1
|
Jastrzębska K. An efficient alternative to DBU in the oxathiaphospholane (OTP) method for the solid phase synthesis of P-stereodefined phosphorothioate analogs. RSC Adv 2024; 14:21174-21179. [PMID: 38966816 PMCID: PMC11223669 DOI: 10.1039/d4ra02833c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/23/2024] [Indexed: 07/06/2024] Open
Abstract
This study presents a modified (extended) 1,3,2-oxathiaphospholane (OTP) method for the synthesis of P-stereodefined phosphorothioate analogs in the presence of previously unused organic bases. TBD (5,7-triazabicyclo[4.4.0]dec-5-ene) and Verkade's proazaphosphatrane (2,8,9-trimethyl-2,5,8,9-tetraaza-1-phosphabicyclo[3.3.3]undecane) are herein used for the first time as efficient organic bases compared to DBU, which is commonly used in the OTP approach.
Collapse
Affiliation(s)
- Katarzyna Jastrzębska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
| |
Collapse
|
2
|
Togawa H, Okubo T, Horiuchi K, Yamaguchi T, Tomita-Sudo E, Akita T, Kawakami J, Obika S. Separation of the diastereomers of phosphorothioated siRNAs by anion-exchange chromatography under non-denaturing conditions. J Chromatogr A 2024; 1721:464847. [PMID: 38552370 DOI: 10.1016/j.chroma.2024.464847] [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: 02/06/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/13/2024]
Abstract
In recent years, several small interfering RNA (siRNA) therapeutics have been approved, and most of them are phosphorothioate (PS)-modified for improving nuclease resistance. This chemical modification induces chirality in the phosphorus atom, leading to the formation of diastereomers. Recent studies have revealed that Sp and Rp configurations of PS modifications of siRNAs have different biological properties, such as nuclease resistance and RNA-induced silencing complex (RISC) loading. These results highlight the importance of determining diastereomeric distribution in quality control. Although various analytical approaches have been used to separate diastereomers (mainly single-stranded oligonucleotides), it becomes more difficult to separate all of them as the number of PS modifications increases. Despite siRNA exhibits efficacy in the double-stranded form, few reports have examined the separation of diastereomers in the double-stranded form. In this study, we investigated the applicability of non-denaturing anion-exchange chromatography (AEX) for the separation of PS-modified siRNA diastereomers. Separation of the four isomers of the two PS bonds tended to improve in the double-stranded form compared to the single-stranded form. In addition, the effects of the analytical conditions and PS-modified position on the separation were evaluated. Moreover, the elution order of the Sp and Rp configurations was confirmed, and the steric difference between them, i.e., the direction of the anionic sulfur atom, appeared to be important for the separation mechanism in non-denaturing AEX. Consequently, all 16 peak tops of the four PS modifications were detected in one sequence, and approximately 30 peak tops were detected out of 64 isomers of six PS bonds, indicating that non-denaturing AEX is a useful technique for the quality control of PS-modified siRNA therapeutics.
Collapse
Affiliation(s)
- Hiroyuki Togawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; CERI Hita, Chemicals Evaluation and Research Institute, Japan, 3-822 Ishii-machi, Hita, Oita 877-0061, Japan
| | - Takashi Okubo
- CERI Hita, Chemicals Evaluation and Research Institute, Japan, 3-822 Ishii-machi, Hita, Oita 877-0061, Japan
| | - Kazuki Horiuchi
- CERI Hita, Chemicals Evaluation and Research Institute, Japan, 3-822 Ishii-machi, Hita, Oita 877-0061, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Elisa Tomita-Sudo
- Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Tomoka Akita
- Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Junji Kawakami
- Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
3
|
Li J, Luo S, Ouyang X, Wu G, Deng Z, He X, Zhao YL. Understanding base and backbone contributions of phosphorothioate DNA for molecular recognition with SBD proteins. Phys Chem Chem Phys 2023; 25:29289-29302. [PMID: 37876253 DOI: 10.1039/d3cp02820h] [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: 10/26/2023]
Abstract
Bacterial DNA phosphorothioate (PT) modification provides a specific anchoring site for sulfur-binding proteins (SBDs). Besides, their recognition patterns include phosphate links and bases neighboring the PT-modified site, thereby bringing about genome sequence-dependent properties in PT-related epigenetics. Here, we analyze the contributions of the DNA backbone (phosphates and deoxyribose) and bases bound with two SBD proteins in Streptomyces pristinaespiralis and coelicolor (SBDSco and SBDSpr). The chalcogen-hydrophobic interactions remained constantly at the anchoring site while the adjacent bases formed conditional and distinctive non-covalent interactions. More importantly, SBD/PT-DNA interactions were not limited within the traditional "4-bp core" range from 5'-I to 3'-III but extended to upstream 5'-II and 5'-III bases and even 5''-I to 5''-III at the non-PT-modified complementary strand. From the epigenetic viewpoint, bases 3'-II, 5''-I, and 5''-III of SBDSpr and 3'-II, 5''-II, and 5''-III of SBDSco present remarkable differentiations in the molecular recognitions. From the protein viewpoint, H102 in SBDSpr and R191 in SBDSco contribute significantly while proline residues at the PT-bound site are strictly conserved for the PT-chalcogen bond. The mutual and make-up mutations are proposed to alter the SBD/PT-DNA recognition pattern, besides additional chiral phosphorothioate modifications on phosphates 5'-II, 5'-II, 3'-I, and 3'-II.
Collapse
Affiliation(s)
- Jiayi Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Shenggan Luo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Xingyu Ouyang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Geng Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
4
|
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.
Collapse
Affiliation(s)
- Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| |
Collapse
|
5
|
Sato K, Nukaga Y, Wada T. Solid-phase synthesis and properties of stereocontrolled boranophosphate/phosphate and phosphorothioate/phosphate chimeric oligouridylates. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230095. [PMID: 37063986 PMCID: PMC10090885 DOI: 10.1098/rsos.230095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
This study describes the stereoselective synthesis of boranophosphate/phosphate (PB/PO) and phosphorothioate/phosphate (PS/PO) chimeric oligouridylates using the solid-phase method. Oxazaphospholidine monomer was used to construct the stereodefined PB and PS linkages. The study introduces modifications to oligouridylate derivatives in the intended positions with the intended stereochemistry of phosphorous atoms. Additionally, biophysical and biochemical properties of the synthesized oligomers were evaluated. Notably, it was found that a (Sp)-PB/PO chimeric oligouridylate had higher hybridization ability than the unmodified counterpart to an unmodified oligoadenylate. This is the first report that elucidates the effect of both stereochemistry and type of P-modification (PB and PS) on properties of oligoribonucleotides.
