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Ge F, Wang Y, Liu J, Yu H, Liu G, Deng Z, He X. Harnessing sulfur-binding domains to separate Sp and Rp isomers of phosphorothioate oligonucleotides. Appl Microbiol Biotechnol 2024; 108:448. [PMID: 39190037 DOI: 10.1007/s00253-024-13283-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024]
Abstract
Chemical synthesis of phosphoromonothioate oligonucleotides (PS-ONs) is not stereo-specific and produces a mixture of Rp and Sp diastereomers, whose disparate reactivity can complicate applications. Although the current methods to separate these diastereomers which rely on chromatography are constantly improving, many Rp and Sp diastereomers are still co-eluted. Here, based on sulfur-binding domains that specifically recognize phosphorothioated DNA and RNA in Rp configuration, we developed a universal separation system for phosphorothioate oligonucleotide isomers using immobilized SBD (SPOIS). With the scalable SPOIS, His-tagged SBD is immobilized onto Ni-nitrilotriacetic acid-coated magnetic beads to form a beads/SBD complex, Rp isomers of the mixture can be completely bound by SBD and separated from Sp isomers unbound in liquid phase, then recovered through suitable elution approach. Using the phosphoromonothioate single-stranded DNA as a model, SPOIS separated PS-ON diastereomers of 4 nt to 50 nt in length at yields of 60-90% of the starting Rp isomers, with PS linkage not locating at 5' or 3' end. Within this length range, PS-ON diastereomers that co-eluted in HPLC could be separated by SPOIS at yields of 84% and 89% for Rp and Sp stereoisomers, respectively. Furthermore, as each Rp phosphorothioate linkage can be bound by SBD, SPOIS allowed the separation of stereoisomers with multiple uniform Sp configurations for multiple phosphorothioate modifications. A second generation of SPOIS was developed using the thermolabile and non-sequence-specific SBDPed, enabling fast and high-yield recovery of PS substrate stereoisomers for the DNAzyme Cd16 and further demonstrating the efficiency of this method. KEY POINTS: • SPOIS allows isomer separations of the Rp and Sp isomers co-eluted on HPLC. • SPOIS can obtain Sp isomers with 5 min and Rp in 20 min from PS-ON diastereomers. • SPOIS was successfully applied to separate isomers of PS substrates of DNAzyme.
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Affiliation(s)
- Fulin Ge
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Yuli Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Jinling Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Hao Yu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China.
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2
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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.
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Affiliation(s)
- Katarzyna Jastrzębska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
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3
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Obexer R, Nassir M, Moody ER, Baran PS, Lovelock SL. Modern approaches to therapeutic oligonucleotide manufacturing. Science 2024; 384:eadl4015. [PMID: 38603508 DOI: 10.1126/science.adl4015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/28/2024] [Indexed: 04/13/2024]
Abstract
Therapeutic oligonucleotides are a powerful drug modality with the potential to treat many diseases. The rapidly growing number of therapies that have been approved and that are in advanced clinical trials will place unprecedented demands on our capacity to manufacture oligonucleotides at scale. Existing methods based on solid-phase phosphoramidite chemistry are limited by their scalability and sustainability, and new approaches are urgently needed to deliver the multiton quantities of oligonucleotides that are required for therapeutic applications. The chemistry community has risen to the challenge by rethinking strategies for oligonucleotide production. Advances in chemical synthesis, biocatalysis, and process engineering technologies are leading to increasingly efficient and selective routes to oligonucleotide sequences. We review these developments, along with remaining challenges and opportunities for innovations that will allow the sustainable manufacture of diverse oligonucleotide products.
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Affiliation(s)
- R Obexer
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
| | - M Nassir
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - E R Moody
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
| | - P S Baran
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - S L Lovelock
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
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4
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Kawsar SMA, Munia NS, Saha S, Ozeki Y. In Silico Pharmacokinetics, Molecular Docking and Molecular Dynamics Simulation Studies of Nucleoside Analogs for Drug Discovery- A Mini Review. Mini Rev Med Chem 2024; 24:1070-1088. [PMID: 37957918 DOI: 10.2174/0113895575258033231024073521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/26/2023] [Accepted: 09/22/2023] [Indexed: 11/15/2023]
Abstract
Nucleoside analogs have been widely used as antiviral, antitumor, and antiparasitic agents due to their ability to inhibit nucleic acid synthesis. Adenosine, cytidine, guanosine, thymidine and uridine analogs such as didanosine, vidarabine, remdesivir, gemcitabine, lamivudine, acyclovir, abacavir, zidovusine, stavudine, and idoxuridine showed remarkable anticancer and antiviral activities. In our previously published articles, our main intention was to develop newer generation nucleoside analogs with acylation-induced modification of the hydroxyl group and showcase their biological potencies. In the process of developing nucleoside analogs, in silico studies play an important role and provide a scientific background for biological data. Molecular interactions between drugs and receptors followed by assessment of their stability in physiological environments, help to optimize the drug development process and minimize the burden of unwanted synthesis. Computational approaches, such as DFT, FMO, MEP, ADMET prediction, PASS prediction, POM analysis, molecular docking, and molecular dynamics simulation, are the most popular tools to culminate all preclinical study data and deliver a molecule with maximum bioactivity and minimum toxicity. Although clinical drug trials are crucial for providing dosage recommendations, they can only indirectly provide mechanistic information through researchers for pathological, physiological, and pharmacological determinants. As a result, in silico approaches are increasingly used in drug discovery and development to provide mechanistic information of clinical value. This article portrays the current status of these methods and highlights some remarkable contributions to the development of nucleoside analogs with optimized bioactivity.
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Affiliation(s)
- Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Nasrin S Munia
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Supriyo Saha
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Premnagar, 248007, Dehradun, Uttarakhand, 248007, India
| | - Yasuhiro Ozeki
- School of Sciences, Yokohama City University, 22-2, Seto, Kanazawa-ku, Yokohama, 236-0027, Japan
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5
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Takahashi Y, Kakuta K, Namioka Y, Igarashi A, Sakamoto T, Iwata Hara R, Sato K, Wada T. Synthesis of P-Modified DNA from Boranophosphate DNA as a Precursor via Acyl Phosphite Intermediates. J Org Chem 2023; 88:10617-10631. [PMID: 37462534 PMCID: PMC10407935 DOI: 10.1021/acs.joc.3c00659] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Indexed: 08/05/2023]
Abstract
In this study, we successfully synthesized several kinds of P-modified nucleic acids from boranophosphate DNAs via an acyl phosphite intermediate in solution and on a solid support. In the solution-phase synthesis, phosphorothioate diester, phosphotriester, and phosphoramidate diester were synthesized in a one-pot reaction from boranophosphodiester via the conversion of an acyl phosphite as a key intermediate. In addition, doubly P-modified nucleic acid derivatives which were difficult to synthesize by the phosphoramidite and H-phosphonate methods were also obtained by the conversion reaction. In the solid-phase synthesis, a boranophosphate derivative was synthesized on a solid support using the H-boranophosphonate method. Then, an acyl phosphite intermediate was formed by treatment with pivaloyl chloride in pyridine, followed by appropriate transformations to obtain the P-modified derivatives such as phosphotriester and phosphorothioate diester. Notably, it was suggested that the conversion reaction of a boranophosphate to a phosphorothioate diester proceeded with retention of the stereochemistry of the phosphorous center. In addition, a phosphorothioate/phosphate chimeric dodecamer was successfully synthesized from a boranophosphate/phosphate chimeric dodecamer using the same strategy. Therefore, boranophosphate derivatives are versatile precursors for the synthesis of P-modified DNA, including chimeric derivatives.
