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Ren Q, Osawa T, Tatsuno M, Obika S. THF peroxide as a factor in generating desulphurised products from the solid-phase synthesis of phosphorothioate-modified oligonucleotides. RSC Adv 2024; 14:21590-21596. [PMID: 38979452 PMCID: PMC11229082 DOI: 10.1039/d4ra03592e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024] Open
Abstract
Antisense oligonucleotides (ASOs) are generally obtained via chemical synthesis on a solid support and phosphorothioate (PS) modification with a phosphate backbone to increase their in vivo stability and activity. However, desulphurised products, in which PS is partially replaced by phosphodiesters, are generally formed during the chemical synthesis of ASO and are difficult to separate from the desired PS-modified ASO by chromatography. Therefore, revealing the unknown factors that cause the formation of desulphurised products and proposing methods to inhibit their formation are highly desirable. In this study, it was found that peroxides in THF, which is used as a solvent for the acetyl capping agent, oxidise phosphite triesters to produce desulphurisation products. The use of THF with antioxidants effectively suppresses the oxidation caused by THF peroxides. Moreover, THF peroxide was found to oxidise phosphoramidites, which are the building blocks of oligonucleotide chemical syntheses, indicating that caution should be taken with the organic solvents used during the synthesis and purification of phosphoramidites.
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Affiliation(s)
- Qin Ren
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita Osaka 565-0871 Japan
| | - Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita Osaka 565-0871 Japan
| | - Michiaki Tatsuno
- 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
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University 1-3 Yamadaoka Suita Osaka 565-0871 Japan
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2
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Zhou X, Kiesman WF, Yan W, Jiang H, Antia FD, Yang J, Fillon YA, Xiao L, Shi X. Development of Kilogram-Scale Convergent Liquid-Phase Synthesis of Oligonucleotides. J Org Chem 2021; 87:2087-2110. [PMID: 34807599 DOI: 10.1021/acs.joc.1c01756] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oligonucleotide drugs show promise to treat diseases afflicting millions of people. To address the need to manufacture large quantities of oligonucleotide therapeutics, the novel convergent liquid-phase synthesis has been developed for an 18-mer oligonucleotide drug candidate. Fragments containing tetra- and pentamers were synthesized and assembled into the 18-mer without column chromatography, which had a similar impurity profile to material made by standard solid-phase oligonucleotide synthesis. Two of the fragments have been synthesized at ∼3 kg/batch sizes and four additional tetra- and pentamer fragments were synthesized at >300-g scale, and a 34-mer was assembled from the fragments. Critical impurities are controlled in the fragment syntheses to provide oligonucleotides of purities suitable for clinical use after applying standard full-length product purification process. Impurity control in the assembly steps demonstrated the potential to eliminate chromatography of full-length oligonucleotides, which should enhance scalability and reduce the environmental impact of the process. The convergent assembly and telescoping of reactions made the long synthesis (>60 reactions) practical by reducing production time, material loss, and chances for impurity generation.
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Affiliation(s)
- Xuan Zhou
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - William F Kiesman
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Wuming Yan
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Hong Jiang
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Firoz D Antia
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Jing Yang
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Yannick A Fillon
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Li Xiao
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Xianglin Shi
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
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3
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Guo X, Stolee JA, Fillon YA, Zou L. Trace-Level Determination of Acrylonitrile Generated in the Manufacturing Process of Oligonucleotides by Static Headspace Gas Chromatography with an Electron Impact(+) Mass Detector. Org Process Res Dev 2021. [DOI: 10.1021/acs.oprd.0c00527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Xun Guo
- Analytical Development, Biogen Inc., Cambridge, Massachusetts 02142, United States
| | - Jessica A. Stolee
- Analytical Development, Biogen Inc., Cambridge, Massachusetts 02142, United States
| | - Yannick A. Fillon
- Antisense Oligonucleotide Development, Biogen Inc., Cambridge, Massachusetts 02142, United States
| | - Lanfang Zou
- Analytical Development, Biogen Inc., Cambridge, Massachusetts 02142, United States
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4
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Sanghvi YS. Large-scale Automated Synthesis of Therapeutic Oligonucleotides: A Status Update. ADVANCES IN NUCLEIC ACID THERAPEUTICS 2019. [DOI: 10.1039/9781788015714-00453] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
An increasing number of therapeutic oligonucleotides are entering human clinical trials, leading to multiple marketed drugs. Thus, large-scale automated synthesis of these products has become a high priority for process chemists. This chapter summarizes the advances in the large-scale solid-support synthesis of oligonucleotides using conventional phosphoramidite chemistry. An overview of the most prevalent modifications currently utilized for the assembly of modified oligonucleotides along with a four-step automated process is presented. A brief description of the post-synthesis processes is also included with protocols for characterization of drug substance. A glimpse of possible future technologies that may tackle the economic and ecological challenges of the 21st century when oligonucleotides will be required in metric-tonne quantity is also discussed.