Collapse
Affiliation(s)
- Kazuki Sato
- Department of Medicinal and Life Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Yohei Nukaga
- Department of Medicinal and Life Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Takeshi Wada
- Department of Medicinal and Life Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| |
Collapse
|
6
|
Sato K, Chiba A, Shiraishi T, Ogawa Y, Hara RI, Wada T. Solid-phase synthesis of N-trichloroacetyl mannosamine 1-phosphate repeating units Mimicking capsular polysaccharide derived from Neisseria meningitidis serotype A. Carbohydr Res 2022; 518:108585. [DOI: 10.1016/j.carres.2022.108585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/02/2022]
|
7
|
Sequence-Specific Recognition of Double-Stranded DNA by Peptide Nucleic Acid Forming Double-Duplex Invasion Complex. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12073677] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Peptide nucleic acid (PNA) is an analog of natural nucleic acids, where the sugar-phosphate backbone of DNA is replaced by an electrostatically neutral N-(2-aminoethyl)glycine backbone. This unique peptide-based backbone enables PNAs to form a very stable duplex with the complementary nucleic acids via Watson–Crick base pairing since there is no electrostatic repulsion between PNA and DNA·RNA. With this high nucleic acid affinity, PNAs have been used in a wide range of fields, from biological applications such as gene targeting, to engineering applications such as probe and sensor developments. In addition to single-stranded DNA, PNA can also recognize double-stranded DNA (dsDNA) through the formation of a double-duplex invasion complex. This double-duplex invasion is hard to achieve with other artificial nucleic acids and is expected to be a promising method to recognize dsDNA in cellula or in vivo since the invasion does not require the prior denaturation of dsDNA. In this paper, we provide basic knowledge of PNA and mainly focus on the research of PNA invasion.
Collapse
|
8
|
Benkovics T, Peng F, Phillips EM, An C, Bade RS, Chung CK, Dance ZEX, Fier PS, Forstater JH, Liu Z, Liu Z, Maligres PE, Marshall NM, Salehi Marzijarani N, McIntosh JA, Miller SP, Moore JC, Neel AJ, Obligacion JV, Pan W, Pirnot MT, Poirier M, Reibarkh M, Sherry BD, Song ZJ, Tan L, Turnbull BWH, Verma D, Waldman JH, Wang L, Wang T, Winston MS, Xu F. Diverse Catalytic Reactions for the Stereoselective Synthesis of Cyclic Dinucleotide MK-1454. J Am Chem Soc 2022; 144:5855-5863. [PMID: 35333525 DOI: 10.1021/jacs.1c12106] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
As practitioners of organic chemistry strive to deliver efficient syntheses of the most complex natural products and drug candidates, further innovations in synthetic strategies are required to facilitate their efficient construction. These aspirational breakthroughs often go hand-in-hand with considerable reductions in cost and environmental impact. Enzyme-catalyzed reactions have become an impressive and necessary tool that offers benefits such as increased selectivity and waste limitation. These benefits are amplified when enzymatic processes are conducted in a cascade in combination with novel bond-forming strategies. In this article, we report a highly diastereoselective synthesis of MK-1454, a potent agonist of the stimulator of interferon gene (STING) signaling pathway. The synthesis begins with the asymmetric construction of two fluoride-bearing deoxynucleotides. The routes were designed for maximum convergency and selectivity, relying on the same benign electrophilic fluorinating reagent. From these complex subunits, four enzymes are used to construct the two bridging thiophosphates in a highly selective, high yielding cascade process. Critical to the success of this reaction was a thorough understanding of the role transition metals play in bond formation.
Collapse
Affiliation(s)
- Tamas Benkovics
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Feng Peng
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Eric M Phillips
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Chihui An
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Rachel S Bade
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Cheol K Chung
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Zachary E X Dance
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Patrick S Fier
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Jacob H Forstater
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Zhijian Liu
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Zhuqing Liu
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Peter E Maligres
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Nicholas M Marshall
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Nastaran Salehi Marzijarani
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - John A McIntosh
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Steven P Miller
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Jeffrey C Moore
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Andrew J Neel
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Jennifer V Obligacion
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Weilan Pan
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Michael T Pirnot
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Marc Poirier
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Mikhail Reibarkh
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Benjamin D Sherry
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Zhiguo Jake Song
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Lushi Tan
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Ben W H Turnbull
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Deeptak Verma
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Jacob H Waldman
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Lu Wang
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Tao Wang
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Matthew S Winston
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Feng Xu
- Department of Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| |
Collapse
|
9
|
Rook ME, Southwell AL. Antisense Oligonucleotide Therapy: From Design to the Huntington Disease Clinic. BioDrugs 2022; 36:105-119. [PMID: 35254632 PMCID: PMC8899000 DOI: 10.1007/s40259-022-00519-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2022] [Indexed: 12/14/2022]
Abstract
Huntington disease (HD) is a fatal progressive neurodegenerative disorder caused by an inherited mutation in the huntingtin (HTT) gene, which encodes mutant HTT protein. Though HD remains incurable, various preclinical studies have reported a favorable response to HTT suppression, emphasizing HTT lowering strategies as prospective disease-modifying treatments. Antisense oligonucleotides (ASOs) lower HTT by targeting transcripts and are well suited for treating neurodegenerative disorders as they distribute broadly throughout the central nervous system (CNS) and are freely taken up by neurons, glia, and ependymal cells. With the FDA approval of an ASO therapy for another disease of the CNS, spinal muscular atrophy, ASOs have become a particularly attractive therapeutic option for HD. However, two types of ASOs were recently assessed in human clinical trials for the treatment of HD, and both were halted early. In this review, we will explore the differences in chemistry, targeting, and specificity of these HTT ASOs as well as preliminary clinical findings and potential reasons for and implications of these halted trials.
Collapse
Affiliation(s)
- Morgan E Rook
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32827, USA.
| | - Amber L Southwell
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32827, USA
| |
Collapse
|
10
|
Hirano Y, Komatsu Y. Promotion of cytoplasmic localization of oligonucleotides by connecting cross-linked duplexes. RSC Adv 2022; 12:24471-24477. [PMID: 36128385 PMCID: PMC9425837 DOI: 10.1039/d2ra04375k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/22/2022] [Indexed: 11/21/2022] Open
Abstract
An interstrand cross-linked duplex (CD) modification promoted antisense oligonucleotide to be localized in the cytoplasm, resulting in effective knockdown microRNA in cytoplasm. In contrast, single-stranded antisense was confined in the nucleus.
Collapse
Affiliation(s)
- Yu Hirano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| |
Collapse
|
11
|
Roussis SG, Cedillo I, Rentel C. Characterizing the Diastereoisomeric Distribution of Phosphorothioate Oligonucleotides by Metal Ion Complexation Chromatography, In-Series Reversed Phase-Strong Anion Exchange Chromatography, and 31P NMR. Anal Chem 2021; 93:16035-16042. [PMID: 34813705 DOI: 10.1021/acs.analchem.1c03593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replacement of a non-bridging oxygen atom of the phosphate diester linkage of an oligonucleotide by sulfur conveys pharmacokinetic benefits, such as increased nuclease resistance and enhanced protein binding. Substitution renders the internucleotide linkages chiral, and so phosphorothioate diester (PS) oligonucleotides comprise complex mixtures of diastereoisomers. Currently, chromatographic separation of individual diastereoisomers is limited to oligonucleotides that contain no more than about four or five PS linkages. The development of therapeutic PS oligonucleotides, which often contain >15 PS linkages, would be greatly aided by methods useful for assessing batch-to-batch stereo-reproducibility. To this effect, the relative sensitivities of metal ion complexation chromatography (MICC), in-series reversed phase-strong anion exchange chromatography (RP-SAX), and 31P NMR toward changes in the diastereoisomeric distributions of therapeutic PS oligonucleotides were compared. Model oligonucleotides synthesized under conditions known to impact PS stereochemistry were used to evaluate the method performance, and all three methods showed excellent sensitivity toward changes in the diastereoisomeric composition. Interactions via the solvent-accessible areas and a combination of hydrophobic and electrostatic forces may be responsible for the selectivity demonstrated by MICC and in-series RP-SAX, respectively.
