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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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Kundu J, Ghosh U, Ghosh A, Pattanayak S, Das A, Sinha S. Synthesis of Chlorophosphoramidate Monomer Morpholinos and PMOs. Curr Protoc 2023; 3:e686. [PMID: 36802170 DOI: 10.1002/cpz1.686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Phosphorodiamidate morpholino oligonucleotides (PMOs) are a successful class of antisense reagents that efficiently modulate gene expression. Because PMOs do not follow standard phosphoramidite chemistry, optimized synthetic protocols for these compounds are relatively scarce in the literature. This paper presents detailed protocols for synthesizing full-length PMOs using chlorophosphoramidate chemistry by manual solid-phase synthesis. We first describe the synthesis of Fmoc-protected morpholino hydroxyl monomers, and the corresponding chlorophosphoramidate monomers, from commercially available protected ribonucleosides. The new Fmoc chemistry necessitates the use of a milder base, such as N-ethylmorpholine (NEM), and coupling reagent, such as 5-(ethylthio)-1H-tetrazole (ETT), which are also tolerated for acid-sensitive trityl chemistry. These chlorophosphoramidate monomers are then employed for PMO synthesis in a manual solid-phase procedure using four sequential steps. The synthetic cycle for each nucleotide incorporation consists of (a) deblocking of the 3'-N protecting group using an acidic deblocking cocktail for trityl and base deblocking for Fmoc, (b) neutralization, (c) coupling in the presence of ETT and NEM, and (d) capping of the unreacted morpholine ring-amine. The method uses safe, stable, and inexpensive reagents, and the process is expected to be scalable. After full-length PMO synthesis and ammonia-mediated cleavage from the solid support and deprotection, a range of PMOs with different lengths can be obtained conveniently and efficiently with reproducible good yields. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of the novel Fmoc-protected morpholino monomers Basic Protocol 2: Synthesis of the phosphorylating reagent (N,N-dimethylphosphoramic dichloride) required for chlorophosphoramidate monomer synthesis Basic Protocol 3: Synthesis of chlorophosphoramidate monomers of Fmoc-protected morpholino monomers Basic Protocol 4: Solution-phase standardization of dimer and trimer PMO synthesis using Fmoc chemistry Basic Protocol 5: Solid-phase synthesis, purification, and characterization of full-length (25-mer) no-tail PMO using both trityl and Fmoc chemistry.
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Affiliation(s)
- Jayanta Kundu
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Ujjwal Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Sankha Pattanayak
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Arnab Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
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3
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Kundu J, Ghosh A, Ghosh U, Das A, Nagar D, Pattanayak S, Ghose A, Sinha S. Synthesis of Phosphorodiamidate Morpholino Oligonucleotides Using Trityl and Fmoc Chemistry in an Automated Oligo Synthesizer. J Org Chem 2022; 87:9466-9478. [PMID: 35839125 DOI: 10.1021/acs.joc.2c00265] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphorodiamidate morpholino oligonucleotides (PMOs) constitute 3 out of the 11 FDA-approved oligonucleotide-based drugs in the last 6 years. PMOs can effectively silence disease-causing genes and modify splicing. However, PMO synthesis has remained challenging for a variety of reasons: inefficient deprotection and coupling methods and instability of monomers. Here, we report the development of a suitable combination of resin supports, deblocking and coupling reagents for synthesizing PMOs using either trityl or Fmoc-protected chlorophosphoramidate monomers. The synthesized PMOs using both the methods on a solid support have been validated for gene silencing in a zebrafish model. The protocol was successfully transferred into an automated DNA synthesizer to make several sequences of PMOs, demonstrating for the first time the adaptation of regular PMOs in a commercial DNA synthesizer. Moreover, PMOs with longer than 20-mer sequences, including FDA-approved Eteplirsen (30-mer), were achieved in >20% overall yield that is superior to previous reports. Hybridization study shows that PMOs exhibit a higher binding affinity toward complementary DNA relative to the DNA/DNA duplex (>6 °C). Additionally, the introduction of Fmoc chemistry into PMOs opens up the possibility for PMO synthesis in commercial peptide synthesizers for future development.
