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Parmar RG, Brown CR, Matsuda S, Willoughby JLS, Theile CS, Charissé K, Foster DJ, Zlatev I, Jadhav V, Maier MA, Egli M, Manoharan M, Rajeev KG. Facile Synthesis, Geometry, and 2'-Substituent-Dependent in Vivo Activity of 5'-(E)- and 5'-(Z)-Vinylphosphonate-Modified siRNA Conjugates. J Med Chem 2018; 61:734-744. [PMID: 29376650 DOI: 10.1021/acs.jmedchem.7b01147] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
(E)-Vinylphosphonate ((E)-VP), a metabolically stable phosphate mimic at the 5'-end of the antisense strand, enhances the in vivo potency of siRNA. Here we describe a straightforward synthetic approach to incorporate a nucleotide carrying a vinylphosphonate (VP) moiety at the 5'-end of oligonucleotides under standard solid-phase synthesis and deprotection conditions by utilizing pivaloyloxymethyl (POM) protected VP-nucleoside phosphoramidites. The POM protection enhances scope and scalability of 5'-VP-modified oligonucleotides and, in a broader sense, the synthesis of oligonucleotides modified with phosphonate moieties. Trivalent N-acetylgalactosamine-conjugated small interfering RNA (GalNAc-siRNA) comprising (E)-geometrical isomer of VP showed improved RISC loading with robust RNAi-mediated gene silencing in mice compared to the corresponding (Z)-isomer despite similar tissue accumulation. We also obtained structural insights into why bulkier 2'-ribosugar substitutions such as 2'-O-[2-(methylamino)-2-oxoethyl] are well tolerated only when combined with 5'-(E)-VP.
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Affiliation(s)
- Rubina Giare Parmar
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Christopher R Brown
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | | | - Christopher S Theile
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Klaus Charissé
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Donald J Foster
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Ivan Zlatev
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Vasant Jadhav
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin A Maier
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin Egli
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine , Nashville, Tennessee 37232, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
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Sable GA, Park J, Kim H, Lim SJ, Jang S, Lim D. Solid-Phase Total Synthesis of the Proposed Structure of Coibamide A and Its Derivative: Highly Methylated Cyclic Depsipeptides. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500697] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Martínez-Montero S, Fernández S, Rodríguez-Pérez T, Sanghvi YS, Wen K, Gotor V, Ferrero M. Improved Synthesis and Isolation of 2′-O-Methyladenosine: Effective and Scalable Enzymatic Separation of 2′/3′-O-Methyladenosine Regioisomers. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900348] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Taj SAS, Narayanan S, Meenakshi SS, Sanghvi YS, Ross BS, Ravikumar VT. Process research on the preparation of DMT protected 2'-O-methoxyethylguanosine for oligonucleotide synthesis in therapeutic applications. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 27:1024-33. [PMID: 18711665 DOI: 10.1080/15257770802271748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
An optimized process to synthesize DMT protected 2 '-O-methoxyethylguanosine is described. A key step involves the enzymatic deamination of a mixture of alkylated products to selectively afford the desired material without resorting to chromatography for purification. This approach was scaled up to kilogram quantities for use in oligonucleotide therapeutics. [Formula: see text].
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McGee DPC, Zhai Y. REACTION OF ANHYDRONUCLEOSIDES WITH MAGNESIUM ALKOXIDES: REGIOSPECIFIC SYNTHESIS OF 2′-O-ALKYLPYRIMIDINE NUCLEOSIDES. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319608002733] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Abstract
An efficient and chemoselective synthesis of 2'-O-methylguanosine (6) has been accomplished in high yield without protection of the guanine base. The salient feature of the synthesis of 6 lies in the application of methylene-bis-(diisopropylsilyl chloride), (MDPSCl(2), 2) as a new 3',5'-O-protecting group for nucleosides. Use of CH(3)Cl as a weak electrophile and NaHMDS as a mild base was crucial to the success of the 2'-O-methylation of 3',5'-O-protected guanosine.
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Affiliation(s)
- Suetying Chow
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla 92093-0358, USA
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Kozai S, Fuzikawa T, Harumoto K, Maruyama T. A new method for the synthesis of 2'-O-benzyladenosine using Mitsunobu reaction. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:145-51. [PMID: 12744602 DOI: 10.1081/ncn-120019506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A new method to introduce a benzyl group onto the 2'-OH of purine ribonucleoside is described. Thus, 6-chloropurine 3'-O-benzoylriboside and its 5'-O-trityl congener were condensed with benzyl alcohol using the Mitsunobu reaction to give the 2'-O-benzyl derivative. The yields were varied from 4.6 to 62.9% depending on the solvent used. The product was converted to adenosine, indicating that the stereochemistry at C-2' is retained.
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Affiliation(s)
- Shigetada Kozai
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
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Roy SK, Tang JY. Efficient Large Scale Synthesis of 2‘-O-Alkyl Pyrimidine Ribonucleosides. Org Process Res Dev 2000. [DOI: 10.1021/op990100t] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saroj K. Roy
- Hybridon Inc., 155 Fortune Boulevard, Milford, Massachusetts 01757
| | - Jin-yan Tang
- Hybridon Inc., 155 Fortune Boulevard, Milford, Massachusetts 01757
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Beigelman L, Haeberli P, Sweedler D, Karpeisky A. Improved Synthetic Approaches Toward 2′-O-Methyl-Adenosine and Guanosine and Their N-Acyl Derivatives. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00002-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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