1
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Rosenqvist P, Saari V, Ora M, Molina AG, Horvath A, Virta P. Tuning the Solubility of Soluble Support Constructs in Liquid Phase Oligonucleotide Synthesis. J Org Chem 2024. [PMID: 39250641 DOI: 10.1021/acs.joc.4c01053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Solubility of the growing oligonucleotide-soluble support constructs in the liquid phase oligonucleotide synthesis (LPOS) is a critical parameter, which affects coupling efficiency, purity, and recovery of the growing oligonucleotides during the chain elongation. In the present study, oligonucleotides have been assembled on a 4-oxoheptanedioic acid (OHDA) linker-derived tetrapodal soluble support using 5'-O-(2-methoxyprop-2-yl)-protected 2'-deoxyribonucleotide phosphoroamidite building blocks with different nucleobase protecting groups [isobutyryl (Gua), 1-butylpyrrolidin-2-ylidene (Gua, Cyt), 2,4-dimethylbenzoyl (Ade, Cyt), and Bz (Thy)]. The solubility of the oligonucleotide-soluble support constructs (molecular mass varying between 3 and 10 kDa) as models of protected tetra-, octa-, dodeca-, hexadeca-, and eicosa-nucleotides was measured in different solvent systems and in potential antisolvents. By tuning the nucleobase protecting group scheme, the solubility can be improved in aprotic organic solvent systems, while the recovery of the constructs in the precipitation, used for the isolation and purification of the growing oligonucleotide intermediates in a protic antisolvent (2-propanol), remained near quantitative. The precipitation-based yield of the protected tetrapodal oligonucleotides varied from a quantitative to 90% yield. Overall yield (for di-: 95%, tri-: 79-96%, tetra-: 82-88%, and pentanucleotides: 68-75%) and purity of the LPOS were evaluated by RP HPLC and MS-spectroscopy of the released oligonucleotide aliquots. In addition, the orthogonality of the OHDA linker was applied to release authentic protected nucleotides from the soluble supports.
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Affiliation(s)
- Petja Rosenqvist
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Verneri Saari
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Mikko Ora
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | | | - Andras Horvath
- Janssen Pharmaceutica N.V., 30 Turnhoutseweg, B-2340 Beerse, Belgium
| | - Pasi Virta
- Department of Chemistry, University of Turku, 20500 Turku, Finland
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2
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Li Q, Sanghvi YS, Yan H. An expanded framework toward improving the detritylation reaction in solid-phase oligonucleotide syntheses - filling the gap. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-9. [PMID: 39120431 DOI: 10.1080/15257770.2024.2388789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/23/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024]
Abstract
A few interactions should be considered during the detritylation reaction of solid-phase oligonucleotide synthesis (SPOS): (i) interaction of solvent with acid; (ii) interaction (or reaction) of solvent with trityl cation, and (iii) interaction of scavenger with acid, with the last one as the focus of this work. Using a stopped-flow setup, commonly used trityl cation scavengers (methanol, thioanisole, 1-dodecanethiol, triisopropylsilane, triethylsilane, and trihexylsilane) were evaluated for their reactivity toward tritylium hexafluorophosphate. Among the scavengers screened, methanol and thioanisole were found to be the most and least reactive, respectively; however, methanol does interact and react with trichloroacetic acid, thus it should not be pre-mixed and stored with acid as deblock solutions. Overall, all aspects of interactions must be taken into consideration while optimizing the detritylation reaction, especially for large scale SPOS.
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Affiliation(s)
- Quanjian Li
- Department of Chemistry, Brock University, St. Catharines, ON, Canada
| | | | - Hongbin Yan
- Department of Chemistry, Brock University, St. Catharines, ON, Canada
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3
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Obexer R, Nassir M, Moody ER, Baran PS, Lovelock SL. Modern approaches to therapeutic oligonucleotide manufacturing. Science 2024; 384:eadl4015. [PMID: 38603508 DOI: 10.1126/science.adl4015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/28/2024] [Indexed: 04/13/2024]
Abstract
Therapeutic oligonucleotides are a powerful drug modality with the potential to treat many diseases. The rapidly growing number of therapies that have been approved and that are in advanced clinical trials will place unprecedented demands on our capacity to manufacture oligonucleotides at scale. Existing methods based on solid-phase phosphoramidite chemistry are limited by their scalability and sustainability, and new approaches are urgently needed to deliver the multiton quantities of oligonucleotides that are required for therapeutic applications. The chemistry community has risen to the challenge by rethinking strategies for oligonucleotide production. Advances in chemical synthesis, biocatalysis, and process engineering technologies are leading to increasingly efficient and selective routes to oligonucleotide sequences. We review these developments, along with remaining challenges and opportunities for innovations that will allow the sustainable manufacture of diverse oligonucleotide products.