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Affiliation(s)
- Yuhei Takahashi
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kiyoshi Kakuta
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yukichi Namioka
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Ayumi Igarashi
- Department
of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Taiichi Sakamoto
- Department
of Life Science, Chiba Institute of Technology, Graduate School of Advanced Engineering, Chiba 275-0016, 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, Tokyo 113-8519, Japan
| | - Kazuki Sato
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takeshi Wada
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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6
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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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7
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Rosenqvist P, Saari V, Pajuniemi E, Gimenez Molina A, Ora M, Horvath A, Virta P. Stereo-Controlled Liquid Phase Synthesis of Phosphorothioate Oligonucleotides on a Soluble Support. J Org Chem 2023. [PMID: 37428953 PMCID: PMC10367069 DOI: 10.1021/acs.joc.3c01006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
5'-O-(2-Methoxyisopropyl) (MIP)-protected 2'-deoxynucleosides as chiral P(V)-building blocks, based on the limonene-derived oxathiaphospholane sulfide, were synthesized and used for the assembly of di-, tri-, and tetranucleotide phosphorothioates on a tetrapodal pentaerythritol-derived soluble support. The synthesis cycle consisted of two reactions and two precipitations: (1) the coupling under basic conditions, followed by neutralization and precipitation and (2) an acid catalyzed 5'-O-deacetalization, followed by neutralization and precipitation. The simple P(V) chemistry together with the facile 5'-O-MIP deprotection proved efficient in the liquid phase oligonucleotide synthesis (LPOS). Ammonolysis released nearly homogeneous Rp or Sp phosphorothioate diastereomers in ca. 80% yield/synthesis cycle.
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Affiliation(s)
- Petja Rosenqvist
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Verneri Saari
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Ella Pajuniemi
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Alejandro Gimenez Molina
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, 2340 Beerse, Belgium
| | - Mikko Ora
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Andras Horvath
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, 2340 Beerse, Belgium
| | - Pasi Virta
- Department of Chemistry, University of Turku, 20500 Turku, Finland
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8
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Genna V, Iglesias-Fernández J, Reyes-Fraile L, Villegas N, Guckian K, Seth P, Wan B, Cabrero C, Terrazas M, Brun-Heath I, González C, Sciabola S, Villalobos A, Orozco M. Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides. Nucleic Acids Res 2023; 51:4713-4725. [PMID: 37099382 PMCID: PMC10250214 DOI: 10.1093/nar/gkad309] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/04/2023] [Accepted: 04/24/2023] [Indexed: 04/27/2023] Open
Abstract
Phosphorothioates (PS) have proven their effectiveness in the area of therapeutic oligonucleotides with applications spanning from cancer treatment to neurodegenerative disorders. Initially, PS substitution was introduced for the antisense oligonucleotides (PS ASOs) because it confers an increased nuclease resistance meanwhile ameliorates cellular uptake and in-vivo bioavailability. Thus, PS oligonucleotides have been elevated to a fundamental asset in the realm of gene silencing therapeutic methodologies. But, despite their wide use, little is known on the possibly different structural changes PS-substitutions may provoke in DNA·RNA hybrids. Additionally, scarce information and significant controversy exists on the role of phosphorothioate chirality in modulating PS properties. Here, through comprehensive computational investigations and experimental measurements, we shed light on the impact of PS chirality in DNA-based antisense oligonucleotides; how the different phosphorothioate diastereomers impact DNA topology, stability and flexibility to ultimately disclose pro-Sp S and pro-Rp S roles at the catalytic core of DNA Exonuclease and Human Ribonuclease H; two major obstacles in ASOs-based therapies. Altogether, our results provide full-atom and mechanistic insights on the structural aberrations PS-substitutions provoke and explain the origin of nuclease resistance PS-linkages confer to DNA·RNA hybrids; crucial information to improve current ASOs-based therapies.
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Affiliation(s)
- Vito Genna
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- NBD | Nostrum Biodiscovery, Baldiri Reixac 10, Barcelona 08028, Spain
| | | | - Laura Reyes-Fraile
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Nuria Villegas
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | | | - Punit Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Brad Wan
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Cristina Cabrero
- Instituto de Química Física Rocasolano, C/ Serrano 119, Madrid 28006, Spain
| | - Montserrat Terrazas
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- Department of Inorganic and Organic Chemistry, Section of Organic Chemistry, IBUB, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Isabelle Brun-Heath
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Carlos González
- Instituto de Química Física Rocasolano, C/ Serrano 119, Madrid 28006, Spain
| | | | | | - Modesto Orozco
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona 08028, Spain
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9
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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.
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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
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Abstract
The discovery of cGAMP in 2012 filled an important gap in our understanding of innate immune signaling. It has been known for over a century that DNA can induce immune responses, but the underlying mechanism was not clear. With the identification of STING as a key player in interferon induction, the DNA detector that activates STING was the last missing link in TBK1-IRF3 signaling. Somewhat unexpectedly, it turns out that nature relays the DNA danger signal through a small molecule. cGAMP is a cyclic dinucleotide produced from cyclodimerization of ATP and GTP upon detection of cytosolic DNA by cGAS, a previously uncharacterized protein, to promote the assembly of the STING signalosome. This article covers a personal account of the discovery of cGAMP, a short history of the relevant nucleotide chemistry, and a summary of the latest development in this field of research in chemistry. It is the author's hope that, with a historic perspective, the readers can better appreciate the synergy between chemistry and biology in drug development.
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Affiliation(s)
- Chuo Chen
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA
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11
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Terada C, Kawamoto S, Yamayoshi A, Yamamoto T. Chemistry of Therapeutic Oligonucleotides That Drives Interactions with Biomolecules. Pharmaceutics 2022; 14:pharmaceutics14122647. [PMID: 36559141 PMCID: PMC9781680 DOI: 10.3390/pharmaceutics14122647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Oligonucleotide therapeutics that can modulate gene expression have been gradually developed for clinical applications over several decades. However, rapid advances have been made in recent years. Artificial nucleic acid technology has overcome many challenges, such as (1) poor target affinity and selectivity, (2) low in vivo stability, and (3) classical side effects, such as immune responses; thus, its application in a wide range of disorders has been extensively examined. However, even highly optimized oligonucleotides exhibit side effects, which limits the general use of this class of agents. In this review, we discuss the physicochemical characteristics that aid interactions between drugs and molecules that belong to living organisms. By systematically organizing the related data, we hope to explore avenues for symbiotic engineering of oligonucleotide therapeutics that will result in more effective and safer drugs.
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12
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Jastrzębska K, Maciaszek A, Dolot R, Tomaszewska-Antczak A, Mikołajczyk B, Guga P. Synthesis and hybridizing properties of P-stereodefined chimeric [PS]-{DNA:RNA} and [PS]-{DNA:(2'-OMe)-RNA} oligomers. RSC Adv 2022; 12:26815-26824. [PMID: 36320848 PMCID: PMC9491215 DOI: 10.1039/d2ra04855h] [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: 08/04/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022] Open
Abstract
Oxathiaphospholane derivatives of 2'-OMe-ribonucleosides and 2'-O-TBDMS-ribonucleosides (MN-OTP and TN-OTP, respectively; nucleobase protected) were synthesized and separated into pure P-diastereomers. X-ray analysis showed the R P absolute configuration of the phosphorus atom in the fast-eluting diastereomer of TA-OTP. The fast- and slow-eluting P-diastereomers of MN-OTP and TN-OTP were used in the solid-phase synthesis of phosphorothioate dinucleotides (MNPST and NPST, respectively), which were subsequently hydrolyzed with R P-selective phosphodiesterase svPDE and S P-selective nuclease P1 to determine the absolute configuration of the phosphorus atoms. P-Stereodefined phosphorothioate ([PS]) 10-mer chimeric oligomers [PS]-{DNA:(2'-OMe)-RNA} and isosequential [PS]-{DNA:RNA} containing two MNPS or NPS units were synthesized. Melting experiments performed for their complexes with Watson-Crick paired DNA matrix showed that MNPS or NPS units decrease the thermal stability of the duplexes (ΔT m = -0.5 ÷ -5.5 °C per modification) regardless of the absolute configuration of the P-atoms. When the (2'-OMe)-RNA matrix was used an increase in T m was noted in all cases (ΔT m = +1 ÷ +7 °C per modification). The changes in thermal stability of the duplexes formed by [PS]-chimeras with DNA and (2'-OMe)-RNA matrices do not correlate with the absolute configuration of the phosphorus atoms.