Collapse
Affiliation(s)
- Stilianos G Roussis
- Ionis Pharmaceuticals, 2855 Gazelle Ct., Carlsbad, California 92010, United States
| | - Isaiah Cedillo
- Ionis Pharmaceuticals, 2855 Gazelle Ct., Carlsbad, California 92010, United States
| | - Claus Rentel
- Ionis Pharmaceuticals, 2855 Gazelle Ct., Carlsbad, California 92010, United States
| |
Collapse
|
12
|
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: 15] [Impact Index Per Article: 5.0] [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.
Collapse
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
| |
Collapse
|
13
|
Advances on Greener Asymmetric Synthesis of Antiviral Drugs via Organocatalysis. Pharmaceuticals (Basel) 2021; 14:ph14111125. [PMID: 34832907 PMCID: PMC8625736 DOI: 10.3390/ph14111125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022] Open
Abstract
Viral infections cause many severe human diseases, being responsible for remarkably high mortality rates. In this sense, both the academy and the pharmaceutical industry are continuously searching for new compounds with antiviral activity, and in addition, face the challenge of developing greener and more efficient methods to synthesize these compounds. This becomes even more important with drugs possessing stereogenic centers as highly enantioselective processes are required. In this minireview, the advances achieved to improve synthetic routes efficiency and sustainability of important commercially antiviral chiral drugs are discussed, highlighting the use of organocatalytic methods.
Collapse
|
14
|
Sato K, Hagio T, Sano M, Muramoto K, Yaoita A, Noro M, Hara RI, Wada T. Solid-Phase Stereocontrolled Synthesis of Oligomeric P-Modified Glycosyl Phosphate Derivatives Using the Oxazaphospholidine Method. ACS OMEGA 2021; 6:20026-20041. [PMID: 34368588 PMCID: PMC8340430 DOI: 10.1021/acsomega.1c03058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/13/2021] [Indexed: 05/09/2023]
Abstract
Glycosyl phosphate repeating units can be found in the glycoconjugates of some bacteria and protozoa parasites. These structures and their P-modified analogs are attractive synthetic targets as antimicrobial, antiparasitic, and vaccine agents. However, P-modified glycosyl phosphates exist in different diastereomeric forms due to the chiral phosphorus atoms, whose configuration would highly affect their physiochemical and biochemical properties. In this study, a stereocontrolled method was developed for the synthesis of P-modified glycosyl phosphate repeating units derived from the lipophosphoglycan of Leishmania using the oxazaphospholidine approach. The solid-phase synthesis facilitated the elongation and purification of the glycosyl phosphate derivatives, while two P-modified glycosyl phosphates (boranophosphate and phosphorothioate) were successfully synthesized with up to three repeating units.
Collapse
Affiliation(s)
- Kazuki Sato
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Tomoya Hagio
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Michi Sano
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kazumasa Muramoto
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Aya Yaoita
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Mihoko Noro
- Department
of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience Building, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Rintaro Iwata Hara
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Department
of Neurology and Neurological Science, Graduate School of Medicinal
and Dental Sciences, Tokyo Medical and Dental
University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Takeshi Wada
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| |
Collapse
|
15
|
Ohkubo A, Muto K, Watanabe R, Ogata D. Chemical Synthesis of Modified Oligonucleotides Containing 5'-Amino-5'-Deoxy-5'-Hydroxymethylthymidine Residues. Curr Protoc 2021; 1:e70. [PMID: 33657278 DOI: 10.1002/cpz1.70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Introduction of cationic modifications into an oligonucleotide can increase its nuclease resistance and duplex- or triplex-forming abilities. In a recent study, we found that the nuclease resistance and RNA binding selectivity of an oligonucleotide containing a 5'-(R)-amino-5'-deoxy-5'-(R)-hydroxymethylthymidine residue were greater than those of the unmodified oligonucleotide. In this article, we describe the synthesis of 5'-amino-5'-deoxy-5'-hydroxymethylthymidine via dihydroxylation of the 5'-alkene derivative using either of two commercial AD (asymmetric dehydroxylation) mixes or via epoxidation and ring opening. We also provide detailed protocols for the syntheses of oligonucleotides containing 5'-amino-5'-deoxy-5'-hydroxymethylthymidine residues. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 5'-amino-5'-deoxy-5'-hydroxymethylthymidine phosphoramidites 9a and 9b Basic Protocol 2: Synthesis of oligonucleotides 1 and 2 containing 5'-amino-5'-deoxy-5'-hydoxymethylthymidine residues (R T and S T).
Collapse
Affiliation(s)
- Akihiro Ohkubo
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kousuke Muto
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Rintaro Watanabe
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Daisuke Ogata
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| |
Collapse
|
16
|
Liang X, Liu M, Komiyama M. Recognition of Target Site in Various Forms of DNA and RNA by Peptide Nucleic Acid (PNA): From Fundamentals to Practical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| |
Collapse
|
17
|
Numan A, Brichacek M. Asymmetric Synthesis of Stereogenic Phosphorus P(V) Centers Using Chiral Nucleophilic Catalysis. Molecules 2021; 26:3661. [PMID: 34203996 PMCID: PMC8232703 DOI: 10.3390/molecules26123661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 11/21/2022] Open
Abstract
Organophosphates have been widely used in agrochemistry, as reagents for organic synthesis, and in biochemistry. Phosphate mimics possessing four unique substituents, and thereby a chirality center, are useful in transition metal catalysis and as nucleotide therapeutics. The catalytic, stereocontrolled synthesis of phosphorus-stereogenic centers is challenging and traditionally depends on a resolution or use of stochiometric auxiliaries. Herein, enantioenriched phosphorus centers have been synthesized using chiral nucleophilic catalysis. Racemic H-phosphinate species were coupled with nucleophilic alcohols under halogenating conditions. Chiral phosphonate products were synthesized in acceptable yields (33-95%) and modest enantioselectivity (up to 62% ee) was observed after identification of an appropriate chiral catalyst and optimization of the solvent, base, and temperature. Nucleophilic catalysis has a tremendous potential to produce enantioenriched phosphate mimics that could be used as prodrugs or chemical biology probes.