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Affiliation(s)
- R Obexer
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
| | - M Nassir
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - E R Moody
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
| | - P S Baran
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - S L Lovelock
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
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4
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Zhou X, Shi X, Fillon Y, Antia F, Pickel T, Yang J, Zhang W, Delavari A, Zhang J. Simplified Oligonucleotide Phosphorus Deprotection Process with Reduced 3-(2-Cyanoethyl) Thymidine Impurities. Nucleic Acid Ther 2024; 34:83-89. [PMID: 38315742 DOI: 10.1089/nat.2023.0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
Oligonucleotides have emerged as valuable new therapeutics. Presently, oligonucleotide manufacturing consists in a series of stepwise additions until the full-length product is obtained. Deprotection of the phosphorus backbone before cleavage and deprotection (C&D) by ammonolysis is necessary to control the 3-(2-cyanoethyl) thymidine (CNET) impurity. In this study, we demonstrate that the use of piperazine as a scavenger of acrylonitrile allows phosphorus deprotection and C&D to be combined in a single step. This reduces solvent consumption, processing time, and CNET levels. Additionally, we showed that substitution of piperazine for triethylamine in the phosphorus deprotection step of supported-synthesis leads to reduced reaction times and lower levels of CNET impurities.
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Affiliation(s)
- Xuan Zhou
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts, USA
| | - Xianglin Shi
- Leal Therapeutics, Worcester, Massachusetts, USA
| | - Yannick Fillon
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts, USA
| | - Firoz Antia
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts, USA
| | - Thomas Pickel
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts, USA
| | - Jing Yang
- Intellia Therapeutics, Inc., Cambridge, Massachusetts, USA
| | - William Zhang
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts, USA
| | - Armin Delavari
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts, USA
| | - Jiabao Zhang
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts, USA
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5
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Banerjee A, Das A, Ghosh A, Gupta A, Sinha S. Synthesis and Biophysical Properties of Triazole-Incorporated PMOs (TzPMOs): A Convergent, Click Ligation Approach. J Org Chem 2024; 89:2895-2903. [PMID: 38344977 DOI: 10.1021/acs.joc.3c02242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The synthesis of phosphorodiamidate morpholino oligonucleotides (PMOs) incorporating single or double triazole rings in the backbone has been achieved via Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC). The synthetic approach implemented is fundamentally convergent, involving the ligation of a 5'-azide PMO fragment to a 3'-alkyne fragment both in solution and on solid support. To access the 3'-alkyne PMO fragment, we synthesized 3'-N-propargyl chlorophosphoramidate morpholino monomers for all four nucleobases. The resulting triazole-incorporated PMOs (TzPMOs) have exhibited comparable or improved binding affinity toward complementary deoxyribonucleic acid (DNA)/ribonucleic acid (RNA) strands compared to its regular analogues. Finally, a full-length TzPMO was designed to target the Nanog gene, demonstrating almost identical hybridization properties when compared to its regular version. Circular dichroism studies revealed a B-type helical conformation for the duplexes formed by TzPMOs.
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Affiliation(s)
- Arpan Banerjee
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Arnab Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Abhishek Gupta
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
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6
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Seliger H, Sanghvi YS. An Update on Protection of 5'-Hydroxyl Functions of Nucleosides and Oligonucleotides. Curr Protoc 2024; 4:e999. [PMID: 38439607 DOI: 10.1002/cpz1.999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
The synthesis of natural and chemically modified nucleosides and oligonucleotides is in great demand due to its increasing number of applications in diverse areas of research. These include tools for diagnostics and proteomics, research reagents for molecular biology, probes for functional genomics, and the design, discovery, development, and manufacture of new therapeutics. The likelihood of success in synthesizing these molecules is often dependent on the correct choice of a protection strategy to block the 5'-hydroxyl group of a carbohydrate moiety, nucleoside, or oligonucleotide. This topic was reviewed extensively in the year 2000. The purpose of this article is to complement and update the original review with recently published methodologies recommended for the protection and deprotection of the 5'-hydroxyl group. © 2024 Wiley Periodicals LLC.