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Affiliation(s)
- Katarzyna Jastrzębska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112. 90-363 Łódź Poland +48-42-6803261 +48-42-6803248
| | - Anna Maciaszek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112. 90-363 Łódź Poland +48-42-6803261 +48-42-6803248
| | - Rafał Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112. 90-363 Łódź Poland +48-42-6803261 +48-42-6803248
| | - Agnieszka Tomaszewska-Antczak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112. 90-363 Łódź Poland +48-42-6803261 +48-42-6803248
| | - Barbara Mikołajczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112. 90-363 Łódź Poland +48-42-6803261 +48-42-6803248
| | - Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112. 90-363 Łódź Poland +48-42-6803261 +48-42-6803248
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13
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Duschmalé J, Schäublin A, Funder E, Schmidt S, Kiełpiński ŁJ, Nymark H, Jensen K, Koch T, Duschmalé M, Koller E, Møller MR, Schadt S, Husser C, Brink A, Sewing S, Minz T, Wengel J, Bleicher K, Li M. Investigating discovery strategies and pharmacological properties of stereodefined phosphorodithioate LNA gapmers. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:176-188. [PMID: 35860384 PMCID: PMC9271985 DOI: 10.1016/j.omtn.2022.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Jörg Duschmalé
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Adrian Schäublin
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Erik Funder
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Steffen Schmidt
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Łukasz J. Kiełpiński
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Helle Nymark
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Klaus Jensen
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Troels Koch
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Martina Duschmalé
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Erich Koller
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Marianne Ravn Møller
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Simone Schadt
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Christophe Husser
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Andreas Brink
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Sabine Sewing
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Tanja Minz
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Konrad Bleicher
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Meiling Li
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
- Corresponding author Meiling Li, Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland.
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14
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Chen T, Tang S, Fu Y, Napolitano JG, Zhang K. Analytical techniques for characterizing diastereomers of phosphorothioated oligonucleotides. J Chromatogr A 2022; 1678:463349. [PMID: 35908512 DOI: 10.1016/j.chroma.2022.463349] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/07/2022] [Accepted: 07/15/2022] [Indexed: 12/18/2022]
Abstract
Oligonucleotides have emerged as powerful therapeutics for treating diverse diseases. To fully unlock the therapeutic potential of oligonucleotides, there is still a great need to further improve their drug-like properties. Numerous chemical modifications have been explored to achieve this goal, with phosphorothioation being one of the most widely used strategies. However, phosphorothioate modification produces diastereomers that are reported to have different properties and performances, demanding detailed characterization of these diastereomers. Here we provide an overview of phosphorothioated oligonucleotide diastereomers, covering their origin and configurations, physicochemical and pharmacological properties, and stereo-selective chemical synthesis, followed by a summary of currently available analytical techniques for characterizing these diastereomers, with a focus on liquid chromatography-based approaches, including ion-pair reversed-phase liquid chromatography, anion exchange chromatography, mixed-mode chromatography, and hybrid approaches. Non-chromatographic techniques, such as capillary electrophoresis, spectroscopy and other methods, are also being reviewed.
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Affiliation(s)
- Tao Chen
- Small Molecule Analytical Chemistry, Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Shijia Tang
- Small Molecule Analytical Chemistry, Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Yige Fu
- Small Molecule Analytical Chemistry, Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - José G Napolitano
- Small Molecule Analytical Chemistry, Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Kelly Zhang
- Small Molecule Analytical Chemistry, Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States.
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15
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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]
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16
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Kiełpiński ŁJ, Funder ED, Schmidt S, Hagedorn PH. Characterization of Escherichia coli RNase H Discrimination of DNA Phosphorothioate Stereoisomers. Nucleic Acid Ther 2021; 31:383-391. [PMID: 34619060 PMCID: PMC8713576 DOI: 10.1089/nat.2021.0055] [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] [Indexed: 12/13/2022] Open
Abstract
Phosphorothioate (PS) modification of antisense oligonucleotides (ASOs) is a
critical factor enabling their therapeutic use. Standard chemical synthesis
incorporates this group in a stereorandom manner; however, significant effort
was made over the years to establish and characterize the impact of chiral
control. In this work, we present our in-depth characterization of interactions
between Escherichia coli RNase H and RNA-DNA heteroduplexes
carrying chirally defined PS groups. First, using a massive parallel assay, we
showed that at least a single Rp-PS group is necessary for
efficient RNase H-mediated cleavage. We followed by demonstrating that this
group needs to be aligned to the phosphate-binding pocket of RNase H, and that
chiral status of other PS groups in close proximity to RNase H does not affect
cleavage efficiency. We have shown that RNase H's PS chiral preference
can be utilized to guide cleavage to a specific chemical bond. Finally, we
present a strategy for ASO optimization by mapping preferred RNase H cleavage
sites of a non-thioated compound, followed by introduction of
Rp-PS in a strategic position. This results in a cleaner
cleavage profile and higher knockdown activity compared with a compound carrying
an Sp-PS at the same location.
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Affiliation(s)
- Łukasz J Kiełpiński
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Erik Daa Funder
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Steffen Schmidt
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Peter H Hagedorn
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, Hørsholm, Denmark
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17
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Knouse KW, Flood DT, Vantourout JC, Schmidt MA, Mcdonald IM, Eastgate MD, Baran PS. Nature Chose Phosphates and Chemists Should Too: How Emerging P(V) Methods Can Augment Existing Strategies. ACS CENTRAL SCIENCE 2021; 7:1473-1485. [PMID: 34584948 PMCID: PMC8461637 DOI: 10.1021/acscentsci.1c00487] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Indexed: 05/27/2023]
Abstract
Phosphate linkages govern life as we know it. Their unique properties provide the foundation for many natural systems from cell biology and biosynthesis to the backbone of nucleic acids. Phosphates are ideal natural moieties; existing as ionized species in a stable P(V)-oxidation state, they are endowed with high stability but exhibit enzymatically unlockable potential. Despite intense interest in phosphorus catalysis and condensation chemistry, organic chemistry has not fully embraced the potential of P(V) reagents. To be sure, within the world of chemical oligonucleotide synthesis, modern approaches utilize P(III) reagent systems to create phosphate linkages and their analogs. In this Outlook, we present recent studies from our laboratories suggesting that numerous exciting opportunities for P(V) chemistry exist at the nexus of organic synthesis and biochemistry. Applications to the synthesis of stereopure antisense oligonucleotides, cyclic dinucleotides, methylphosphonates, and phosphines are reviewed as well as chemoselective modification to peptides, proteins, and nucleic acids. Finally, an outlook into what may be possible in the future with P(V) chemistry is previewed, suggesting these examples represent just the tip of the iceberg.
