woods B, El-Sagheer AH, Brown T. Synthesis and biophysical properties of carbamate-locked nucleic acid (LNA) oligonucleotides with potential antisense applications. Org Biomol Chem 2019; 17:5341-5348. [PMID: 31099373 PMCID: PMC6686644 DOI: 10.1039/c9ob00691e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/09/2019] [Indexed: 12/13/2022]
Abstract
Antisense oligonucleotides (ASOs) are becoming important drugs for hard to treat diseases. Modifications to their DNA backbones are essential to inhibit degradation in vivo, but they can reduce binding affinity to RNA targets. To address this problem we have combined the enzymatic resistance of carbamate (CBM) DNA backbone analogues with the thermodynamic stability conferred by locked nucleic acid sugars (LNA). Using a dinucleotide phosphoramidite strategy and automated solid phase synthesis, we have synthesised a set of oligonucleotides modified with multiple LNA-CBM units. The LNA sugars restore binding affinity to RNA targets, and in this respect LNA position with respect to the CBM linkage is important. Oligonucleotides containing carbamate flanked on its 5'and 3'-sides by LNA form stable duplexes with RNA and unstable duplexes with DNA, which is desirable for antisense applications. Carbamate-LNA modified oligonucleotides also show increased stability in the presence of snake venom and foetal bovine serum compared to LNA or CBM backbones alone.
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Affiliation(s)
- Cameron Thorpe
- Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford OX1 3TA
, UK
.
| | - Sven Epple
- Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford OX1 3TA
, UK
.
| | - Benjamin Woods
- Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford OX1 3TA
, UK
.
| | - Afaf H. El-Sagheer
- Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford OX1 3TA
, UK
.
- Chemistry Branch
, Department of Science and Mathematics
, Faculty of Petroleum and Mining Engineering
, Suez University
,
Suez 43721
, Egypt
| | - Tom Brown
- Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford OX1 3TA
, UK
.
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Basílio Barbosa V, de Oliveira Martins E, Weber G. Nearest-neighbour parameters optimized for melting temperature prediction of DNA/RNA hybrids at high and low salt concentrations. Biophys Chem 2019; 251:106189. [PMID: 31129553 DOI: 10.1016/j.bpc.2019.106189] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 11/28/2022]
Abstract
Gene editing technologies sparked a renewed interest in the hybridization of DNA/RNA duplexes, yet little improvement on nearest-neighbour parameters was made over the past two decades. For low sodium concentration no parameter set was yet calculated. Here, we revised the existing experimental datasets and used an expanded set of sequences from which we recalculated the nearest-neighbour parameters, reducing the average temperature prediction uncertainty to 1.6 °C. Two experimental sets using temperatures extracted via different methods were used with similar results, with the curve-fitting method achieving a slight advantage in prediction quality over other methods. Additionally, we obtained new parameters for low salt with an average uncertainty of 0.98 °C. We also tested several types of salt correction factors and concluded that it is advisable to use those originally developed for RNA/RNA rather than for DNA/DNA.
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Affiliation(s)
- Vivianne Basílio Barbosa
- Departamento de Fsica, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Erik de Oliveira Martins
- Escola Politécnica, Centro Universitário do Leste de Minas Gerais, 35170-056 Coronel Fabriciano, MG, Brazil
| | - Gerald Weber
- Departamento de Fsica, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil.
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10
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Li Y, Yang Q, Yang L, Lei N, Zheng K. A scalable electrochemical dehydrogenative cross-coupling of P(O)H compounds with RSH/ROH. Chem Commun (Camb) 2019; 55:4981-4984. [PMID: 30968096 DOI: 10.1039/c9cc01378d] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A practical, scalable electrochemical dehydrogenative cross-coupling of P(O)H compounds with thiols, phenols and alcohols in both an undivided cell and a continuous-flow setup is disclosed. Its broad substrate scope (>50 examples), good functional-group tolerance and scalability (>10 g) show potential for practical synthesis. A preliminary mechanistic study suggests that the phosphorus radicals are involved in the catalytic cycle.
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Affiliation(s)
- Yujun Li
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
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