Collapse
|
18
|
Wang M, Zhang L, Huo X, Zhang Z, Yuan Q, Li P, Chen J, Zou Y, Wu Z, Zhang W. Catalytic Asymmetric Synthesis of the anti‐COVID‐19 Drug Remdesivir. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011527] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Mo Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Frontiers Science Center for Transformative Molecules School of Chemistry and Chemical Engineering Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
- School of Pharmacy Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Lu Zhang
- School of Pharmacy Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Xiaohong Huo
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Frontiers Science Center for Transformative Molecules School of Chemistry and Chemical Engineering Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Zhenfeng Zhang
- School of Pharmacy Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Qianjia Yuan
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Frontiers Science Center for Transformative Molecules School of Chemistry and Chemical Engineering Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Panpan Li
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Frontiers Science Center for Transformative Molecules School of Chemistry and Chemical Engineering Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Jianzhong Chen
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Frontiers Science Center for Transformative Molecules School of Chemistry and Chemical Engineering Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Yashi Zou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Frontiers Science Center for Transformative Molecules School of Chemistry and Chemical Engineering Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Zhengxing Wu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Frontiers Science Center for Transformative Molecules School of Chemistry and Chemical Engineering Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Wanbin Zhang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Frontiers Science Center for Transformative Molecules School of Chemistry and Chemical Engineering Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
- School of Pharmacy Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| |
Collapse
|
19
|
Wang M, Zhang L, Huo X, Zhang Z, Yuan Q, Li P, Chen J, Zou Y, Wu Z, Zhang W. Catalytic Asymmetric Synthesis of the anti-COVID-19 Drug Remdesivir. Angew Chem Int Ed Engl 2020; 59:20814-20819. [PMID: 32870563 DOI: 10.1002/anie.202011527] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Indexed: 01/12/2023]
Abstract
The catalytic asymmetric synthesis of the anti-COVID-19 drug Remdesivir has been realized by the coupling of the P-racemic phosphoryl chloride with protected nucleoside GS441524. The chiral bicyclic imidazole catalyst used is crucial for the dynamic kinetic asymmetric transformation (DyKAT) to proceed smoothly with high reactivity and excellent stereoselectivity (96 % conv., 22:1 SP :RP ). Mechanistic studies showed that this DyKAT is a first-order visual kinetic reaction dependent on the catalyst concentration. The unique chiral bicyclic imidazole skeleton and carbamate substituent of the catalyst are both required for the racemization process, involving the phosphoryl chloride, and subsequent stereodiscriminating step. A 10 gram scale reaction was also conducted with comparably excellent results, showing its potential for industrial application.
Collapse
Affiliation(s)
- Mo Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.,School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Lu Zhang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xiaohong Huo
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Zhenfeng Zhang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Qianjia Yuan
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Panpan Li
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jianzhong Chen
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yashi Zou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Zhengxing Wu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Wanbin Zhang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.,School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| |
Collapse
|
20
|
Kawaguchi D, Kodama A, Abe N, Takebuchi K, Hashiya F, Tomoike F, Nakamoto K, Kimura Y, Shimizu Y, Abe H. Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Daisuke Kawaguchi
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Ayumi Kodama
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Naoko Abe
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- Research Center for Materials Science Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Kei Takebuchi
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Fumiaki Tomoike
- Research Center for Materials Science Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Kosuke Nakamoto
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Yasuaki Kimura
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Yoshihiro Shimizu
- Biodynamics Research Center (BDR) RIKEN 6-2-3, Furuedai Suita Osaka 565-0874 Japan
| | - Hiroshi Abe
- Chemistry Department Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- Research Center for Materials Science Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- CREST (Japan) Science and Technology Agency 7, Gobancho, Chiyoda-ku Tokyo 102-0076 Japan
- Institute for Glyco-core Research Tokai National Higher Education and Research System Furo-cho, Chikusa-ku Nagoya Aichi 464-8601 Japan
| |
Collapse
|
21
|
Kawaguchi D, Kodama A, Abe N, Takebuchi K, Hashiya F, Tomoike F, Nakamoto K, Kimura Y, Shimizu Y, Abe H. Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis. Angew Chem Int Ed Engl 2020; 59:17403-17407. [PMID: 32627275 DOI: 10.1002/anie.202007111] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Indexed: 01/19/2023]
Abstract
Messenger RNAs (mRNAs) with phosphorothioate modification (PS-mRNA) to the phosphate site of A, G, C, and U with all 16 possible combinations were prepared, and the translation reaction was evaluated using an E. coli cell-free translation system. Protein synthesis from PS-mRNA increased in 12 of 15 patterns when compared with that of unmodified mRNA. The protein yield increased 22-fold when the phosphorothioate modification at A/C sites was introduced into the region from the 5'-end to the initiation codon. Single-turnover analysis of PS-mRNA translation showed that phosphorothioate modification increases the number of translating ribosomes, thus suggesting that the rate of translation initiation (rate of ribosome complex formation) is positively affected by the modification. The method provides a new strategy for improving translation by using non-natural mRNA.
Collapse
Affiliation(s)
- Daisuke Kawaguchi
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Ayumi Kodama
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Naoko Abe
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kei Takebuchi
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Fumiaki Tomoike
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kosuke Nakamoto
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yasuaki Kimura
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yoshihiro Shimizu
- Biodynamics Research Center (BDR), RIKEN, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Hiroshi Abe
- Chemistry Department, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,CREST (Japan) Science and Technology Agency, 7, Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.,Institute for Glyco-core Research, Tokai National Higher Education and Research System, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| |
Collapse
|
22
|
Sato K, Wada T. Development of Efficient Synthetic Methods of Boranophosphate Oligonucleotides. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences, Tokyo University of Science
| |
Collapse
|
23
|
Hyjek-Składanowska M, Vickers TA, Napiórkowska A, Anderson BA, Tanowitz M, Crooke ST, Liang XH, Seth PP, Nowotny M. Origins of the Increased Affinity of Phosphorothioate-Modified Therapeutic Nucleic Acids for Proteins. J Am Chem Soc 2020; 142:7456-7468. [PMID: 32202774 DOI: 10.1021/jacs.9b13524] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The phosphorothioate backbone modification (PS) is one of the most widely used chemical modifications for enhancing the drug-like properties of nucleic acid-based drugs, including antisense oligonucleotides (ASOs). PS-modified nucleic acid therapeutics show improved metabolic stability from nuclease-mediated degradation and exhibit enhanced interactions with plasma, cell-surface, and intracellular proteins, which facilitates their tissue distribution and cellular uptake in animals. However, little is known about the structural basis of the interactions of PS nucleic acids with proteins. Here, we report a crystal structure of the DNA-binding domain of a model ASO-binding protein PC4, in complex with a full PS 2'-OMe DNA gapmer ASO. To our knowledge this is the first structure of a complex between a protein and fully PS nucleic acid. Each PC4 dimer comprises two DNA-binding interfaces. In the structure one interface binds the 5'-terminal 2'-OMe PS flank of the ASO, while the other interface binds the regular PS DNA central part in the opposite polarity. As a result, the ASO forms a hairpin-like structure. ASO binding also induces the formation of a dimer of dimers of PC4, which is stabilized by base pairing between homologous regions of the ASOs bound by each dimer of PC4. The protein interacts with the PS nucleic acid through a network of electrostatic and hydrophobic interactions, which provides insights into the origins for the enhanced affinity of PS for proteins. The importance of these contacts was further confirmed in a NanoBRET binding assay using a Nano luciferase tagged PC4 acting as the BRET donor, to a fluorescently conjugated ASO acting as the BRET acceptor. Overall, our results provide insights into the molecular forces that govern the interactions of PS ASOs with cellular proteins and provide a potential model for how these interactions can template protein-protein interactions causative of cellular toxicity.