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Affiliation(s)
- Kyle W. Knouse
- Elsie
Biotechnologies, 4955
Directors Place, San Diego, California 92121, United States
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dillon T. Flood
- Elsie
Biotechnologies, 4955
Directors Place, San Diego, California 92121, United States
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Julien C. Vantourout
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael A. Schmidt
- Chemical
and Synthetic Development, Bristol Myers
Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Ivar M. Mcdonald
- Small
Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Martin D. Eastgate
- Chemical
and Synthetic Development, Bristol Myers
Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Phil S. Baran
- Elsie
Biotechnologies, 4955
Directors Place, San Diego, California 92121, United States
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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18
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Anderson BA, Freestone GC, Low A, De-Hoyos CL, Iii WJD, Østergaard ME, Migawa MT, Fazio M, Wan WB, Berdeja A, Scandalis E, Burel SA, Vickers TA, Crooke ST, Swayze EE, Liang X, Seth PP. Towards next generation antisense oligonucleotides: mesylphosphoramidate modification improves therapeutic index and duration of effect of gapmer antisense oligonucleotides. Nucleic Acids Res 2021; 49:9026-9041. [PMID: 34417625 PMCID: PMC8450106 DOI: 10.1093/nar/gkab718] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/30/2021] [Accepted: 08/19/2021] [Indexed: 12/12/2022] Open
Abstract
The PS modification enhances the nuclease stability and protein binding properties of gapmer antisense oligonucleotides (ASOs) and is one of very few modifications that support RNaseH1 activity. We evaluated the effect of introducing stereorandom and chiral mesyl-phosphoramidate (MsPA) linkages in the DNA gap and flanks of gapmer PS ASOs and characterized the effect of these linkages on RNA-binding, nuclease stability, protein binding, pro-inflammatory profile, antisense activity and toxicity in cells and in mice. We show that all PS linkages in a gapmer ASO can be replaced with MsPA without compromising chemical stability and RNA binding affinity but these designs reduced activity. However, replacing up to 5 PS in the gap with MsPA was well tolerated and replacing specific PS linkages at appropriate locations was able to greatly reduce both immune stimulation and cytotoxicity. The improved nuclease stability of MsPA over PS translated to significant improvement in the duration of ASO action in mice which was comparable to that of enhanced stabilized siRNA designs. Our work highlights the combination of PS and MsPA linkages as a next generation chemical platform for identifying ASO drugs with improved potency and therapeutic index, reduced pro-inflammatory effects and extended duration of effect.
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Affiliation(s)
| | | | - Audrey Low
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | | | | | - Michael T Migawa
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Michael Fazio
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - W Brad Wan
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Andres Berdeja
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Eli Scandalis
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | | | - Stanley T Crooke
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Xuehai Liang
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
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19
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Huang Y, Knouse KW, Qiu S, Hao W, Padial NM, Vantourout JC, Zheng B, Mercer SE, Lopez-Ogalla J, Narayan R, Olson RE, Blackmond DG, Eastgate MD, Schmidt MA, McDonald IM, Baran PS. A P(V) platform for oligonucleotide synthesis. Science 2021; 373:1265-1270. [PMID: 34516793 PMCID: PMC8579956 DOI: 10.1126/science.abi9727] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The promise of gene-based therapies is being realized at an accelerated pace, with more than 155 active clinical trials and multiple U.S. Food and Drug Administration approvals for therapeutic oligonucleotides, by far most of which contain modified phosphate linkages. These unnatural linkages have desirable biological and physical properties but are often accessed with difficulty using phosphoramidite chemistry. We report a flexible and efficient [P(V)]–based platform that can install a wide variety of phosphate linkages at will into oligonucleotides. This approach uses readily accessible reagents and can install not only stereodefined or racemic thiophosphates but any combination of (S, R or rac)–PS with native phosphodiester (PO2) and phosphorodithioate (PS2) linkages into DNA and other modified nucleotide polymers. This platform easily accesses this diversity under a standardized coupling protocol with sustainably prepared, stable P(V) reagents.
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Affiliation(s)
- Yazhong Huang
- Small Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney St., Cambridge, MA 02142
| | - Kyle W. Knouse
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Elsie Biotechnologies, 4955 Directors Pl, San Diego, CA 92121
| | - Shenjie Qiu
- Chemical Process Development, Bristol Myers Squibb, One Squibb Dr., New Brunswick, NJ 08903
| | - Wei Hao
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Natalia M. Padial
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Julien C. Vantourout
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Bin Zheng
- Chemical Process Development, Bristol Myers Squibb, One Squibb Dr., New Brunswick, NJ 08903
| | - Stephen E. Mercer
- Small Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney St., Cambridge, MA 02142
| | - Javier Lopez-Ogalla
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Rohan Narayan
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Richard E. Olson
- Small Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney St., Cambridge, MA 02142
| | - Donna G. Blackmond
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Martin D. Eastgate
- Chemical Process Development, Bristol Myers Squibb, One Squibb Dr., New Brunswick, NJ 08903
| | - Michael A. Schmidt
- Chemical Process Development, Bristol Myers Squibb, One Squibb Dr., New Brunswick, NJ 08903
| | - Ivar M. McDonald
- Small Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney St., Cambridge, MA 02142
| | - Phil S. Baran
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
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20
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Zheng YY, Wu Y, Begley TJ, Sheng J. Sulfur modification in natural RNA and therapeutic oligonucleotides. RSC Chem Biol 2021; 2:990-1003. [PMID: 34458821 PMCID: PMC8341892 DOI: 10.1039/d1cb00038a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/22/2021] [Indexed: 11/21/2022] Open
Abstract
Sulfur modifications have been discovered on both DNA and RNA. Sulfur substitution of oxygen atoms at nucleobase or backbone locations in the nucleic acid framework led to a wide variety of sulfur-modified nucleosides and nucleotides. While the discovery, regulation and functions of DNA phosphorothioate (PS) modification, where one of the non-bridging oxygen atoms is replaced by sulfur on the DNA backbone, are important topics, this review focuses on the sulfur modification in natural cellular RNAs and therapeutic nucleic acids. The sulfur modifications on RNAs exhibit diversity in terms of modification location and cellular function, but the various sulfur modifications share common biosynthetic strategies across RNA species, cell types and domains of life. The first section reviews the post-transcriptional sulfur modifications on nucleobases with an emphasis on thiouridine on tRNA and phosphorothioate modification on RNA backbones, as well as the functions of the sulfur modifications on different species of cellular RNAs. The second section reviews the biosynthesis of different types of sulfur modifications and summarizes the general strategy for the biosynthesis of sulfur-containing RNA residues. One of the main goals of investigating sulfur modifications is to aid the genomic drug development pipeline and enhance our understandings of the rapidly growing nucleic acid-based gene therapies. The last section of the review focuses on the current drug development strategies employing sulfur substitution of oxygen atoms in therapeutic RNAs.
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Affiliation(s)
- Ya Ying Zheng
- Department of Chemistry, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| | - Ying Wu
- Department of Chemistry, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| | - Thomas J Begley
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- Department of Biological Science, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| | - Jia Sheng
- Department of Chemistry, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
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21
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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.
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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
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22
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Hara RI, Sato K, Wada T. Synthesis of Glycosyl Phosphate Repeats and Their Analogues. J SYN ORG CHEM JPN 2021. [DOI: 10.5059/yukigoseikyokaishi.79.558] [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
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23
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Clavé G, Reverte M, Vasseur JJ, Smietana M. Modified internucleoside linkages for nuclease-resistant oligonucleotides. RSC Chem Biol 2021; 2:94-150. [PMID: 34458777 PMCID: PMC8341215 DOI: 10.1039/d0cb00136h] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.
