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Duchamp E, Vasquez G, Firoozi N, Freestone GC, Oestergaard M, Seth PP, Hanessian S. Towards combining backbone and sugar constraint in 3'-3' bis-phosphonate tethered 2'-4' bridged LNA oligonucleotide trimers. RSC Adv 2024; 14:23583-23591. [PMID: 39070250 PMCID: PMC11276400 DOI: 10.1039/d4ra04277h] [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: 06/12/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024] Open
Abstract
Therapeutic oligonucleotides are chemically modified to enhance their drug-like properties - including binding affinity for target RNA. Many nucleic acid analogs that enhance RNA binding affinity constrain the furanose sugar in an RNA-like sugar pucker. The improvements in binding affinity result primarily from increased off-rates with minimal effects on on-rates for hybridization. To identify alternate chemical modification strategies that can modulate on- and off-rates for oligonucleotide hybridization, we hypothesized that extending conformational restraint across multiple nucleotides could modulate hybridization kinetics by restricting rotational freedom of the sugar-phosphate backbone. As part of that effort, we recently reported that using hydrocarbon tethers to bridge adjacent phosphodiester linkages as phosphonate tethered bridges can pre-organize nucleic acids in conformations conducive for Watson-Crick base-pairing and modulate hybridization kinetics. In this report, we describe the synthesis of locked nucleic acid (LNA) trimers linked through alkylphosphonate tethers which restrict conformation of the furanose sugar in addition to restricting conformational mobility of the sugar-phosphate backbone across three nucleotide units.
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Affiliation(s)
- Edouard Duchamp
- Department of Chemistry, Université de Montréal Québec H3C 3J7 Canada
| | - Guillermo Vasquez
- Department of Medicinal Chemistry, Ionis Pharmaceuticals Carlsbad CA 92010 USA
| | - Neda Firoozi
- Department of Chemistry, Université de Montréal Québec H3C 3J7 Canada
| | - Graeme C Freestone
- Department of Medicinal Chemistry, Ionis Pharmaceuticals Carlsbad CA 92010 USA
| | - Michael Oestergaard
- Department of Medicinal Chemistry, Ionis Pharmaceuticals Carlsbad CA 92010 USA
| | - Punit P Seth
- Alnylam Pharmaceuticals 675 West Kendall St Cambridge MA 0214 USA
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal Québec H3C 3J7 Canada
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697 USA
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2
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Hanessian S. My 50-Plus Years of Academic Research Collaborations with Industry. A Retrospective. J Org Chem 2024; 89:9147-9186. [PMID: 38865159 DOI: 10.1021/acs.joc.4c00652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
A retrospective is presented highlighting the synthesis of selected "first-in-kind" natural products, their synthetic analogues, structure elucidations, and rationally designed bioactive synthetic compounds that were accomplished because of collaborations with past and present pharmaceutical and agrochemical companies. Medicinal chemistry projects involving structure-based design exploiting cocrystal structures of small molecules with biologically relevant enzymes, receptors, and bacterial ribosomes with synthetic small molecules leading to marketed products, clinical candidates, and novel drug prototypes were realized in collaboration. Personal reflections, historical insights, behind the scenes stories from various long-term projects are shared in this retrospective article.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Succ. Centre-ville, Montréal, Québec, Canada H3C 3J7
- Department of Pharmaceutical Sciences, University of California, Irvine, California 91266, United States
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3
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Osawa T, Akino T, Obika S. Synthesis, Duplex-Forming Ability, and Enzymatic Stability of Oligonucleotides Modified with Amide-Linked Dinucleotides Containing a 3',4'-Tetrahydropyran-Bridged Nucleic Acid. J Org Chem 2024; 89:269-280. [PMID: 38064209 DOI: 10.1021/acs.joc.3c02019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Replacement of a phosphodiester linkage with an amide linkage can improve the binding affinity of oligonucleotides to complementary RNA and their stability toward nucleases. In addition, restricting the conformation of the sugar moiety and the phosphate backbone in oligonucleotides effectively improves duplex stability. In this study, we designed amide-linked dinucleotides containing a 3',4'-tetrahydropyran-bridged nucleic acid (3',4'-tpBNA) with a constrained sugar conformation as well as a torsion angle ε. Phosphoramidites of the designed dinucleotides were synthesized and incorporated into oligonucleotides. Conformational analysis of the synthesized dinucleotides showed that the sugar conformation of the S-isomer of the amide-linked dinucleotide containing 3',4'-tpBNA was N-type, which has the same conformation as that of the RNA duplex, while that of another R-isomer was S-type. Tm analysis indicated that the oligonucleotides containing the synthesized S-isomer showed RNA-selective hybridizing ability, although their duplex-forming ability was slightly inferior to that of natural oligonucleotides. Interestingly, the stability of the oligonucleotides toward endonucleases was significantly improved by modification with the two types of amide-linked dinucleotides developed in this study.