Collapse
Affiliation(s)
- Malwina Hyjek-Składanowska
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland.,Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland
| | - Timothy A Vickers
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Agnieszka Napiórkowska
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland.,Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland
| | - Brooke A Anderson
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Michael Tanowitz
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Stanley T Crooke
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Xue-Hai Liang
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P Seth
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Marcin Nowotny
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland.,Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland
| |
Collapse
|
24
|
Islam MA, Fujisaka A, Kawakami J, Yamaguchi T, Obika S. Different reactivity of Sp and Rp isomers of phosphorothioate-modified oligonucleotides in a duplex structure. Bioorg Med Chem Lett 2020; 30:127166. [PMID: 32527537 DOI: 10.1016/j.bmcl.2020.127166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 10/24/2022]
Abstract
The presence of a stereoisomeric center at the phosphorus atom in phosphorothioate-modified oligonucleotides (PS-ONs) has been recognized as an important feature since the early stages of their development. Therefore, several studies have been conducted on the chirality of PS-ONs. In this study, we evaluated the stereo-biased chemistry of PS-ON duplexes. Depending on their absolute configurations, PS-ON duplexes were found to have significantly different and stereospecific reactivities towards simple alkylating reagent.
Collapse
Affiliation(s)
- Md Ariful Islam
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali 3814, Bangladesh
| | - Aki Fujisaka
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Faculty of Pharmacy, Osaka Ohtani University, Nishikiori-Kita 3-11-1, Tondabayashi, Osaka 584-8540, Japan
| | - Junji Kawakami
- Faculty of Frontiers of Innovative Research in Science and Technology, Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Takao Yamaguchi
- 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.
| |
Collapse
|
25
|
Duschmalé J, Hansen HF, Duschmalé M, Koller E, Albaek N, Møller MR, Jensen K, Koch T, Wengel J, Bleicher K. In vitro and in vivo properties of therapeutic oligonucleotides containing non-chiral 3' and 5' thiophosphate linkages. Nucleic Acids Res 2020; 48:63-74. [PMID: 31754711 PMCID: PMC6943131 DOI: 10.1093/nar/gkz1099] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 10/28/2019] [Accepted: 11/07/2019] [Indexed: 11/12/2022] Open
Abstract
The introduction of non-bridging phosphorothioate (PS) linkages in oligonucleotides has been instrumental for the development of RNA therapeutics and antisense oligonucleotides. This modification offers significantly increased metabolic stability as well as improved pharmacokinetic properties. However, due to the chiral nature of the phosphorothioate, every PS group doubles the amount of possible stereoisomers. Thus PS oligonucleotides are generally obtained as an inseparable mixture of a multitude of diastereoisomeric compounds. Herein, we describe the introduction of non-chiral 3′ thiophosphate linkages into antisense oligonucleotides and report their in vitro as well as in vivo activity. The obtained results are carefully investigated for the individual parameters contributing to antisense activity of 3′ and 5′ thiophosphate modified oligonucleotides (target binding, RNase H recruitment, nuclease stability). We conclude that nuclease stability is the major challenge for this approach. These results highlight the importance of selecting meaningful in vitro experiments particularly when examining hitherto unexplored chemical modifications.
Collapse
Affiliation(s)
- Jörg Duschmalé
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
- To whom correspondence should be addressed. Tel: +41 61 68 86081; Fax: +41 61 68 88714;
| | - Henrik Frydenlund Hansen
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Martina Duschmalé
- Pharmaceutical Sciences, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Erich Koller
- Pharmaceutical Sciences, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Nanna Albaek
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Marianne Ravn Møller
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Klaus Jensen
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Troels Koch
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Konrad Bleicher
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| |
Collapse
|
26
|
Diastereoselective Synthesis of Phosphorodiamidate Morpholino Dimers. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.11958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
27
|
Sakamuri S, Eltepu L, Liu D, Lam S, Meade BR, Liu B, Dello Iacono G, Kabakibi A, Luukkonen L, Leedom T, Foster M, Bradshaw CW. Impact of Phosphorothioate Chirality on Double-Stranded siRNAs: A Systematic Evaluation of Stereopure siRNA Designs. Chembiochem 2020; 21:1304-1308. [PMID: 31863714 DOI: 10.1002/cbic.201900630] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/19/2019] [Indexed: 12/16/2022]
Abstract
Oligonucleotides are important therapeutic approaches, as evidenced by recent clinical successes with antisense oligonucleotides (ASOs) and double-stranded short interfering RNAs (siRNAs). Phosphorothioate (PS) modifications are a standard feature in the current generation of oligonucleotide therapeutics, but generate isomeric mixtures, leading to 2n isomers. All currently marketed therapeutic oligonucleotides (ASOs and siRNAs) are complex isomeric mixtures. Recent chemical methodologies for stereopure PS insertions have resulted in preliminary rules for ASOs, with multiple stereopure ASOs moving into clinical development. Although siRNAs have comparatively fewer PSs, the field has yet to embrace the idea of stereopure siRNAs. Herein, it has been investigated whether the individual isomers contribute equally to the in vivo activity of a representative siRNA. The results of a systematic evaluation of stereopure PS incorporation into antithrombin-3 (AT3) siRNA are reported and demonstrate that individual PS isomers dramatically affect in vivo activity. A standard siRNA design with six PS insertions was investigated and it was found that only about 10 % of the 64 possible isomers were as efficacious as the stereorandom control. Based on this data, it can be concluded that G1R stereochemistry is critical, G2R is important, G21S is preferable, and G22 and P1/P2 tolerate both isomers. Surprisingly, the disproportionate loss of efficacy for most isomers does not translate into significant gain for the productive isomers, and thus, warrants further mechanistic studies.
Collapse
Affiliation(s)
- Sukumar Sakamuri
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | - Laxman Eltepu
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | - Dingguo Liu
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | - Son Lam
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | - Bryan R Meade
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | - Bin Liu
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | | | - Ayman Kabakibi
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | - Lena Luukkonen
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | - Tom Leedom
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | - Mark Foster
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | - Curt W Bradshaw
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| |
Collapse
|
28
|
Sakamuri S, Liu D, Eltepu L, Liu B, Reboton LJ, Preston R, Bradshaw CW. Identification of a Tricyclic P III Chiral Auxiliary for Solid-Supported Synthesis of Stereopure Phosphorothioate-Containing Oligonucleotides. Chembiochem 2020; 21:1298-1303. [PMID: 31863718 DOI: 10.1002/cbic.201900631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/19/2019] [Indexed: 12/27/2022]
Abstract
Since the recognition of oligonucleotides as a therapeutic modality, significant work has been devoted to improving therapeutic properties, including nuclease stability. Phosphorothioate (PS) modifications of phosphodiesters are one of the most explored chemical modification and integral to currently approved oligonucleotide therapeutics, including antisense oligonucleotides (ASOs) and short interfering RNAs (siRNAs). Insertion of sulfur into the phosphate bridge in an n-mer leads to 2n isomeric mixtures of PSs, with different nuclease stability and protein-binding properties. Efforts to create stereopure PS-containing oligonucleotides has spurred interest in identifying new synthetic methods. Herein, work on a novel and practical tricyclic PIII chiral auxiliary and its application in solid-supported synthesis of stereopure PS-containing oligonucleotides is reported.