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5
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Yang J, Stolee JA, Jiang H, Xiao L, Kiesman WF, Antia FD, Fillon YA, Ng A, Shi X. Solid-Phase Synthesis of Phosphorothioate Oligonucleotides Using Sulfurization Byproducts for in Situ Capping. J Org Chem 2018; 83:11577-11585. [PMID: 30179468 DOI: 10.1021/acs.joc.8b01553] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Oligonucleotides containing phosphorothioate (PS) linkages have recently demonstrated significant clinical utility. PS oligonucleotides are manufactured via a solid-phase chain elongation process in which a four-reaction cycle consisting of detritylation, coupling, sulfurization, and failure sequence capping with Ac2O is repeated. In the capping step, uncoupled sequences are acetylated at the 5'-OH to stop the chain growth and control the levels of deletion, or ( n-1), impurities. Herein, we report that the byproducts of commonly used sulfurization reagents react with the 5'-OH and cap the failure sequences. The standard Ac2O capping step can therefore be eliminated, and this 3-reaction cycle process affords a higher yield and higher or comparable overall purity compared to the conventional 4-reaction synthesis. This improvement results in reducing the number of reactions from ∼80 to ∼60 for the synthesis of a typical length 20-mer oligonucleotide. For every kilogram of an oligonucleotide intermediate synthesized, > 500 L of reagents and organic solvents is saved, and the E-factor is decreased to <1500 from ∼2000.
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Affiliation(s)
- Jimin Yang
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - Jessica A Stolee
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - Hong Jiang
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - Li Xiao
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - William F Kiesman
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - Firoz D Antia
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - Yannick A Fillon
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - Austen Ng
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - Xianglin Shi
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
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6
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Scotson JL, Andrews BI, Laws AP, Page MI. Phosphorothioate anti-sense oligonucleotides: the kinetics and mechanism of the sulfurisation of phosphites by phenylacetyl disulfide (PADS). Org Biomol Chem 2018; 14:10840-10847. [PMID: 27805225 DOI: 10.1039/c6ob02108e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In the pharmaceutical industry the sulfurisation of nucleotide-phosphites to produce more biologically stable thiophosphates is often achieved using 'aged' solutions of phenylacetyl disulfide (PADS) which consist of a mixture of polysulfides that are more efficient sulfur transfer reagents. However, both 'fresh' and 'aged' solutions of PADS are capable of the sulfurisation of phosphites. The rates of both processes in acetonitrile are first order in sulfurising agent, phosphite and a pyridine base, although with 'aged' PADS the rate becomes independent of base at high concentrations. The Brönsted β values for sulfurisation using 'fresh' and 'aged' PADS with substituted pyridines are 0.43 and 0.26, respectively. With 'fresh' PADS the Brönsted βnuc = 0.51 for substituted trialkyl phosphites is consistent with a mechanism involving nucleophilic attack of the phosphite on the PADS disulfide bond to reversibly generate a phosphonium intermediate, the rate-limiting breakdown of which occurs by a base catalysed elimination process, confirmed by replacing the ionisable hydrogens in PADS with methyl groups. The comparable polysulfide phosphonium ion intermediate seen with 'aged' PADS presents a more facile pathway for product formation involving S-S bond fission as opposed to C-S bond fission.