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Affiliation(s)
- Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Taiki Akino
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 1-3, Suita, Osaka 565-0871, Japan
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4
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Munir R, Zahoor AF, Javed S, Parveen B, Mansha A, Irfan A, Khan SG, Irfan A, Kotwica-Mojzych K, Mojzych M. Simmons-Smith Cyclopropanation: A Multifaceted Synthetic Protocol toward the Synthesis of Natural Products and Drugs: A Review. Molecules 2023; 28:5651. [PMID: 37570621 PMCID: PMC10420228 DOI: 10.3390/molecules28155651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023] Open
Abstract
Simmons-Smith cyclopropanation is a widely used reaction in organic synthesis for stereospecific conversion of alkenes into cyclopropane. The utility of this reaction can be realized by the fact that the cyclopropane motif is a privileged synthetic intermediate and a core structural unit of many biologically active natural compounds such as terpenoids, alkaloids, nucleosides, amino acids, fatty acids, polyketides and drugs. The modified form of Simmons-Smith cyclopropanation involves the employment of Et2Zn and CH2I2 (Furukawa reagent) toward the total synthesis of a variety of structurally complex natural products that possess broad range of biological activities including anticancer, antimicrobial and antiviral activities. This review aims to provide an intriguing glimpse of the Furukawa-modified Simmons-Smith cyclopropanation, within the year range of 2005 to 2022.
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Affiliation(s)
- Ramsha Munir
- Medicinal Chemistry Research Lab, Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (R.M.); (B.P.); (A.M.); (S.G.K.); (A.I.)
| | - Ameer Fawad Zahoor
- Medicinal Chemistry Research Lab, Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (R.M.); (B.P.); (A.M.); (S.G.K.); (A.I.)
| | - Sadia Javed
- Department of Biochemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan;
| | - Bushra Parveen
- Medicinal Chemistry Research Lab, Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (R.M.); (B.P.); (A.M.); (S.G.K.); (A.I.)
| | - Asim Mansha
- Medicinal Chemistry Research Lab, Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (R.M.); (B.P.); (A.M.); (S.G.K.); (A.I.)
| | - Ahmad Irfan
- Department of Chemistry, College of Science, King Khalid University, Abha 61413, Saudi Arabia;
| | - Samreen Gul Khan
- Medicinal Chemistry Research Lab, Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (R.M.); (B.P.); (A.M.); (S.G.K.); (A.I.)
| | - Ali Irfan
- Medicinal Chemistry Research Lab, Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (R.M.); (B.P.); (A.M.); (S.G.K.); (A.I.)
| | - Katarzyna Kotwica-Mojzych
- Laboratory of Experimental Cytology, Medical University of Lublin, Radziwiłłowska 11, 20-080 Lublin, Poland;
| | - Mariusz Mojzych
- Department of Chemistry, Siedlce University of Natural Sciences and Humanities, 3-go Maja 54, 08-110 Siedlce, Poland
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Bege M, Herczeg M, Bereczki I, Debreczeni N, Bényei A, Herczegh P, Borbás A. Triaza-tricyclanos - synthesis of a new class of tricyclic nucleoside analogues by stereoselective cascade cyclocondensation. Org Biomol Chem 2023; 21:2213-2219. [PMID: 36804654 DOI: 10.1039/d3ob00154g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Herein, we report a stereoselective synthesis of a novel type of conformationally constrained nucleoside analogue in which the sugar part is replaced by a new symmetrical tricycle consisting of a morpholine ring condensed with two imidazolidines. 1,5-Dialdehydes obtained from trityl- and dimethoxytrityl-protected uridine, ribothymidine, inosine, cytidine, adenosine and guanosine by metaperiodate oxidation were reacted with N1,N3-dibenzyl-1,2,3-triaminopropane; the latter reactant was produced using a new method that avoids explosive intermediates. Reactions of dialdehydes with propane-triamine via cascade tricyclization resulted in the corresponding triaza-tricyclic derivatives bearing three new stereogenic centers in high yields. Out of the eight possible diastereoisomers, one stereoisomer was formed in each case due to the chiral control of the starting nucleoside-dialdehydes and the steric constraint of the condensed ring system. The absolute configuration of the new stereotriad was determined by X-ray diffraction and NMR experiments. A mechanistic study performed under reductive conditions to trap the presumed bicyclic intermediate showed that the triamine reactant first attacks the 2'-aldehyde group, followed by a rapid bicyclization to form the imidazolidino-morpholine unit.