Collapse
Affiliation(s)
- Sukumar Sakamuri
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | - Dingguo Liu
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | - Laxman Eltepu
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | - Bin Liu
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | - Lisa Jo Reboton
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | - Ryan Preston
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| | - Curt W Bradshaw
- Solstice Biologics, 9535 Waples Street, San Diego, CA, 92121, USA
| |
Collapse
|
29
|
Simulescu V, Ilia G. Solid-phase Synthesis of Phosphorus Derivatives. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190213112019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The solid-phase synthesis (SPS) of phosphorus-containing compounds is based mainly on the fact that the chemical process is conducted in a two-phase system. One of the components is connected via covalent bonds to a solid support, which is in general an insoluble polymer, representing the solid phase of the process. The other components involved into the process are solubilized in a solution. The method is suitable to be applied to almost any organic compounds. A common example of using solid-phase synthesis is for obtaining products nucleotide containing, similar to nucleic acids. During the whole process, the nucleotide is always on the solid phase, after the condensation reaction, except for the last step, when the synthesis is already finished. Then, the product is released and separated very easily by filtration. The obtained polymer-oligonucleotide product can participate further in condensation reactions as well. Other important biomolecules synthesized by solid-phase approach during the last decades are nucleoside di- and triphosphates, nucleoside diphosphate sugars and dinucleoside polyphosphates. Those products are precursors of deoxysugars, aminodeoxysugars, uronic acids or glycoconjugates, and are also necessary for DNA and RNA synthesis. The use of the solid-phase method in the context of immobilized oligomers is of great interest nowadays. The solid-phase synthesis offers many advantages in comparison with the conventional solution-phase method, because it takes much less time, it is highly stereoselective, the products are separated and purified usually by a simple filtration or decantation, solvents with high boiling points could be used, the whole process is based on solid polymer support and the obtained compounds should not be isolated.
Collapse
Affiliation(s)
- Vasile Simulescu
- Institute of Chemistry Timisoara of Romanian Academy, 24 Mihai Viteazul Bvd., 300223 Timisoara, Romania
| | - Gheorghe Ilia
- Institute of Chemistry Timisoara of Romanian Academy, 24 Mihai Viteazul Bvd., 300223 Timisoara, Romania
| |
Collapse
|
30
|
Shigi N, Mizuno Y, Kunifuda H, Matsumura K, Komiyama M. Promotion of Single-Strand Invasion of PNA to Double-Stranded DNA by Pseudo-Complementary Base Pairing. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Narumi Shigi
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yuki Mizuno
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Department of Materials Science & Engineering, Shibaura Institute of Technology, 3-7-5 Toyosu, Koto-ku, Tokyo 135-8548, Japan
| | - Hiroko Kunifuda
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Kazunari Matsumura
- Department of Materials Science & Engineering, Shibaura Institute of Technology, 3-7-5 Toyosu, Koto-ku, Tokyo 135-8548, Japan
| | - Makoto Komiyama
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| |
Collapse
|
31
|
Hibino M, Aiba Y, Watanabe Y, Shoji O. Peptide Nucleic Acid Conjugated with Ruthenium-Complex Stabilizing Double-Duplex Invasion Complex Even under Physiological Conditions. Chembiochem 2018; 19:1601-1604. [PMID: 29797750 DOI: 10.1002/cbic.201800256] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Indexed: 02/03/2023]
Abstract
Peptide nucleic acid (PNA) can form a stable duplex with DNA, and, accordingly, directly recognize double-stranded DNA through the formation of a double-duplex invasion complex, wherein a pair of complementary PNA strands form two PNA/DNA duplexes. Because invasion does not require prior denaturation of DNA, PNA holds great potential for in cellulo or in vivo applications. To broaden the applicability of PNA invasion, we developed a new conjugate of PNA with a ruthenium complex. This Ru-PNA conjugate exhibits higher DNA-binding affinity, which results in enhanced invasion efficiency, even under physiological conditions.
Collapse
Affiliation(s)
- Masaki Hibino
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-Cho Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-Cho Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| | - Yoshihito Watanabe
- Research Center for Materials Science, Nagoya University, Furo-Cho Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-Cho Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| |
Collapse
|
32
|
Islam MA, Fujisaka A, Mori S, Ito KR, Yamaguchi T, Obika S. Synthesis and biophysical properties of 5'-thio-2',4'-BNA/LNA oligonucleotide. Bioorg Med Chem 2018; 26:3634-3638. [PMID: 29886084 DOI: 10.1016/j.bmc.2018.05.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 10/16/2022]
Abstract
Phosphorothioate modification of oligonucleotides is one of the most promising chemical modifications in nucleic acid therapeutics. Structurally similar 5'-thio or phosphorothiolate-modified nucleotides, in which the 5'-bridging oxygen atom is replaced with a sulfur atom, are attracting attention and gaining importance in oligonucleotide-based research. In our present study, we synthesized 5'-thio-2',4'-BNA/LNA monomers bearing thymine or 5-methylcytosine nucleobase. The 5'-thio-2',4'-BNA/LNA monomers were successfully incorporated into target oligonucleotides, and their nuclease stability and binding affinity with complementary strands were evaluated.
Collapse
Affiliation(s)
- Md Ariful Islam
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali 3814, Bangladesh
| | - Aki Fujisaka
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Faculty of Pharmacy, Osaka Ohtani University, Nishikiori-Kita 3-11-1, Tondabayashi, Osaka 584-8540, Japan
| | - Shohei Mori
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kosuke Ramon Ito
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takao Yamaguchi
- 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.
| |
Collapse
|
33
|
Granger E, Solomianko K, Young C, Erb J. Exploration of chiral Lewis acid Mg 2+ catalysts in the synthesis of aryl organophosphate triesters from phosphorus oxychloride through a three-step, two-pot substitution sequence. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.02.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
34
|
Kuwabara K, Maekawa Y, Minoura M, Murai T. Hydrolysis of Phosphonothioates with a Binaphthyl Group: P-Stereogenic O-Binaphthyl Phosphonothioic Acids and Their Use as Optically Active Ligands and Chiral Discriminating Agents. Org Lett 2018; 20:1375-1379. [PMID: 29431445 DOI: 10.1021/acs.orglett.8b00147] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The hydrolysis of phosphonothioates with a binaphthyl group afforded the first example of O-(2'-hydroxy)binaphthyl phosphonothioic acids in good to high yields and >95:5 diastereoselectivity. The reaction proceeds via an axis-to-center chirality-transfer reaction. The ability of these acids to act as chiral molecular auxiliaries was demonstrated by using them as optically active ligands for the asymmetric ethylation of benzaldehyde and as a chiral discriminating agent for chiral aliphatic amines.