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Affiliation(s)
- James L Scotson
- Department of Chemistry, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
| | - Benjamin I Andrews
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Andrew P Laws
- Department of Chemistry, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
| | - Michael I Page
- Department of Chemistry, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
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7
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Scotson JL, Andrews BI, Laws AP, Page MI. Phosphorothioate anti-sense oligonucleotides: the kinetics and mechanism of the generation of the sulfurising agent from phenylacetyl disulfide (PADS). Org Biomol Chem 2016; 14:8301-8. [PMID: 27531007 DOI: 10.1039/c6ob01531j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The synthesis of phosphorothioate oligonucleotides is often accomplished in the pharmaceutical industry by the sulfurisation of the nucleotide-phosphite using phenylacetyl disulfide (PADS) which has an optimal combination of properties. This is best achieved by an initial 'ageing' of PADS for 48 h in acetonitrile with 3-picoline to generate polysulfides. The initial base-catalysed degradation of PADS occurs by an E1cB-type elimination to generate a ketene and acyldisulfide anion. Proton abstraction to reversibly generate a carbanion is demonstrated by H/D exchange, the rate of which is greatly increased by electron-withdrawing substituents in the aromatic ring of PADS. The ketene can be trapped intramolecularly by an o-allyl group. The disulfide anion generated subsequently attacks unreacted PADS on sulfur to give polysulfides, the active sulfurising agent. The rate of degradation of PADS is decreased by less basic substituted pyridines and is only first order in PADS indicating that the rate-limiting step is formation of the disulfide anion from the carbanion.
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Affiliation(s)
- James L Scotson
- Department of Chemistry, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
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8
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Smith M, Beck T. Quantitation of a low level coeluting impurity present in a modified oligonucleotide by both LC-MS and NMR. J Pharm Biomed Anal 2015; 118:34-40. [PMID: 26512997 DOI: 10.1016/j.jpba.2015.10.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/07/2015] [Accepted: 10/13/2015] [Indexed: 01/13/2023]
Abstract
This paper describes the use of two complementary techniques, LC-MS and NMR, to quantify a low level mono phosphate substituted impurity in an oligonucleotide drug substance. This impurity is the result of a sulphurisation failure, leading to the production of a sequence where a phosphorothioate linkage is replaced by a phosphate. Few quantitative methods are possible to analyse these challenging molecules especially if reversed phase ion pair chromatography, one of the most commonly used techniques for the separation of oligonucleotides, is unable to resolve the impurity in question. With the use of a standard addition method it could be demonstrated that both analytical techniques show equivalency and furthermore, the LC-MS method alone with additional validation has the potential to perform this quantitative assay with a high degree of accuracy.
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Affiliation(s)
- Marco Smith
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, UK.
| | - Tony Beck
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, UK
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9
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Rydzak JW, White DE, Airiau CY, Sterbenz JT, York BD, Clancy DJ, Dai Q. Real-Time Process Analytical Technology Assurance for Flow Synthesis of Oligonucleotides. Org Process Res Dev 2014. [DOI: 10.1021/op500035j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- James W. Rydzak
- Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - David E. White
- Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Christian Y. Airiau
- Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Jeffrey T. Sterbenz
- Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Brian D. York
- Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Donald J. Clancy
- Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Qunying Dai
- Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
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10
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To Market, To Market—2013. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2014. [DOI: 10.1016/b978-0-12-800167-7.00027-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
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11
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Wu L, White DE, Ye C, Vogt FG, Terfloth GJ, Matsuhashi H. Desulfurization of phosphorothioate oligonucleotides via the sulfur-by-oxygen replacement induced by the hydroxyl radical during negative electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:836-844. [PMID: 22791250 DOI: 10.1002/jms.3022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
While the occurrence of desulfurization of phosphorothioate oligonucleotides in solution is well established, this study represents the first attempt to investigate the basis of the unexpected desulfurization via the net sulfur-by-oxygen (S-O) replacement during negative electrospray ionization (ESI). The current work, facilitated by quantitative mass deconvolution, demonstrates that considerable desulfurization can take place even under common negative ESI operating conditions. The extent of desulfurization is dependent on the molar phosphorothioate oligonucleotide-to-hydroxyl radical ratio, which is consistent with the corona discharge-induced origin of the hydroxyl radical leading to the S-O replacement. This hypothesis is supported by the fact that an increase of the high-performance liquid chromatography (HPLC) flow rate and the on-column concentration of a phosphorothioate oligonucleotide, as well as a decrease of the electrospray voltage reduce the degree of desulfurization. Comparative LC-tandem mass spectrometry (MS/MS) sequencing of a phosphorothioate oligonucleotide and its corresponding desulfurization product revealed evidence that the S-O replacement occurs at multiple phosphorothioate internucleotide linkage sites. In practice, the most convenient and effective strategy for minimizing this P = O artifact is to increase the LC flow rate and the on-column concentration of phosphorothioate oligonucleotides. Another approach to mitigate possible detrimental effects of the undesired desulfurization is to operate the ESI source at a very low electrospray voltage to diminish the corona discharge; however this will significantly compromise sensitivity when analyzing the low-level P = O impurities in phosphorothioate oligonucleotides.