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Affiliation(s)
| | - Maeva Reverte
- IBMM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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24
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Scharner J, Aznarez I. Clinical Applications of Single-Stranded Oligonucleotides: Current Landscape of Approved and In-Development Therapeutics. Mol Ther 2020; 29:540-554. [PMID: 33359792 PMCID: PMC7854307 DOI: 10.1016/j.ymthe.2020.12.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/19/2020] [Accepted: 12/15/2020] [Indexed: 02/07/2023] Open
Abstract
Single-stranded oligonucleotides have been explored as a therapeutic modality for more than 20 years. Only during the last 5 years have single-stranded oligonucleotides become a modality of choice in the fields of precision medicine and targeted therapeutics. Recently, there have been a number of development efforts involving this modality that have led to treatments for genetic diseases that were once untreatable. This review highlights key applications of single-stranded oligonucleotides that function in a sequence-dependent manner when applied to modulate precursor (pre-)mRNA splicing, gene expression, and immune pathways. These applications have been used to address diseases that range from neurological to muscular to metabolic, as well as to develop vaccines. The wide range of applications denotes the versatility of single-stranded oligonucleotides as a robust therapeutic platform. The focus of this review is centered on approved single-stranded oligonucleotide therapies and the evolution of oligonucleotide therapeutics into novel applications currently in clinical development.
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25
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Andrews BI, Antia FD, Brueggemeier SB, Diorazio LJ, Koenig SG, Kopach ME, Lee H, Olbrich M, Watson AL. Sustainability Challenges and Opportunities in Oligonucleotide Manufacturing. J Org Chem 2020; 86:49-61. [PMID: 33253568 PMCID: PMC8154579 DOI: 10.1021/acs.joc.0c02291] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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With a renewed and growing interest
in therapeutic oligonucleotides
across the pharmaceutical industry, pressure is increasing on drug
developers to take more seriously the sustainability ramifications
of this modality. With 12 oligonucleotide drugs reaching the market
to date and hundreds more in clinical trials and preclinical development,
the current state of the art in oligonucleotide production poses a
waste and cost burden to manufacturers. Legacy technologies make use
of large volumes of hazardous reagents and solvents, as well as energy-intensive
processes in synthesis, purification, and isolation. In 2016, the
American Chemical Society (ACS) Green Chemistry Institute Pharmaceutical
Roundtable (GCIPR) identified the development of greener processes
for oligonucleotide Active Pharmaceutical Ingredients (APIs) as a
critical unmet need. As a result, the Roundtable formed a focus team
with the remit of identifying green chemistry and engineering improvements
that would make oligonucleotide production more sustainable. In this
Perspective, we summarize the present challenges in oligonucleotide
synthesis, purification, and isolation; highlight potential solutions;
and encourage synergies between academia; contract research, development
and manufacturing organizations; and the pharmaceutical industry.
A critical part of our assessment includes Process Mass Intensity
(PMI) data from multiple companies to provide preliminary baseline
metrics for current oligonucleotide manufacturing processes.
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Affiliation(s)
- Benjamin I Andrews
- Chemical Development, GlaxoSmithKline, Stevenage SG1 2NY, United Kingdom
| | - Firoz D Antia
- Biogen, Inc., Cambridge, Massachusetts 02142, United States
| | | | - Louis J Diorazio
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield SK10 4TF, United Kingdom
| | - Stefan G Koenig
- Genentech, Inc., A Member of the Roche Group, South San Francisco, California 94080, United States
| | - Michael E Kopach
- Eli Lilly and Company, 1400 West Raymond Street, Indianapolis, Indiana 46285, United States
| | - Heewon Lee
- Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States
| | | | - Anna L Watson
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield SK10 4TF, United Kingdom
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26
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Kumar P, Caruthers MH. DNA Analogues Modified at the Nonlinking Positions of Phosphorus. Acc Chem Res 2020; 53:2152-2166. [PMID: 32885957 DOI: 10.1021/acs.accounts.0c00078] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chemically modified oligonucleotides are being developed as a new class of medicines for curing conditions that previously remained untreatable. Three primary classes of therapeutic oligonucleotides are single-stranded antisense oligonucleotides (ASOs), double stranded small interfering RNAs (siRNAs), and oligonucleotides that induce exon skipping. Recently, ASOs, siRNAs, and exon skipping oligonucleotides have been approved for patients with unmet medical needs, and many other candidates are being tested in late stage clinical trials. In coming years, therapeutic oligonucleotides may match the promise of small molecules and antibodies. Interestingly, in the 1980s when we developed chemical methods for synthesizing oligonucleotides, no one would have imagined that these highly charged macromolecules could become future medicines. Indeed, the anionic nature and poor metabolic stability of the natural phosphodiester backbone provided a major challenge for the use of oligonucleotides as therapeutic drugs. Thus, chemical modifications of oligonucleotides were essential in order to improve their pharmacokinetic properties. Keeping this view in mind, my laboratory has developed a series of novel oligonucleotides where one or both nonbridging oxygens in the phosphodiester backbone are replaced with an atom or molecule that introduces molecular properties that enhance biological activity. We followed two complementary approaches. One was the use of phosphoramidites that could act directly as synthons for the solid phase synthesis of oligonucleotide analogues. This approach sometimes was not feasible due to instability of various synthons toward the reagents used during synthesis of oligonucleotides. Therefore, using a complementary approach, we developed phosphoramidite synthons that can be incorporated into oligonucleotides with minimum changes in the solid phase DNA synthesis protocols but contain a handle for generating appropriate analogues postsynthetically.This Account summarizes our efforts toward preparing these types of analogues over the past three decades and discusses synthesis and properties of backbone modified oligonucleotides that originated from the Caruthers' laboratory. For example, by replacing one of the internucleotide oxygens with an acetate group, we obtained so-called phosphonoacetate oligonucleotides that were stable to nucleases and, when delivered as esters, entered into cells unaided. Alternatively oligonucleotides bearing borane phosphonate linkages were found to be RNase H active and compatible with the endogenous RNA induced silencing complex (RISC). Oligonucleotides containing an alkyne group directly linked to phosphorus in the backbone were prepared as well and used to attach molecules such as amino acids and peptides.
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Affiliation(s)
- Pawan Kumar
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, 450 Main Street, Cambridge, Massachusetts 02142, United States
| | - Marvin H. Caruthers
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, United States
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27
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Radzikowska E, Kaczmarek R, Korczyński D, Krakowiak A, Mikołajczyk B, Baraniak J, Guga P, Wheeler KA, Pawlak T, Nawrot B. P-stereocontrolled synthesis of oligo(nucleoside N3'→O5' phosphoramidothioate)s - opportunities and limitations. RSC Adv 2020; 10:35185-35197. [PMID: 35515667 PMCID: PMC9056831 DOI: 10.1039/d0ra04987e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/15/2020] [Indexed: 12/29/2022] Open
Abstract
3'-N-(2-Thio-1,3,2-oxathiaphospholane) derivatives of 5'-O-DMT-3'-amino-2',3'-dideoxy-ribonucleosides (NOTP-N), that bear a 4,4-unsubstituted, 4,4-dimethyl, or 4,4-pentamethylene substituted oxathiaphospholane ring, were synthesized. Within these three series, NOTP-N differed by canonical nucleobases (i.e., AdeBz, CytBz, GuaiBu, or Thy). The monomers were chromatographically separated into P-diastereomers, which were further used to prepare NNPSN' dinucleotides (3), as well as short P-stereodefined oligo(deoxyribonucleoside N3'→O5' phosphoramidothioate)s (NPS-) and chimeric NPS/PO- and NPS/PS-oligomers. The condensation reaction for NOTP-N monomers was found to be 5-6 times slower than the analogous OTP derivatives. When the 5'-end nucleoside of a growing oligomer adopts a C3'-endo conformation, a conformational 'clash' with the incoming NOTP-N monomer takes place, which is a main factor decreasing the repetitive yield of chain elongation. Although both isomers of NNPSN' were digested by the HINT1 phosphoramidase enzyme, the isomers hydrolyzed at a faster rate were tentatively assigned the R P absolute configuration. This assignment is supported by X-ray analysis of the protected dinucleotide DMTdGiBu NPSMeTOAc, which is P-stereoequivalent to the hydrolyzed faster P-diastereomer of dGNPST.