Collapse
Affiliation(s)
- Kazuma Kuwabara
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University , Yanagido, Gifu 501-1193, Japan
| | - Yuuki Maekawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University , Yanagido, Gifu 501-1193, Japan
| | - Mao Minoura
- Department of Chemistry, Graduate School of Science, Rikkyo University , Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Toshiaki Murai
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University , Yanagido, Gifu 501-1193, Japan
| |
Collapse
|
35
|
El Zahar NM, Magdy N, El-Kosasy AM, Bartlett MG. Chromatographic approaches for the characterization and quality control of therapeutic oligonucleotide impurities. Biomed Chromatogr 2017; 32. [PMID: 28869310 DOI: 10.1002/bmc.4088] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/13/2017] [Accepted: 08/28/2017] [Indexed: 12/16/2022]
Abstract
Phosphorothioate (PS) oligonucleotides are a rapidly rising class of drugs with significant therapeutic applications. However, owing to their complex structure and multistep synthesis and purification processes, generation of low-level impurities and degradation products are common. Therefore, they require significant investment in quality control and impurity identification. This requires the development of advanced methods for analysis, characterization and quantitation. In addition, the presence of the PS linkage leads to the formation of chiral centers which can affect their biological properties and therapeutic efficiency. In this review, the different types of oligonucleotide impurities and degradation products, with an emphasis on their origin, mechanism of formation and methods to reduce, prevent or even eliminate their production, will be extensively discussed. This review will focus mainly on the application of chromatographic techniques to determine these impurities but will also discuss other approaches such as mass spectrometry, capillary electrophoresis and nuclear magnetic resonance spectroscopy. Finally, the chirality and formation of diastereomer mixtures of PS oligonucleotides will be covered as well as approaches used for their characterization and the application for the development of stereochemically-controlled PS oligonucleotides.
Collapse
Affiliation(s)
- N M El Zahar
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.,Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, USA
| | - N Magdy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - A M El-Kosasy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, USA
| |
Collapse
|
36
|
Iwamoto N, Butler DCD, Svrzikapa N, Mohapatra S, Zlatev I, Sah DWY, Meena, Standley SM, Lu G, Apponi LH, Frank-Kamenetsky M, Zhang JJ, Vargeese C, Verdine GL. Control of phosphorothioate stereochemistry substantially increases the efficacy of antisense oligonucleotides. Nat Biotechnol 2017; 35:845-851. [PMID: 28829437 DOI: 10.1038/nbt.3948] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 07/26/2017] [Indexed: 12/26/2022]
Abstract
Whereas stereochemical purity in drugs has become the standard for small molecules, stereoisomeric mixtures containing as many as a half million components persist in antisense oligonucleotide (ASO) therapeutics because it has been feasible neither to separate the individual stereoisomers, nor to synthesize stereochemically pure ASOs. Here we report the development of a scalable synthetic process that yields therapeutic ASOs having high stereochemical and chemical purity. Using this method, we synthesized rationally designed stereopure components of mipomersen, a drug comprising 524,288 stereoisomers. We demonstrate that phosphorothioate (PS) stereochemistry substantially affects the pharmacologic properties of ASOs. We report that Sp-configured PS linkages are stabilized relative to Rp, providing stereochemical protection from pharmacologic inactivation of the drug. Further, we elucidated a triplet stereochemical code in the stereopure ASOs, 3'-SpSpRp, that promotes target RNA cleavage by RNase H1 in vitro and provides a more durable response in mice than stereorandom ASOs.
Collapse
Affiliation(s)
| | | | | | | | - Ivan Zlatev
- Wave Life Sciences, Cambridge, Massachusetts, USA
| | | | - Meena
- Wave Life Sciences, Cambridge, Massachusetts, USA
| | | | - Genliang Lu
- Wave Life Sciences, Cambridge, Massachusetts, USA
| | | | | | | | | | - Gregory L Verdine
- Wave Life Sciences, Cambridge, Massachusetts, USA.,Department of Stem Cell and Regenerative Biology, Department of Chemistry and Chemical Biology, Harvard University and Harvard Medical School, Cambridge, Massachusetts, USA
| |
Collapse
|
37
|
Li M, Lightfoot HL, Halloy F, Malinowska AL, Berk C, Behera A, Schümperli D, Hall J. Synthesis and cellular activity of stereochemically-pure 2'-O-(2-methoxyethyl)-phosphorothioate oligonucleotides. Chem Commun (Camb) 2017; 53:541-544. [PMID: 27966701 DOI: 10.1039/c6cc08473g] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Stereochemically-pure 2'-O-(2-methoxyethyl)-phosphorothioate (PS-MOE) oligonucleotides were synthesized from new chiral oxazaphospholidine-containing nucleosides. Thermal stability studies showed that the incorporation of Rp-PS linkages increased RNA-binding affinity. In cells, a full Rp-PS-MOE splice-switching oligonucleotide targeting part of the ferrochelatase gene was more potent than its Sp-PS counterpart, but of similar potency to the stereorandom PS-parent sequence.
Collapse
Affiliation(s)
- M Li
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.
| | - H L Lightfoot
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.
| | - F Halloy
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.
| | - A L Malinowska
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.
| | - C Berk
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.
| | - A Behera
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.
| | - D Schümperli
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - J Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.
| |
Collapse
|
38
|
Islam MA, Waki R, Fujisaka A, Ito KR, Obika S. In vitro and in vivo biophysical properties of oligonucleotides containing 5'-thio nucleosides. Drug Discov Ther 2017; 10:263-270. [PMID: 27890900 DOI: 10.5582/ddt.2016.01055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Phosphorothioate modification is one of the most widely investigated and promising chemical modifications in oligonucleotide (ON) based therapeutics. Structurally similar 5'-thio or phosphorothiolate-modified nucleotides, in which a 5'-bridging oxygen is replaced with a sulfur atom, are gaining importance for ON-based research. Several reports have been published describing the synthesis of 5'-thio-modified ONs but no detailed in vitro and in vivo data are available. Here, we report the synthesis of 5'-thio-modified 2'-deoxy-5-methylcytidine. 5'-Thio-modified thymidine and 2'-deoxy-5-methylcytidine were incorporated into target ONs, then we evaluated their binding affinity, nuclease stability, RNase H mediated scission, stability in blood serum, and in vitro and in vivo activity. This is the first report showing the influence of 5'-thio-modified antisense ONs in in vitro and in vivo experiments.