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Affiliation(s)
- Lianming Wu
- API Chemistry and Analysis, Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA 19406, USA.
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12
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Mukhlall JA, Hersh WH. Sulfurization of dinucleoside phosphite triesters with chiral disulfides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2012; 30:706-25. [PMID: 21902473 DOI: 10.1080/15257770.2011.597366] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Sixteen chiral analogues of phenylacetyl disulfide (PADS) and 5-methyl-3H-1,2,4-dithiazol-3-one (MEDITH) were used to sulfurize five dithymidine phosphite triesters, each incorporating a β-cyanoethoxy or siloxy group. Each mixture of S(P):R(P) phosphite triester diastereomers was combined with approximately one fourth of an equivalent of each of the sulfurizing reagents, and the R(PS):S(PS) diastereomer ratios of the resulting phosphite sulfides or phosphorothioates were determined by reverse-phase HPLC. Diastereoselectivities and corresponding diastereomeric excess (de) values were calculated by correcting for the starting triester diastereomer ratios. The highest de values for R(PS) and S(PS) phosphorothioates were 14.7% and 7.9%, respectively, both using MEDITH analogues.
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Affiliation(s)
- Joshua A Mukhlall
- Department of Chemistry and Biochemistry, Queens College and the Graduate Center of the City University of New York, Flushing, New York, USA
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13
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Sanghvi YS. A status update of modified oligonucleotides for chemotherapeutics applications. ACTA ACUST UNITED AC 2012; Chapter 4:Unit 4.1.1-22. [PMID: 21901670 DOI: 10.1002/0471142700.nc0401s46] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This unit presents an update of recent developments and clinical progress in chemically modified oliogonucleotides useful for therapeutic applications. During the last decade, the number of therapeutic oligonucleotides in clinical trials has nearly tripled. This is primarily due to advances in the synthesis protocols, better understanding of the biology, improved delivery, and better formulation technologies. Currently, over 100 clinical trials with oligonucleotide-based drugs are ongoing in the United States for potential treatment of a variety of life-threatening diseases. Among various oligonucleotides, antisense technology has been at the forefront, with one product on the market. Antisense technologies represent about half of the active clinical trials. Similarly, siRNA, aptamers, spiegelmers microRNA, shRNA, IMO, and CpG have been other active classes of oligonucleotides that are also undergoing clinical trials. This review attempts to summarize the current status of synthesis, chemical modifications, purification, and analysis in light of the rapid progress with multitude of oligonucleotides pursued as therapeutic modality.