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7
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Brzezinska J, Trzciński S, Strzelec J, Chmielewski MK. From CPG to hybrid support: Review on the approaches in nucleic acids synthesis in various media. Bioorg Chem 2023; 140:106806. [PMID: 37660625 DOI: 10.1016/j.bioorg.2023.106806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/26/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023]
Abstract
Solid-phase synthesis is, to date, the preferred method for the manufacture of oligonucleotides, in quantities ranging from a few micrograms for research purposes to several kilograms for therapeutic or commercial use. But for large-scale oligonucleotide manufacture, scaling up and hazardous waste production pose challenges that necessitate the investigation of alternate synthetic techniques. Despite the disadvantages of glass supports, using soluble supports as a substitute presents difficulties because of their high overall yield and complex purification steps. To address these challenges, various independent approaches have been developed; however, other problems such as insufficient cycle efficiency and synthesis of oligonucleotide chains of desired length continue to exist. In this study, we present a review of the current developments, advantages, and difficulties of recently reported alternatives to supports based on controlled pore glass, and discuss the importance of a support choice to resolve issues arising during oligonucleotide synthesis.
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Affiliation(s)
- Jolanta Brzezinska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Stanisław Trzciński
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Joanna Strzelec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marcin K Chmielewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; FutureSynthesis sp. z o.o., ul. Rubież 46B, 61-612 Poznan, Poland.
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8
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Paul S, Gray D, Caswell J, Brooks J, Ye W, Moody TS, Radinov R, Nechev L. Convergent Biocatalytic Mediated Synthesis of siRNA. ACS Chem Biol 2023; 18:2183-2187. [PMID: 37061926 DOI: 10.1021/acschembio.3c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
New technologies are required to combat the challenges faced with manufacturing commercial quantities of oligonucleotide drug substances which are required for treating large patient populations. Herein we report a convergent biocatalytic synthesis strategy for an Alnylam model siRNA. The siRNA chemical structure includes several of the unnatural modifications and conjugations typical of siRNA drug substances. Using Almac's 3-2-3-2 hybrid RNA ligase enzyme strategy that sequentially ligates short oligonucleotide fragments (blockmers), the target siRNA was produced to high purity at 1 mM concentration. Additional strategies were investigated including the use of polynucleotide kinase phosphorylation and the use of crude blockmer starting materials without chromatographic purification. These findings highlight a path toward a convergent synthesis of siRNAs for large-scale manufacture marrying both enzymatic liquid and classical solid-phase synthesis.
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Affiliation(s)
- Stephanie Paul
- Almac Sciences, Department of Technology, Almac House, 20 Seagoe Industrial Estate, Craigavon, Northern Ireland BT63 5QD, United Kingdom
| | - Darren Gray
- Almac Sciences, Department of Technology, Almac House, 20 Seagoe Industrial Estate, Craigavon, Northern Ireland BT63 5QD, United Kingdom
| | - Jill Caswell
- Almac Sciences, Department of Technology, Almac House, 20 Seagoe Industrial Estate, Craigavon, Northern Ireland BT63 5QD, United Kingdom
| | - Joshua Brooks
- Alnylam Pharmaceuticals Inc., 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Wenjie Ye
- Alnylam Pharmaceuticals Inc., 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Thomas S Moody
- Almac Sciences, Department of Technology, Almac House, 20 Seagoe Industrial Estate, Craigavon, Northern Ireland BT63 5QD, United Kingdom
- Arran Chemical Company, Unit 1 Monksland Industrial Estate, Athlone, Co., Roscommon, N37 DN24, Ireland
| | - Roumen Radinov
- Alnylam Pharmaceuticals Inc., 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Lubomir Nechev
- Alnylam Pharmaceuticals Inc., 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
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9
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Tsurusaki T, Sato K, Imai H, Hirai K, Takahashi D, Wada T. Convergent synthesis of phosphorodiamidate morpholino oligonucleotides (PMOs) by the H-phosphonate approach. Sci Rep 2023; 13:12576. [PMID: 37537221 PMCID: PMC10400599 DOI: 10.1038/s41598-023-38698-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/13/2023] [Indexed: 08/05/2023] Open
Abstract
Phosphorodiamidate morpholino oligonucleotides (PMOs) are a promising type of antisense oligonucleotides, but their challenging synthesis makes them difficult to access. This research presents an efficient synthetic approach for PMOs using the H-phosphonate approach. The use of phosphonium-type condensing reagents significantly reduced coupling times compared with the current synthetic approach. Furthermore, phosphonium-type condensing reagents facilitated the fragment condensation of PMO, synthesizing up to 8-mer containing all four nucleobases with remarkable coupling efficacy. This is the first report on the convergent synthesis of PMOs. This approach would facilitate the large-scale synthesis of PMOs and accelerate their popularity and accessibility as a next-generation therapy.