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Affiliation(s)
- Jayanta Kundu
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Ujjwal Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Arnab Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Dhriti Nagar
- Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Sankha Pattanayak
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Aurnab Ghose
- Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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Li C, Callahan AJ, Simon MD, Totaro KA, Mijalis AJ, Phadke KS, Zhang G, Hartrampf N, Schissel CK, Zhou M, Zong H, Hanson GJ, Loas A, Pohl NLB, Verhoeven DE, Pentelute BL. Fully automated fast-flow synthesis of antisense phosphorodiamidate morpholino oligomers. Nat Commun 2021; 12:4396. [PMID: 34285203 PMCID: PMC8292409 DOI: 10.1038/s41467-021-24598-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/11/2021] [Indexed: 11/11/2022] Open
Abstract
Rapid development of antisense therapies can enable on-demand responses to new viral pathogens and make personalized medicine for genetic diseases practical. Antisense phosphorodiamidate morpholino oligomers (PMOs) are promising candidates to fill such a role, but their challenging synthesis limits their widespread application. To rapidly prototype potential PMO drug candidates, we report a fully automated flow-based oligonucleotide synthesizer. Our optimized synthesis platform reduces coupling times by up to 22-fold compared to previously reported methods. We demonstrate the power of our automated technology with the synthesis of milligram quantities of three candidate therapeutic PMO sequences for an unserved class of Duchenne muscular dystrophy (DMD). To further test our platform, we synthesize a PMO that targets the genomic mRNA of SARS-CoV-2 and demonstrate its antiviral effects. This platform could find broad application not only in designing new SARS-CoV-2 and DMD antisense therapeutics, but also for rapid development of PMO candidates to treat new and emerging diseases.
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MESH Headings
- Animals
- COVID-19/virology
- Chemistry Techniques, Synthetic/instrumentation
- Chemistry, Pharmaceutical/instrumentation
- Chlorocebus aethiops
- Communicable Diseases, Emerging/drug therapy
- Communicable Diseases, Emerging/microbiology
- Disease Models, Animal
- High-Throughput Screening Assays/instrumentation
- High-Throughput Screening Assays/methods
- Humans
- Morpholinos/chemical synthesis
- Morpholinos/pharmacology
- Morpholinos/therapeutic use
- Muscular Dystrophy, Duchenne/drug therapy
- Muscular Dystrophy, Duchenne/genetics
- Oligonucleotides, Antisense/chemical synthesis
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- Precision Medicine/methods
- RNA, Messenger/antagonists & inhibitors
- RNA, Viral/antagonists & inhibitors
- SARS-CoV-2/genetics
- Time Factors
- Vero Cells
- COVID-19 Drug Treatment
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Affiliation(s)
- Chengxi Li
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alex J Callahan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mark D Simon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kyle A Totaro
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexander J Mijalis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kruttika-Suhas Phadke
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Genwei Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nina Hartrampf
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- University of Zurich, Department of Chemistry, Zurich, Switzerland
| | - Carly K Schissel
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ming Zhou
- Sarepta Therapeutics, Cambridge, MA, USA
| | - Hong Zong
- Sarepta Therapeutics, Cambridge, MA, USA
| | | | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicola L B Pohl
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - David E Verhoeven
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Hofmeister A, Jahn-Hofmann K, Krack A, Müller A, Kurz M, Scheidler S. Novel Dioxane and Morpholino Nucleotide Analogues: Syntheses and RNA-Hybridization Properties. Chembiochem 2020; 22:1072-1078. [PMID: 33112485 DOI: 10.1002/cbic.202000693] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/26/2020] [Indexed: 11/09/2022]
Abstract
A novel class of nucleotide analogues with a dioxane ring as central scaffold has been developed. Synthetic routes in two diastereomeric series were realized, and the final thymidine analogues were synthesized with common functionalities for the automated oligonucleotide synthesis. The chemical space of the initially derived nucleotides was expanded by changing the central dioxane to analogous morpholine derivatives. This opens up the possibility for further derivatization by attaching different substituents at the morpholine nitrogen. The novel nucleotide building blocks were incorporated into double-stranded RNA sequences, and their hybridization properties investigated by melting-temperature analysis. Both scaffolds, dioxanes and morpholines, had an equal impact on double-strand stability, but Tm values differed depending on the chirality in the six-membered ring.