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14
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Noll B, Seiffert S, Vornlocher HP, Roehl I. Characterization of small interfering RNA by non-denaturing ion-pair reversed-phase liquid chromatography. J Chromatogr A 2011; 1218:5609-17. [PMID: 21737080 DOI: 10.1016/j.chroma.2011.06.057] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 05/31/2011] [Accepted: 06/11/2011] [Indexed: 01/27/2023]
Abstract
Small interfering RNAs (siRNA) are emerging as a novel therapeutic modality for the specific inhibition of target gene expression. siRNA are typically formed by annealing of two complementary single stranded oligoribonucleotides. Compared to purity determination of non-hybridized single strands by denaturing chromatographic methods, characterization of the hybridized duplex is challenging. Here we are reporting a non-denaturing ion pairing-reversed phase (IP-RP) chromatography method capable of separating optimal duplex (full-length single strands only) from non-optimal duplex variants (containing shortmers, longmers and 2',5'-isomers) using ultraviolet- and mass spectrometric detection. The impact of different annealing conditions on siRNA composition was investigated. Optimized annealing conditions lead to a significant increase in optimal duplex, while total duplex content remained constant. The non-denaturing method reported herein showed high mass spectrometric sensitivity and superior separation efficiencies compared to other IP-RP buffer systems. The method is useful for in-process control and release testing of therapeutic double stranded nucleic acids such as siRNA.
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15
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Mukhlall JA, Noll BC, Hersh WH. Synthesis of chiral disulfides: potential reagents for enantioselective sulfurization. J Sulphur Chem 2011. [DOI: 10.1080/17415993.2011.580346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Joshua A. Mukhlall
- a Department of Chemistry and Biochemistry , Queens College and the Graduate Center of the City University of New York , Flushing , NY , 11367–1597 , USA
| | - Bruce C. Noll
- b Bruker AXS, Inc., 5465 East Cheryl Parkway, Madison , WI , 53711 , USA
| | - William H. Hersh
- a Department of Chemistry and Biochemistry , Queens College and the Graduate Center of the City University of New York , Flushing , NY , 11367–1597 , USA
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16
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Seiffert S, Debelak H, Hadwiger P, Jahn-Hofmann K, Roehl I, Vornlocher HP, Noll B. Characterization of side reactions during the annealing of small interfering RNAs. Anal Biochem 2011; 414:47-57. [PMID: 21376008 DOI: 10.1016/j.ab.2011.02.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 02/25/2011] [Accepted: 02/25/2011] [Indexed: 10/18/2022]
Abstract
Small interfering RNAs (siRNAs) are emerging as a novel therapeutic modality for the specific inhibition of target gene expression. The development of siRNA-based therapeutics requires in-depth knowledge of the manufacturing process as well as adequate analytical methods to characterize this class of molecules. Here the impurity formation during the annealing of siRNA was investigated. Two siRNAs containing common chemical RNA modifications (2'-O-methyl, 2'-deoxy-2'-fluoro, 2'-deoxy-ribose, and phosphorothioate linkages) were used to determine major side reactions-such as 2',3'-isomerization, strand scission, and HF elimination-depending on annealing parameters such as RNA concentration, presence of cations, temperature, and time. Individual impurities were characterized using analytical size exclusion chromatography, denaturing and nondenaturing ion-pair reversed-phase high-performance liquid chromatography, differential scanning calorimetry, and ultraviolet spectrometry. The degradation pathways described in this work can lead to significantly reduced product quality and compromised drug activity. The data reported here provide background to successfully address challenges associated with the manufacture of siRNAs and other nucleic acid therapeutics such as aptamers, spiegelmers, and decoy and antisense oligonucleotides.