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Affiliation(s)
- Taiki Tsurusaki
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Kazuki Sato
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Hiroki Imai
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Kunihiro Hirai
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, Kanagawa, 210-8681, Japan
| | - Daisuke Takahashi
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, Kanagawa, 210-8681, Japan
| | - Takeshi Wada
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
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10
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Rosenqvist P, Saari V, Pajuniemi E, Gimenez Molina A, Ora M, Horvath A, Virta P. Stereo-Controlled Liquid Phase Synthesis of Phosphorothioate Oligonucleotides on a Soluble Support. J Org Chem 2023. [PMID: 37428953 PMCID: PMC10367069 DOI: 10.1021/acs.joc.3c01006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
5'-O-(2-Methoxyisopropyl) (MIP)-protected 2'-deoxynucleosides as chiral P(V)-building blocks, based on the limonene-derived oxathiaphospholane sulfide, were synthesized and used for the assembly of di-, tri-, and tetranucleotide phosphorothioates on a tetrapodal pentaerythritol-derived soluble support. The synthesis cycle consisted of two reactions and two precipitations: (1) the coupling under basic conditions, followed by neutralization and precipitation and (2) an acid catalyzed 5'-O-deacetalization, followed by neutralization and precipitation. The simple P(V) chemistry together with the facile 5'-O-MIP deprotection proved efficient in the liquid phase oligonucleotide synthesis (LPOS). Ammonolysis released nearly homogeneous Rp or Sp phosphorothioate diastereomers in ca. 80% yield/synthesis cycle.
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Affiliation(s)
- Petja Rosenqvist
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Verneri Saari
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Ella Pajuniemi
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Alejandro Gimenez Molina
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, 2340 Beerse, Belgium
| | - Mikko Ora
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Andras Horvath
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, 2340 Beerse, Belgium
| | - Pasi Virta
- Department of Chemistry, University of Turku, 20500 Turku, Finland
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11
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Moody ER, Obexer R, Nickl F, Spiess R, Lovelock SL. An enzyme cascade enables production of therapeutic oligonucleotides in a single operation. Science 2023; 380:1150-1154. [PMID: 37319201 DOI: 10.1126/science.add5892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
Therapeutic oligonucleotides have emerged as a powerful drug modality with the potential to treat a wide range of diseases; however, the rising number of therapies poses a manufacturing challenge. Existing synthetic methods use stepwise extension of sequences immobilized on solid supports and are limited by their scalability and sustainability. We report a biocatalytic approach to efficiently produce oligonucleotides in a single operation where polymerases and endonucleases work in synergy to amplify complementary sequences embedded within catalytic self-priming templates. This approach uses unprotected building blocks and aqueous conditions. We demonstrate the versatility of this methodology through the synthesis of clinically relevant oligonucleotide sequences containing diverse modifications.
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Affiliation(s)
- E R Moody
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - R Obexer
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - F Nickl
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - R Spiess
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - S L Lovelock
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
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12
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Hall J. Future directions for medicinal chemistry in the field of oligonucleotide therapeutics. RNA (NEW YORK, N.Y.) 2023; 29:423-433. [PMID: 36693762 PMCID: PMC10019366 DOI: 10.1261/rna.079511.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/09/2023] [Indexed: 05/13/2023]
Abstract
In the last decade, the field of oligonucleotide therapeutics has matured, with the regulatory approval of several single-stranded and double-stranded RNA drugs. In this Perspective, I discuss enabling developments and likely future directions in the field from the perspective of oligonucleotide chemistry.
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Affiliation(s)
- Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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13
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Van Giesen KJ, Thompson MJ, Meng Q, Lovelock SL. Biocatalytic Synthesis of Antiviral Nucleosides, Cyclic Dinucleotides, and Oligonucleotide Therapies. JACS AU 2023; 3:13-24. [PMID: 36711092 PMCID: PMC9875237 DOI: 10.1021/jacsau.2c00481] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/11/2022] [Accepted: 11/11/2022] [Indexed: 05/27/2023]
Abstract
Nucleosides, nucleotides, and oligonucleotides modulate diverse cellular processes ranging from protein production to cell signaling. It is therefore unsurprising that synthetic analogues of nucleosides and their derivatives have emerged as a versatile class of drug molecules for the treatment of a wide range of disease areas. Despite their great therapeutic potential, the dense arrangements of functional groups and stereogenic centers present in nucleic acid analogues pose a considerable synthetic challenge, especially in the context of large-scale manufacturing. Commonly employed synthetic methods rely on extensive protecting group manipulations, which compromise step-economy and result in high process mass intensities. Biocatalytic approaches have the potential to address these limitations, enabling the development of more streamlined, selective, and sustainable synthetic routes. Here we review recent achievements in the biocatalytic manufacturing of nucleosides and cyclic dinucleotides along with progress in developing enzymatic strategies to produce oligonucleotide therapies. We also highlight opportunities for innovations that are needed to facilitate widespread adoption of these biocatalytic methods across the pharmaceutical industry.