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Affiliation(s)
- Armin Hofmeister
- Sanofi R&D, Industrial Park Hoechst, G838, 65926, Frankfurt am Main, Germany
| | | | - Arne Krack
- Sanofi R&D, Industrial Park Hoechst, G838, 65926, Frankfurt am Main, Germany
| | - Armin Müller
- Sanofi R&D, Industrial Park Hoechst, G838, 65926, Frankfurt am Main, Germany
| | - Michael Kurz
- Sanofi R&D, Industrial Park Hoechst, G838, 65926, Frankfurt am Main, Germany
| | - Sabine Scheidler
- Sanofi R&D, Industrial Park Hoechst, G838, 65926, Frankfurt am Main, Germany
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Krishna H, Jastrzebska K, Caruthers M. Exploring site-specific activation of bis-N,N'-dialkylaminophosphordiamidites and the synthesis of morpholinophosphoramidate oligonucleotides. FEBS Lett 2019; 593:1459-1467. [PMID: 31206627 DOI: 10.1002/1873-3468.13492] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 11/05/2022]
Abstract
Morpholinos are six-membered rings that may provide higher conformational rigidity when incorporated into an oligonucleotide (ODN) backbone. Phosphorodiamidate morpholinos are chemically modified ODNs containing morpholinos in place of 2'-deoxyribose moieties throughout their backbone and have garnered much interest in recent years due to their ability to function as highly effective steric blockers in exon skipping therapy. To further explore the biophysical and biological properties of ODNs derived from morpholino nucleosides, we have replaced the 2'-deoxyribonucleotides of phosphodiester DNA with morpholinonucleotides to generate phosphoramidate ODNs. Here, we evaluate the mechanistic pathways observed during the solution-phase synthesis of morpholinonucleoside phosphoramidites, solid-phase synthesis of morpholinonucleotide phosphoramidates of mA, mG, mC and mT (prefix 'm' represents morpholino) and our first attempts directed at the solid-phase synthesis of chimeric DNA-phosphoramidate ODNs, as well as fully modified 22-mer phosphoramidate ODNs.
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Paul S, Caruthers MH. Synthesis of Phosphorodiamidate Morpholino Oligonucleotides and Their Chimeras Using Phosphoramidite Chemistry. J Am Chem Soc 2016; 138:15663-15672. [PMID: 27934012 DOI: 10.1021/jacs.6b08854] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Phosphorodiamidate morpholinos (PMOs) and PMO-DNA chimeras have been prepared on DNA synthesizers using phosphoramidite chemistry. This was possible by first generating boranephosphoroamidate morpholino internucleotide linkages followed by oxidative substitution with four different amines: N,N-dimethylamine, N-methylamine, ammonia, and morpholine. When compared to a natural DNA duplex, the amino modified PMO was found to have a higher melting temperature with either complementary DNA or RNA, whereas the remaining PMO analogues having morpholino, dimethylamino, or N-methylamino phosphorodiamidate linkages had melting temperatures that were either comparable or reduced. Additionally the N,N-dimethylamino PMO-DNA chimeras were found to stimulate RNaseH1 activity. Treatment of HeLa cells with fluorescently labeled PMO chimeras demonstrated that these analogues were efficiently taken up by cells in the presence of a lipid transfection reagent. Because of the simplistic synthesis procedures, various PMO analogues are now readily available and should therefore open new pathways for research into the antisense, diagnostic, and nanotechnology oligonucleotide fields.
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Affiliation(s)
- Sibasish Paul
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309, United States
| | - Marvin H Caruthers
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309, United States
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Bhadra J, Kundu J, Ghosh KC, Sinha S. Synthesis of phosphorodiamidate morpholino oligonucleotides by H-phosphonate method. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.05.080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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9
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Lithium bromide–DBU mediated synthesis of chlorophosphoramidate-activated morpholino nucleoside subunits. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.09.126] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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