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17
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Ravikumar VT, Kumar RK, Olsen P, Moore MN, Carty RL, Andrade M, Gorman D, Zhu X, Cedillo I, Wang Z, Mendez L, Scozzari AN, Aguirre G, Somanathan R, Berneès S. UnyLinker: An Efficient and Scaleable Synthesis of Oligonucleotides Utilizing a Universal Linker Molecule: A Novel Approach To Enhance the Purity of Drugs. Org Process Res Dev 2008. [DOI: 10.1021/op8000178] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vasulinga T. Ravikumar
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - R. Krishna Kumar
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Phil Olsen
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Max N. Moore
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Recaldo L. Carty
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Mark Andrade
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Dennis Gorman
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Xuefeng Zhu
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Isaiah Cedillo
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Zhiwei Wang
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Lucio Mendez
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Anthony N. Scozzari
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Gerardo Aguirre
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Ratnasamy Somanathan
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Sylvain Berneès
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
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18
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Wang Z, Olsen P, Ravikumar VT. A novel universal linker for efficient synthesis of phosphorothioate oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 26:259-69. [PMID: 17454735 DOI: 10.1080/15257770701257277] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A versatile and conformationally preorganized universal linker molecule is reported here for efficient synthesis of phosphorothioate oligonucleotides. With respect to nucleoside loaded support, comparable yield and quality based on ion-pair LC-MS are obtained for both deoxy and 2'-O-methoxyethyl modified phosphorothioate oligonucleotides. No 3'-phosphate or phosphorothioate monoester or any modification of universal molecule still attached to oligonucleotide was observed. [structure: see text]
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Affiliation(s)
- Zhiwei Wang
- Isis Pharmaceuticals, Carlsbad, California 92008. USA
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19
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Kumar RK, Olsen P, Ravikumar VT. An alternative advantageous protocol for efficient synthesis of phosphorothioate oligonucleotides utilizing phenylacetyl disulfide (PADS). NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 26:181-8. [PMID: 17365796 DOI: 10.1080/15257770601112739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Phosphorothioate oligonucleotides could be synthesized using a 0.2 M solution of phenylacetyl disulfide (PADS) in a mixture of pyridine and acetonitrile (1:1, v/v) with > 99.9% step-wise efficiency. Unlike most other sulfurizing reagents that need to be stable in solution for performance, PADS needs to degrade and "age" in solution and hence performs efficiently even after storing the solution at room temperature for over a month. High yield and quality of oligonucleotides are produced thereby offering an alternative attractive protocol for use of this efficient sulfurizing reagent.
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20
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Kumar RK, Guzaev AP, Rentel C, Ravikumar VT. Efficient synthesis of antisense phosphorothioate oligonucleotides using a universal solid support. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.02.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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21
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Cheruvallath ZS, Eleuteri A, Turney B, Ravikumar VT. (2-Acetoxyphenoxy)ethyl (APOE) as a Phosphate Protecting Group in Solid-Phase Synthesis of Oligonucleotides via the Phosphoramidite Approach. Org Process Res Dev 2006. [DOI: 10.1021/op0502147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Alessandra Eleuteri
- Isis Pharmaceuticals, Inc., 2282 Faraday Avenue, Carlsbad, California 92008, U.S.A
| | - Brett Turney
- Isis Pharmaceuticals, Inc., 2282 Faraday Avenue, Carlsbad, California 92008, U.S.A
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22
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Ravikumar VT, Andrade M, Carty RL, Dan A, Barone S. Development of siRNA for therapeutics: efficient synthesis of phosphorothioate RNA utilizing phenylacetyl disulfide (PADS). Bioorg Med Chem Lett 2006; 16:2513-7. [PMID: 16481168 DOI: 10.1016/j.bmcl.2006.01.081] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 01/20/2006] [Accepted: 01/20/2006] [Indexed: 12/01/2022]
Abstract
Efficient synthesis of phosphorothioate RNA (PS-RNA) is demonstrated by using phenylacetyl disulfide (PADS) in a mixture of pyridine and acetonitrile (1:1, v/v) for 3 min. Sulfurization is achieved with >99.8% stepwise efficiency. This reagent also performs efficiently during synthesis of RNA containing PS:PO mixed backbone.
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23
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Krotz AH, Hang A, Gorman D, Scozzari AN. Polysulfide reagent in solid-phase synthesis of phosphorothioate oligonucleotides: greater than 99.8% sulfurization efficiency. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:1293-9. [PMID: 16252666 DOI: 10.1080/15257770500230384] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A solution of sulfur (0.1 M) and sodium sulfide (0.01M) in 3-picoline, referred to as polysulfide reagent, rapidly converts trialkyl and triaryl phosphite triesters to the corresponding phosphorothioate derivatives. Greater than 99.8% average stepwise sulfurization efficiency is obtained in the solid-phase synthesis of DNA and RNA phosphorothioate olgonucleotides via the phosphoramidite approach.
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Affiliation(s)
- Achim H Krotz
- Isis Pharmaceuticals, Inc., Carlsbad, California 92008, USA
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