Acetylated and Methylated β-Cyclodextrins as Viable Soluble Supports for the Synthesis of Short 2′-Oligodeoxyribo-nucleotides in Solution

Molina, Alejandro Gimenez; Kungurtsev, Vyacheslav; Virta, Pasi; Lönnberg, Harri

doi:10.3390/molecules171012102

Cited by 24 publications

(37 citation statements)

References 34 publications

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“…Instead, other acid-labile protecting groups should be explored. For example, the methoxy isopropyl acetal protecting group (MW 74) employed by Molina et al 43,44 to synthesize 3-mer oligos on a cyclodextran support could be applied.…”

Section: Further Discussion: Advantages and Current Challengesmentioning

confidence: 99%

Organic Solvent Nanofiltration (OSN): A New Technology Platform for Liquid-Phase Oligonucleotide Synthesis (LPOS)

Kim

Gaffney

Valtcheva

et al. 2016

Org. Process Res. Dev.

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Organic Solvent Nanofiltration (OSN) technology is a membrane process for molecular separation in harsh organic media. However, despite having well-documented potential applications, development hurdles have hindered the widespread uptake of OSN technology. One of the most promising areas of application is as an iterative synthesis platform, for instance for oligonucleotides or peptides, where a thorough purification step is required after each synthesis cycle, preferably in the same working solvent. In this work, we report a process development study for liquid-phase oligonucleotide synthesis (LPOS) using OSN technology. Oligonucleotide (oligo) based drugs are being advanced as a new generation of therapeutics functioning at the protein expression level. Currently, over one hundred oligo based drugs are undergoing clinical trials, suggesting that it will soon be necessary to produce oligos at a scale of metric tons per year. However, there are as yet no synthesis platforms that can manufacture oligos at >10 kg batch-scale. With the process developed here, we have successfully carried out 8 iterative cycles of chain extension and synthesized 5-mer and 9-mer 2'-O-methyl oligoribonucleotide phosphorothioates, all in liquid phase media. This paper discusses the key challenges, both anticipated and unexpected, faced during development of this process, and suggests solutions to reduce the development period. An economic analysis has been carried out, highlighting the potential competitiveness of the LPOS-OSN process, and the necessity for a solvent recovery unit.

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Section: Further Discussion: Advantages and Current Challengesmentioning

confidence: 99%

Organic Solvent Nanofiltration (OSN): A New Technology Platform for Liquid-Phase Oligonucleotide Synthesis (LPOS)

Kim

Gaffney

Valtcheva

et al. 2016

Org. Process Res. Dev.

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“…Current Protocols in Nucleic Acid Chemistry β-Cyclodextrin (Molina et al, 2012) 5-mer (5 nucleotides, 1-arm) C (×1) + E (×1) 1.5 eq. (DNA)…”

Section: Of 17mentioning

confidence: 99%

“…During the last decade, various chemical protocols for LPOS have been a subject of significant interest due to the increasing demand for large quantities of therapeutic ONs. This effort includes extraction (de Koning et al, 2006), precipitation (Donga et al, 2006;Kim et al, 2013;Kungurtsev et al, 2013;Matsuno et al, 2016;Molina et al, 2015;Molina et al, 2014;Schwenger et al, 2017), chromatography (Molina et al, 2012), and OSNbased (Gaffney et al, 2015;Kim et al, 2016) purification techniques for scale up of ONs. Although some of these methods provide possible avenues for large-scale LPOS, none have been demonstrated at scales useful for the commercial production of ONs.…”

Section: Summary and Future Predictions Toward Green Manufacturing Ofmentioning

confidence: 99%

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Liquid‐Phase Oligonucleotide Synthesis: Past, Present, and Future Predictions

Molina

Sanghvi²

2019

CP Nucleic Acid Chemistry

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Therapeutic oligonucleotides have emerged as a powerful paradigm with the ability to treat a wide range of the human diseases. As a result, we have witnessed more than one hundred oligonucleotides currently in active clinical trials and eight Food and Drug Administration (FDA)‐approved drugs. Until now, the demand for oligonucleotide‐based drugs has been fulfilled by conventional solid‐phase synthesis in an effective manner. However, there are products in advanced stages of clinical trials projecting a collective demand of metric ton quantities in the near future. Therefore, large‐scale manufacturing of these products has become a high priority for process chemists. This article summarizes the advances in liquid‐phase oligonucleotide synthesis (LPOS) as a possible alternative strategy to meet the scale‐up challenge. A review of the literature describing major efforts in developing LPOS technologies is presented. Gratifyingly, serious attempts are under way to develop an efficient environmentally benign green chemistry protocol that is scalable and cost effective for the manufacturing of oligonucleotides. A summary of the most innovative LPOS protocols has been included to provide a glimpse of what may be possible in the future for large‐scale production of oligonucleotides. © 2019 by John Wiley & Sons, Inc.

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“…Much later chromatographic separation was exploited for the assembly of short ODNs from base-moiety-protected 5´-(1-methoxy-1-methylethyl)-2´-deoxyribonucleoside 3´-phosphoramidites on a fully methylated β-cyclodextrin support [ 60 ]. The 1-methoxy-1-methylethyl group may be removed by acid-catalyzed methanolysis approximately as readily as the DMTr group, but it gives only volatile products.…”

Section: Reviewmentioning

confidence: 99%

Synthesis of oligonucleotides on a soluble support

Lönnberg¹

2017

Beilstein J. Org. Chem.

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Oligonucleotides are usually prepared in lab scale on a solid support with the aid of a fully automated synthesizer. Scaling up of the equipment has allowed industrial synthesis up to kilogram scale. In spite of this, solution-phase synthesis has received continuous interest, on one hand as a technique that could enable synthesis of even larger amounts and, on the other hand, as a gram scale laboratory synthesis without any special equipment. The synthesis on a soluble support has been regarded as an approach that could combine the advantageous features of both the solution and solid-phase syntheses. The critical step of this approach is the separation of the support-anchored oligonucleotide chain from the monomeric building block and other small molecular reagents and byproducts after each coupling, oxidation and deprotection step. The techniques applied so far include precipitation, extraction, chromatography and nanofiltration. As regards coupling, all conventional chemistries, viz. phosphoramidite, H-phosphonate and phosphotriester strategies, have been attempted. While P(III)-based phosphoramidite and H-phosphonate chemistries are almost exclusively used on a solid support, the “outdated” P(V)-based phosphotriester chemistry still offers one major advantage for the synthesis on a soluble support; the omission of the oxidation step simplifies the coupling cycle. Several of protocols developed for the soluble-supported synthesis allow the preparation of both DNA and RNA oligomers of limited length in gram scale without any special equipment, being evidently of interest for research groups that need oligonucleotides in large amounts for research purposes. However, none of them has really tested at such a scale that the feasibility of their industrial use could be critically judged.

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Acetylated and Methylated β-Cyclodextrins as Viable Soluble Supports for the Synthesis of Short 2′-Oligodeoxyribo-nucleotides in Solution

Cited by 24 publications

References 34 publications

Organic Solvent Nanofiltration (OSN): A New Technology Platform for Liquid-Phase Oligonucleotide Synthesis (LPOS)

Organic Solvent Nanofiltration (OSN): A New Technology Platform for Liquid-Phase Oligonucleotide Synthesis (LPOS)

Liquid‐Phase Oligonucleotide Synthesis: Past, Present, and Future Predictions

Synthesis of oligonucleotides on a soluble support

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