Collapse
Affiliation(s)
- Md Ariful Islam
- Graduate School of Pharmaceutical Sciences, Osaka University
| | | | | | | | | |
Collapse
|
39
|
A new and convenient approach for the synthesis of P-stereogenic intermediates bearing a tert-butyl(methyl)phosphino group. RESEARCH ON CHEMICAL INTERMEDIATES 2017. [DOI: 10.1007/s11164-017-2923-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
40
|
Shoji T, Kim S, Chiba K. Synthesis of Azanucleosides by Anodic Oxidation in a Lithium Perchlorate-Nitroalkane Medium and Diversification at the 4′-Nitrogen Position. Angew Chem Int Ed Engl 2017; 56:4011-4014. [DOI: 10.1002/anie.201700547] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Takao Shoji
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu Tokyo 183-8509 Japan
| | - Shokaku Kim
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu Tokyo 183-8509 Japan
| | - Kazuhiro Chiba
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu Tokyo 183-8509 Japan
| |
Collapse
|
41
|
Shoji T, Kim S, Chiba K. Synthesis of Azanucleosides by Anodic Oxidation in a Lithium Perchlorate-Nitroalkane Medium and Diversification at the 4′-Nitrogen Position. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700547] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Takao Shoji
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu Tokyo 183-8509 Japan
| | - Shokaku Kim
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu Tokyo 183-8509 Japan
| | - Kazuhiro Chiba
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu Tokyo 183-8509 Japan
| |
Collapse
|
42
|
Murayama K, Asanuma H. Effect of Methyl Group on Acyclic Serinol Scaffold for Tethering Dyes on the DNA Duplex Stability. Chembiochem 2016; 18:142-149. [DOI: 10.1002/cbic.201600558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Keiji Murayama
- Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| |
Collapse
|
43
|
Zhong YL, Yasuda N, Li H, McLaughlin M, Tschaen D. Process Chemistry in Antiviral Research. Top Curr Chem (Cham) 2016; 374:77. [PMID: 27807768 DOI: 10.1007/s41061-016-0076-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/03/2016] [Indexed: 10/20/2022]
Abstract
This article reviews antiviral therapies that have been approved for human use during the last decade, with a focus on the process chemistry that enabled access to these important drugs. In particular, process chemistry highlights from the practical syntheses of the HCV drugs sofosbuvir (Gilead), grazoprevir (Merck), and elbasvir (Merck), the HIV therapy darunavir (Tibotec) and the influenza treatment peramivir (BioCryst) are presented.
Collapse
Affiliation(s)
- Yong-Li Zhong
- Department of Process Chemistry, Merck and Co., Inc., PO Box 2000, Rahway, NJ, 07065, USA.
| | - Nobuyoshi Yasuda
- Department of Process Chemistry, Merck and Co., Inc., PO Box 2000, Rahway, NJ, 07065, USA
| | - Hongming Li
- Department of Process Chemistry, Merck and Co., Inc., PO Box 2000, Rahway, NJ, 07065, USA
| | - Mark McLaughlin
- Department of Process Chemistry, Merck and Co., Inc., PO Box 2000, Rahway, NJ, 07065, USA
| | - David Tschaen
- Department of Process Chemistry, Merck and Co., Inc., PO Box 2000, Rahway, NJ, 07065, USA
| |
Collapse
|
44
|
Kaczyński TP, Manszewski T, Chmielewski MK. StereoselectiveP-Cyclisation and Diastereoisomeric Purification of 5-Phenyl-3-(pyridin-2-yl)-1,3,2-oxazaphospholidine Formed from a Thermolabile Protecting Group. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
45
|
Nukaga Y, Oka N, Wada T. Stereocontrolled Solid-Phase Synthesis of Phosphate/Phosphorothioate (PO/PS) Chimeric Oligodeoxyribonucleotides on an Automated Synthesizer Using an Oxazaphospholidine–Phosphoramidite Method. J Org Chem 2016; 81:2753-62. [DOI: 10.1021/acs.joc.5b02793] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Yohei Nukaga
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Natsuhisa Oka
- Department
of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Takeshi Wada
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| |
Collapse
|
46
|
Affiliation(s)
- Natsuhisa Oka
- Department of Biomolecular Science, Faculty of Engineering, Gifu University
| | - Takeshi Wada
- Department of Medicinal and Life Science, Faculty of Pharmaceutical Sciences, Tokyo University of Science
| |
Collapse
|
47
|
Dutartre M, Bayardon J, Jugé S. Applications and stereoselective syntheses of P-chirogenic phosphorus compounds. Chem Soc Rev 2016; 45:5771-5794. [DOI: 10.1039/c6cs00031b] [Citation(s) in RCA: 233] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This review reports the best stereoselective or asymmetric syntheses, the most efficient P*-building blocks and functionalisation of P-chirogenic compounds, in the light of chiral phosphorus compound applications.
Collapse
Affiliation(s)
- Mathieu Dutartre
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB-StéréochIM)
- UMR CNRS 6302
- 21078 Dijon Cedex
- France
| | - Jérôme Bayardon
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB-StéréochIM)
- UMR CNRS 6302
- 21078 Dijon Cedex
- France
| | - Sylvain Jugé
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB-StéréochIM)
- UMR CNRS 6302
- 21078 Dijon Cedex
- France
| |
Collapse
|
48
|
Berger O, Montchamp JL. General synthesis of P-stereogenic compounds: the menthyl phosphinate approach. Org Biomol Chem 2016; 14:7552-62. [DOI: 10.1039/c6ob01413e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Easily prepared menthyl phosphinates of high diastereoisomeric purity provide versatile intermediates for the synthesis of P-stereogenic compounds.
Collapse
Affiliation(s)
- Olivier Berger
- Chemistry and Biochemistry
- Texas Christian University
- Fort Worth
- USA
| | | |
Collapse
|
49
|
Radzikowska E, Baraniak J. Synthesis of PS/PO-chimeric oligonucleotides using mixed oxathiaphospholane and phosphoramidite chemistry. Org Biomol Chem 2015; 13:269-76. [PMID: 25363356 DOI: 10.1039/c4ob01837k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chimeric oligonucleotides containing phosphodiester and phosphorothioate linkages have been obtained using the solid phase synthesis. The oligonucleotide parts possessing natural internucleotide phosphate bonds were assembled using commercially available nucleoside 3'-O-(2-cyanoethyl-N,N-diisopropylamino)phosphoramidites 7 whereas the phosphorothioate segment was built using nucleoside 3'-O-(2-thio-1,3,2-oxathiaphospholanes) 3. The oxidation steps, crucial for the conversion of phosphite linkages into the phosphate moieties, were conducted using tert-butylperoxy-trimethylsilane, and this reagent was not harmful to the diester phosphorothioate linkages. When P-diastereopure nucleoside 3'-O-(2-thio-1,3,2-oxathiaphospholane) monomers were employed the resulting chimeric backbone retained the P-stereoregularity of the phosphorothioate units.
Collapse
Affiliation(s)
- Ewa Radzikowska
- Department of Bioorganic Chemistry, Center of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | | |
Collapse
|
50
|
Recent advances in H-phosphonate chemistry. Part 1. H-phosphonate esters: synthesis and basic reactions. Top Curr Chem (Cham) 2015; 361:137-77. [PMID: 25370520 DOI: 10.1007/128_2014_562] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This review covers recent progress in the preparation of H-phosphonate mono- and diesters, basic studies on mechanistic and stereochemical aspects of this class of phosphorus compounds, and their fundamental chemistry in terms of transformation of P-H bonds into P-heteroatom bonds. Selected recent applications of H-phosphonate derivatives in basic organic phosphorus chemistry and in the synthesis of biologically important phosphorus compounds are also discussed.
Collapse
|