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Affiliation(s)
- Ewa Radzikowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Renata Kaczmarek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Dariusz Korczyński
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Agnieszka Krakowiak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Barbara Mikołajczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Janina Baraniak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Kraig A Wheeler
- Whitworth University, Department of Chemistry 300 W. Hawthorne Rd. Spokane WA 99251 USA
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
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28
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Funder ED, Albæk N, Moisan A, Sewing S, Koch T. Refining LNA safety profile by controlling phosphorothioate stereochemistry. PLoS One 2020; 15:e0232603. [PMID: 32530964 PMCID: PMC7292364 DOI: 10.1371/journal.pone.0232603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 04/17/2020] [Indexed: 01/01/2023] Open
Abstract
Drug discovery with phosphorothioate oligonucleotides is an area of intensive research. In this study we have controlled the stereochemistry of the phosphorothioate backbone of LNA oligonucleotides to investigate the differences in safety profile, target mRNA knock down, and cellular uptake in vitro. The study reveals that controlling only four stereocenters in an isomeric phosphorothioate mixture can improve the therapeutic index significantly by improving safety without compromising activity.
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Affiliation(s)
| | - Nanna Albæk
- Roche Innovation Center Copenhagen A/S, Hørsholm, Denmark
| | - Annie Moisan
- Roche Innovation Center Basel, Basel, Switzerland
| | | | - Troels Koch
- Roche Innovation Center Copenhagen A/S, Hørsholm, Denmark
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29
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Glazier DA, Liao J, Roberts BL, Li X, Yang K, Stevens CM, Tang W. Chemical Synthesis and Biological Application of Modified Oligonucleotides. Bioconjug Chem 2020; 31:1213-1233. [PMID: 32227878 DOI: 10.1021/acs.bioconjchem.0c00060] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA plays a myriad of roles in the body including the coding, decoding, regulation, and expression of genes. RNA oligonucleotides have garnered significant interest as therapeutics via antisense oligonucleotides or small interfering RNA strategies for the treatment of diseases ranging from hyperlipidemia, HCV, and others. Additionally, the recently developed CRISPR-Cas9 mediated gene editing strategy also relies on Cas9-associated RNA strands. However, RNA presents numerous challenges as both a synthetic target and a potential therapeutic. RNA is inherently unstable, difficult to deliver into cells, and potentially immunogenic by itself or upon modification. Despite these challenges, with the help of chemically modified oligonucleotides, multiple RNA-based drugs have been approved by the FDA. The progress is made possible due to the nature of chemically modified oligonucleotides bearing advantages of nuclease stability, stronger binding affinity, and some other unique properties. This review will focus on the chemical synthesis of RNA and its modified versions. How chemical modifications of the ribose units and of the phosphatediester backbone address the inherent issues with using native RNA for biological applications will be discussed along the way.
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Affiliation(s)
- Daniel A Glazier
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Junzhuo Liao
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Brett L Roberts
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Xiaolei Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Ka Yang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Christopher M Stevens
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Weiping Tang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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30
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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.
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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
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31
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Hara RI, Yoshino R, Nukaga Y, Maeda Y, Sato K, Wada T. Synthesis and properties of DNA oligomers containing stereopure phosphorothioate linkages and C-5 modified deoxyuridine derivatives. RSC Adv 2020; 10:34006-34013. [PMID: 35519073 PMCID: PMC9056737 DOI: 10.1039/d0ra06970a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/03/2020] [Indexed: 12/25/2022] Open
Abstract
Phosphorothioate (PS) modification, where a non-bridging oxygen atom in a phosphodiester linkage is replaced by a sulfur atom, is widely used to improve the properties of nucleic acid drugs. Each PS linkage can be found in two stereoisomers, Rp and Sp. Since one non-bridging oxygen or sulfur atom in Sp-PS or Rp-PS, respectively, is located close to the C-5 substituent of uracil in a DNA/RNA hybrid duplex, the combination of the stereochemistry of the PS linkages and the type of the C-5 modification of uracil bases is expected to affect the properties of the hybrid duplexes. Herein, DNA oligomers containing both stereopure phosphorohioate linkages and C-5 modified deoxyuridine derivatives were synthesized. The thermodynamic stability of the DNA/RNA and DNA/DNA duplexes and RNase H activity of the DNA/RNA duplexes were evaluated. The combination of 5-propynyluracil and (Rp)-PS linkages in a DNA strand could significantly increase the thermal stability of a DNA/RNA hybrid duplex without reducing its RNase H activity. The combination of 5-propynyluracil and (Rp)-PS linkages in a DNA strand could significantly increase the thermal stability of a DNA/RNA hybrid duplex.![]()
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Affiliation(s)
- Rintaro Iwata Hara
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
- Department of Neurology and Neurological Science
| | - Reijiro Yoshino
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
| | - Yohei Nukaga
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
| | - Yusuke Maeda
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
| | - Kazuki Sato
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
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32
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Maciaszek A, Jastrzębska K, Guga P. Homopurine R P-stereodefined phosphorothioate analogs of DNA with hampered Watson-Crick base pairings form Hoogsteen paired parallel duplexes with (2'-OMe)-RNAs. Org Biomol Chem 2019; 17:4611-4620. [PMID: 31017142 DOI: 10.1039/c8ob03112f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
3'-O-(2-Thio-4,4-pentamethylene-1,3,2-oxathiaphospholane) derivatives of 5'-O-DMT-N6-methyl-deoxyadenosine and 5'-O-DMT-N2,N2-dimethyl-O6-diphenylcarbamoyl-deoxyguanosine (OTP-NY, NY = DMT-m6dA or DMT-m,m2dGDPC) were synthesized, resolved onto pure P-diastereomers, and used in P-stereocontrolled synthesis of dinucleoside 3',5,-phosphorothioates NXPST (NX = m6dA or m,m2dG), in which the absolute configuration of the stereogenic phosphorus atom was established enzymatically. Diastereomerically pure OTP-NY and standard OTP-N (N = DMT-dABz or DMT-dGBz,DPC) were used in the synthesis of chimeric RP-stereodefined phosphorothioate oligomers ((RP-PS)-DN(NX)A) with hampered Watson-Crick base pairings. It was found that the m6dA units slightly reduce the thermodynamic stability of antiparallel duplexes formed with RNA and (2'-OMe)-RNA matrices, whereas m,m2dG units prevent their formation. The m6dA units stabilize (by up to 4.5 °C per modified unit) the parallel duplexes formed by (RP-PS)-DN(NX)A with Hoogsteen-paired (2'-OMe)-RNA templates compared to the analogous reference duplex containing only unmodified nucleobases. In contrast, the m,m2dG units destabilize such duplexes by up to 3 °C per modified unit. Both units prevent the formation of the corresponding parallel triplexes.
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Affiliation(s)
- Anna Maciaszek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, 90-363 Łódź, Poland.