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Affiliation(s)
| | | | | | - Sarah L. Lovelock
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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14
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Borths CJ, Burr T, Figuccia A, Ford JG, Guan B, Jones MT, Klingeleers D, Lochner S, Rodriguez AA, Wetter C. Nitrosamine Risk Assessments in Oligonucleotides. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.2c00330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Tracey Burr
- Ionis Pharmaceuticals Inc., Carlsbad, California 92010, United States
| | - Aude Figuccia
- Novartis AG, Lichtstrasse 35, CH-4056 Basel, Switzerland
| | - J. Gair Ford
- AstraZeneca, Macclesfield SK10 2NA, United Kingdom
| | - Bing Guan
- Biogen, Cambridge, Massachusetts 02142, United States
| | - Michael T. Jones
- Pfizer, 875 Chesterfield Parkway West, Chesterfield, Missouri 63017, United States
| | | | | | | | - Christian Wetter
- F. Hoffmann-La Roche AG, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
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15
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Senthilvelan A, Shanmugasundaram M, Kore AR. Solution‐Phase Chemical Synthesis of Modified RNA Dinucleotides. Curr Protoc 2022; 2:e583. [PMID: 36342272 DOI: 10.1002/cpz1.583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This article describes a simple, reliable, efficient, and improved solution-phase method for the gram-scale chemical synthesis of RNA dinucleotides such as pAm pA, pAm pG, and pAm pU that utilizes phosphoramidite chemistry. The overall synthetic strategy involves three steps. The first step involves the coupling reaction between 5'-O-MMT protected nucleoside-3'-O-phosphoramidite and a protected nucleoside containing a free 5'-OH group in the presence of tetrazole, followed by the oxidation of phosphite triester using tert-butyl hydroperoxide to give the corresponding protected Nm pN. Next, the 5'-O-MMT is cleaved under 3% trichloroacetic acid in dichloromethane conditions. Finally, the 5'-hydroxyl group is phosphorylated by the use of an activated bis(2-cyanoethyl)-N,N-diisopropyl phosphoramidite using tetrazole, followed by the oxidation of trivalent to pentavalent phosphorus using tert-butyl hydroperoxide and subsequent deprotection using ammonium hydroxide to afford the corresponding RNA dinucleotide, pNm pN, in good yields with high purity (>99.5%). © 2022 Wiley Periodicals LLC.
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16
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Senthilvelan A, Shanmugasundaram M, Kore AR. Efficient and Improved Solution-Phase Synthesis of Modified RNA Dinucleotides: Versatile Synthons in Cap 1 mRNA Therapeutics. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.2c00218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Annamalai Senthilvelan
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, Texas 78744-1832, United States
| | - Muthian Shanmugasundaram
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, Texas 78744-1832, United States
| | - Anilkumar R. Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, Texas 78744-1832, United States
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17
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Cosgrove SC, Miller GJ. Advances in biocatalytic and chemoenzymatic synthesis of nucleoside analogues. Expert Opin Drug Discov 2022; 17:355-364. [PMID: 35133222 DOI: 10.1080/17460441.2022.2039620] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Nucleoside analogues represent a cornerstone of achievement in drug discovery, rising to prominence particularly in the fields of antiviral and anticancer discovery over the last 60 years. Traditionally accessed using chemical synthesis, a paradigm shift to include the use of biocatalytic synthesis is now apparent. AREAS COVERED Herein, the authors discuss the recent advances using this technology to access nucleoside analogues. Two key aspects are covered, the first surrounding methodology concepts, effectively using enzymes to access diverse nucleoside analogue space and also for producing key building blocks. The second focuses on the use of biocatalytic cascades for de novo syntheses of nucleoside analogue drugs. Finally, recent advances in technologies for effecting enzymatic nucleoside synthesis are considered, chiefly immobilization and flow. EXPERT OPINION Enzymatic synthesis of nucleoside analogues is maturing but has yet to usurp chemical synthesis as a first-hand synthesis technology, with scalability and substrate modification primary issues. Moving forward, tandem approaches that harness expertise across molecular microbiology and chemical synthesis will be vital to unlocking the potential of next generation nucleoside analogue drug discovery.
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Affiliation(s)
- Sebastian C Cosgrove
- Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, UK.,Centre for Glycoscience Research, Keele University, Keele, Staffordshire, UK
| | - Gavin J Miller
- Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, UK.,Centre for Glycoscience Research, Keele University, Keele, Staffordshire, UK
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