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33
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Chen X, Pu M, Cheng H, Sperger T, Schoenebeck F. Arylation of Axially Chiral Phosphorothioate Salts by Dinuclear Pd I Catalysis. Angew Chem Int Ed Engl 2019; 58:11395-11399. [PMID: 31190467 PMCID: PMC6771726 DOI: 10.1002/anie.201906063] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Indexed: 01/10/2023]
Abstract
S-aryl phosphorothioates are privileged motifs in pharmaceuticals, agrochemicals, and catalysts; yet, the challenge of devising a straightforward synthetic route to enantioenriched S-aryl phosphorothioates has remained unsolved to date. We demonstrate herein the first direct C-SP(=O)(OR')(OR'') coupling of diverse and chiral phosphorothioate salts with aryl iodides, enabled by an air- and moisture-stable PdI dimer. Our mechanistic and computational data suggest distinct dinuclear PdI catalysis to be operative, which allows for operationally simple couplings with broad scope and full retention of stereochemistry.
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Affiliation(s)
- Xiang‐Yu Chen
- Institute of Organic ChemistryRWTH Aachen UniversityLandoltweg 152074AachenGermany
| | - Maoping Pu
- Institute of Organic ChemistryRWTH Aachen UniversityLandoltweg 152074AachenGermany
| | - Hong‐Gang Cheng
- Institute of Organic ChemistryRWTH Aachen UniversityLandoltweg 152074AachenGermany
| | - Theresa Sperger
- Institute of Organic ChemistryRWTH Aachen UniversityLandoltweg 152074AachenGermany
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34
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Campos KR, Coleman PJ, Alvarez JC, Dreher SD, Garbaccio RM, Terrett NK, Tillyer RD, Truppo MD, Parmee ER. The importance of synthetic chemistry in the pharmaceutical industry. Science 2019; 363:363/6424/eaat0805. [PMID: 30655413 DOI: 10.1126/science.aat0805] [Citation(s) in RCA: 242] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Innovations in synthetic chemistry have enabled the discovery of many breakthrough therapies that have improved human health over the past century. In the face of increasing challenges in the pharmaceutical sector, continued innovation in chemistry is required to drive the discovery of the next wave of medicines. Novel synthetic methods not only unlock access to previously unattainable chemical matter, but also inspire new concepts as to how we design and build chemical matter. We identify some of the most important recent advances in synthetic chemistry as well as opportunities at the interface with partner disciplines that are poised to transform the practice of drug discovery and development.
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Affiliation(s)
- Kevin R Campos
- Global Chemistry, Merck & Co. Inc., Kenilworth, NJ 07033, USA.
| | - Paul J Coleman
- Global Chemistry, Merck & Co. Inc., Kenilworth, NJ 07033, USA.
| | - Juan C Alvarez
- Global Chemistry, Merck & Co. Inc., Kenilworth, NJ 07033, USA
| | | | | | | | | | | | - Emma R Parmee
- Global Chemistry, Merck & Co. Inc., Kenilworth, NJ 07033, USA
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35
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Chen X, Pu M, Cheng H, Sperger T, Schoenebeck F. Arylation of Axially Chiral Phosphorothioate Salts by Dinuclear Pd
I
Catalysis. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xiang‐Yu Chen
- Institute of Organic ChemistryRWTH Aachen University Landoltweg 1 52074 Aachen Germany
| | - Maoping Pu
- Institute of Organic ChemistryRWTH Aachen University Landoltweg 1 52074 Aachen Germany
| | - Hong‐Gang Cheng
- Institute of Organic ChemistryRWTH Aachen University Landoltweg 1 52074 Aachen Germany
| | - Theresa Sperger
- Institute of Organic ChemistryRWTH Aachen University Landoltweg 1 52074 Aachen Germany
| | - Franziska Schoenebeck
- Institute of Organic ChemistryRWTH Aachen University Landoltweg 1 52074 Aachen Germany
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36
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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.
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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
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37
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Hara RI, Saito T, Kogure T, Hamamura Y, Uchiyama N, Nukaga Y, Iwamoto N, Wada T. Stereocontrolled Synthesis of Boranophosphate DNA by an Oxazaphospholidine Approach and Evaluation of Its Properties. J Org Chem 2019; 84:7971-7983. [PMID: 31140804 DOI: 10.1021/acs.joc.9b00658] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In this paper, we describe the first stereocontrolled synthesis and properties of boranophosphate DNA (PB-DNA), which contains all of the four nucleobases longer than 10mer. Synthesis was accomplished via an oxazaphospholidine approach combined with acid-labile protecting groups on nucleobases. It was demonstrated that there were significant differences between all-( Rp)- and all-( Sp)-PB-DNA in terms of the duplex-formation ability, nuclease resistance, and ribonuclease H (RNase H) activity. In particular, all-( Sp)-PB-DNA was demonstrated to show a duplex-formation ability with RNA and RNase H activity, both of which are necessary for antisense-type nucleic acid therapeutics.
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Affiliation(s)
- Rintaro Iwata Hara
- Faculty of Pharmaceutical Sciences , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan.,Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences , Tokyo Medical and Dental University , 1-5-45 Yushima , Bunkyo-ku , Tokyo 113-8519 , Japan
| | - Tatsuya Saito
- Faculty of Pharmaceutical Sciences , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
| | - Tomoki Kogure
- Faculty of Pharmaceutical Sciences , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
| | - Yuka Hamamura
- Graduate School of Frontier Sciences , The University of Tokyo , 5-1-5 Kashiwanoha , Kashiwa , Chiba 277-8562 , Japan
| | - Naoki Uchiyama
- Graduate School of Frontier Sciences , The University of Tokyo , 5-1-5 Kashiwanoha , Kashiwa , Chiba 277-8562 , Japan
| | - Yohei Nukaga
- Faculty of Pharmaceutical Sciences , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
| | - Naoki Iwamoto
- Graduate School of Frontier Sciences , The University of Tokyo , 5-1-5 Kashiwanoha , Kashiwa , Chiba 277-8562 , Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
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38
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Knouse KW, deGruyter JN, Schmidt MA, Zheng B, Vantourout JC, Kingston C, Mercer SE, Mcdonald IM, Olson RE, Zhu Y, Hang C, Zhu J, Yuan C, Wang Q, Park P, Eastgate MD, Baran PS. Unlocking P(V): Reagents for chiral phosphorothioate synthesis. Science 2018; 361:1234-1238. [PMID: 30072577 DOI: 10.1126/science.aau3369] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/12/2018] [Indexed: 12/21/2022]
Abstract
Phosphorothioate nucleotides have emerged as powerful pharmacological substitutes of their native phosphodiester analogs with important translational applications in antisense oligonucleotide (ASO) therapeutics and cyclic dinucleotide (CDN) synthesis. Stereocontrolled installation of this chiral motif has long been hampered by the systemic use of phosphorus(III) [P(III)]-based reagent systems as the sole practical means of oligonucleotide assembly. A fundamentally different approach is described herein: the invention of a P(V)-based reagent platform for programmable, traceless, diastereoselective phosphorus-sulfur incorporation. The power of this reagent system is demonstrated through the robust and stereocontrolled synthesis of various nucleotidic architectures, including ASOs and CDNs, via an efficient, inexpensive, and operationally simple protocol.
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Affiliation(s)
- Kyle W Knouse
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Justine N deGruyter
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael A Schmidt
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA.
| | - Bin Zheng
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Julien C Vantourout
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Cian Kingston
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Stephen E Mercer
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Ivar M Mcdonald
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Richard E Olson
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Ye Zhu
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Chao Hang
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Jason Zhu
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Changxia Yuan
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Qinggang Wang
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Peter Park
- Department of Discovery Chemistry, Bristol-Myers Squibb, P.O. Box 5400, Princeton, NJ 08543, USA
| | - Martin D Eastgate
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA.
| | - Phil S Baran
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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39
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Hagedorn PH, Persson R, Funder ED, Albæk N, Diemer SL, Hansen DJ, Møller MR, Papargyri N, Christiansen H, Hansen BR, Hansen HF, Jensen MA, Koch T. Locked nucleic acid: modality, diversity, and drug discovery. Drug Discov Today 2017; 23:101-114. [PMID: 28988994 DOI: 10.1016/j.drudis.2017.09.018] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/01/2017] [Accepted: 09/27/2017] [Indexed: 01/05/2023]
Abstract
Over the past 20 years, the field of RNA-targeted therapeutics has advanced based on discoveries of modified oligonucleotide chemistries, and an ever-increasing understanding of how to apply cellular assays to identify oligonucleotides with improved pharmacological properties in vivo. Locked nucleic acid (LNA), which exhibits high binding affinity and potency, is widely used for this purpose. Our understanding of RNA biology has also expanded tremendously, resulting in new approaches to engage RNA as a therapeutic target. Recent observations indicate that each oligonucleotide is a unique entity, and small structural differences between oligonucleotides can often lead to substantial differences in their pharmacological properties. Here, we outline new principles for drug discovery exploiting oligonucleotide diversity to identify rare molecules with unique pharmacological properties.
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Affiliation(s)
- Peter H Hagedorn
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Robert Persson
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Erik D Funder
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Nanna Albæk
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Sanna L Diemer
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Dennis J Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Marianne R Møller
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Natalia Papargyri
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Helle Christiansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Bo R Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Henrik F Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Mads A Jensen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Troels Koch
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark.
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40
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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.
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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
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41
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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.
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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
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42
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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.
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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.
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43
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Valeur E, Guéret SM, Adihou H, Gopalakrishnan R, Lemurell M, Waldmann H, Grossmann TN, Plowright AT. New Modalities for Challenging Targets in Drug Discovery. Angew Chem Int Ed Engl 2017; 56:10294-10323. [PMID: 28186380 DOI: 10.1002/anie.201611914] [Citation(s) in RCA: 246] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 01/31/2017] [Indexed: 12/11/2022]
Abstract
Our ever-increasing understanding of biological systems is providing a range of exciting novel biological targets, whose modulation may enable novel therapeutic options for many diseases. These targets include protein-protein and protein-nucleic acid interactions, which are, however, often refractory to classical small-molecule approaches. Other types of molecules, or modalities, are therefore required to address these targets, which has led several academic research groups and pharmaceutical companies to increasingly use the concept of so-called "new modalities". This Review defines for the first time the scope of this term, which includes novel peptidic scaffolds, oligonucleotides, hybrids, molecular conjugates, as well as new uses of classical small molecules. We provide the most representative examples of these modalities to target large binding surface areas such as those found in protein-protein interactions and for biological processes at the center of cell regulation.
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Affiliation(s)
- Eric Valeur
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Stéphanie M Guéret
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Hélène Adihou
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Malin Lemurell
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Herbert Waldmann
- Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany.,Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Germany
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.,Department of Chemistry & Pharmaceutical Sciences, VU University Amsterdam, The Netherlands
| | - Alleyn T Plowright
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
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44
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Valeur E, Guéret SM, Adihou H, Gopalakrishnan R, Lemurell M, Waldmann H, Grossmann TN, Plowright AT. Neue Modalitäten für schwierige Zielstrukturen in der Wirkstoffentwicklung. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611914] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Eric Valeur
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
| | - Stéphanie M. Guéret
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Hélène Adihou
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Malin Lemurell
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
| | - Herbert Waldmann
- Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
- Fakultät für Chemie and Chemische Biologie; Technische Universität Dortmund; Deutschland
| | - Tom N. Grossmann
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; Niederlande
| | - Alleyn T. Plowright
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
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45
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Hara RI, Ogawa Y, Noro M, Wada T. Stereocontrolled Synthesis of P-Modified N-Acetylmannosamine-α-1-phosphate Analogs. CHEM LETT 2017. [DOI: 10.1246/cl.170349] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Rintaro Iwata Hara
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
| | - Yuki Ogawa
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
| | - Mihoko Noro
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience Building 702, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
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46
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Overcoming cellular barriers for RNA therapeutics. Nat Biotechnol 2017; 35:222-229. [PMID: 28244992 DOI: 10.1038/nbt.3802] [Citation(s) in RCA: 724] [Impact Index Per Article: 103.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 01/19/2017] [Indexed: 02/07/2023]
Abstract
RNA-based therapeutics, such as small-interfering (siRNAs), microRNAs (miRNAs), antisense oligonucleotides (ASOs), aptamers, synthetic mRNAs and CRISPR-Cas9, have great potential to target a large part of the currently undruggable genes and gene products and to generate entirely new therapeutic paradigms in disease, ranging from cancer to pandemic influenza to Alzheimer's disease. However, for these RNA modalities to reach their full potential, they first need to overcome a billion years of evolutionary defenses that have kept RNAs on the outside of cells from invading the inside of cells. Overcoming the lipid bilayer to deliver RNA into cells has remained the major problem to solve for widespread development of RNA therapeutics, but recent chemistry advances have begun to penetrate this evolutionary armor.
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47
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Abstract
Oligonucleotide-based therapeutics have made rapid progress in the clinic for treatment of a variety of disease indications. Unmodified oligonucleotides are polyanionic macromolecules with poor drug-like properties. Over the past two decades, medicinal chemists have identified a number of chemical modification and conjugation strategies which can improve the nuclease stability, RNA-binding affinity, and pharmacokinetic properties of oligonucleotides for therapeutic applications. In this perspective, we present a summary of the most commonly used nucleobase, sugar and backbone modification, and conjugation strategies used in oligonucleotide medicinal chemistry.
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Affiliation(s)
- W Brad Wan
- Department of Medicinal Chemistry, Ionis Pharmaceuticals , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P Seth
- Department of Medicinal Chemistry, Ionis Pharmaceuticals , 2855 Gazelle Court, Carlsbad, California 92010, United States
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48
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Jastrzębska K, Maciaszek A, Dolot R, Bujacz G, Guga P. Thermal stability and conformation of antiparallel duplexes formed by P-stereodefined phosphorothioate DNA/LNA chimeric oligomers with DNA and RNA matrices. Org Biomol Chem 2016; 13:10032-40. [PMID: 26293357 DOI: 10.1039/c5ob01474c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
3'-O-(2-Thio-4,4-pentamethylene-1,3,2-oxathiaphospholane) derivatives of LNA-type nucleosides (LNA-OTPs, 2a-d; B' = Thy, Ade(Bz), Cyt(Bz), Gua(dmf), respectively) were synthesized and separated into pure P-diastereomers. X-ray analysis allowed for assignment of the absolute configuration of the phosphorus atom in the detritylated, fast-eluting diastereomer 2a. The diastereomerically pure LNA-OTP monomers were used in solid phase synthesis of P-stereodefined chimeric PS-(DNA/LNA) 11-mers containing 2-3 LNA units. Formally, among the phosphorothioate oligomers the biggest enhancement in thermal stability of Watson-Crick paired duplexes was found for [SP-PS]-(DNA/LNA)/RNA duplexes (on average 8.2 °C per LNA nucleotide), followed by [RP-PS]-(DNA/LNA)/RNA (6.3 °C), [RP-PS]-(DNA/LNA)/DNA (3.8 °C) and [SP-PS]-(DNA/LNA)/DNA (2.4 °C per LNA nucleotide). However, detailed analysis of the thermal dissociation data showed that the thermal stability of (PS-LNA)-containing duplexes does not depend on the spatial orientation of the sulfur atoms. This conclusion received support from CD measurements.
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Affiliation(s)
- Katarzyna Jastrzębska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, 90-363 Łódź, Poland.
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49
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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
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50
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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
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