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Affiliation(s)
- Miklós Bege
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary. .,Institute of Healthcare Industry, University of Debrecen, Nagyerdei krt 98, 4032 Debrecen, Hungary.,MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Mihály Herczeg
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary.
| | - Ilona Bereczki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary. .,National Laboratory of Virology, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary.,Pharmamodul Research Group, University of Debrecen, Nagyerdei krt 98, 4032 Debrecen, Hungary
| | - Nóra Debreczeni
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary.
| | - Attila Bényei
- X-ray Diffraction Laboratory, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Pál Herczegh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary.
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary. .,National Laboratory of Virology, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
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Kajino R, Sakamoto S, Ueno Y. Synthesis, gene silencing activity, thermal stability, and serum stability of siRNA containing four ( S)-5'- C-aminopropyl-2'- O-methylnucleosides (A, adenosine; U, uridine; G, guanosine; and C, cytidine). RSC Adv 2022; 12:11454-11476. [PMID: 35425057 PMCID: PMC9002251 DOI: 10.1039/d2ra00705c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/30/2022] [Indexed: 11/29/2022] Open
Abstract
Herein, we report the synthesis of (S)-5'-C-aminopropyl-2'-O-methyladenosine and (S)-5'-C-aminopropyl-2'-O-methylguanosine phosphoramidites and the properties of small interfering RNAs (siRNAs) containing four (S)-5'-C-aminopropyl-2'-O-methylnucleosides (A, adenosine; U, uridine; G, guanosine; and C, cytidine). The siRNAs containing (S)-5'-C-aminopropyl-nucleosides at the 3'- and 5'-regions of the passenger strand were well tolerated for RNA interference (RNAi) activity. Conversely, the (S)-5'-C-aminopropyl modification in the central region of the passenger strand decreased the RNAi activity. Furthermore, the siRNAs containing three or four consecutive (S)-5'-C-aminopropyl-2'-O-methylnucleosides at the 3'- and 5'-regions of the passenger strand exhibited RNAi activity similar to that of the corresponding 2'-O-methyl-modified siRNAs. Finally, it was observed that (S)-5'-C-aminopropyl modifications effectively improved the serum stability of the siRNAs, compared with 2'-O-methyl modifications. Therefore, (S)-5'-C-aminopropyl-2'-O-methylnucleosides would be useful for improving the serum stability of therapeutic siRNA molecules without affecting their RNAi activities.
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Affiliation(s)
- Ryohei Kajino
- United Graduate School of Agricultural Science, Gifu University Japan +81-58-293-2919 +81-58-293-2919
| | - Shuichi Sakamoto
- Institute of Microbial Chemistry (BIKAKEN) Numazu Branch, Microbial Chemistry Research Foundation 18-24 Miyamoto Numazu Shizuoka 410-0301 Japan
| | - Yoshihito Ueno
- United Graduate School of Agricultural Science, Gifu University Japan +81-58-293-2919 +81-58-293-2919
- Department of Life Science and Chemistry, The Graduate School of Natural Science and Technology, Gifu University Japan
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University Japan
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University 1-1 Yanagido Gifu 501-1193 Japan
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7
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Osawa T, Yano N, Aoyama H, Obika S. Synthesis, Duplex-Forming Ability, and Nuclease Resistance of Oligonucleotides Containing a Thymidine Derivative with a 1-Oxaspiro[4.5]decane Skeleton. Chem Pharm Bull (Tokyo) 2022; 70:699-706. [PMID: 36184452 DOI: 10.1248/cpb.c22-00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chemically modified nucleic acids are essential for the therapeutic application of oligonucleotides. In this study, 6'-C-spiro-thymidine exhibiting a fixed torsion angle γ was designed, synthesized, and incorporated into oligonucleotides. The conformational analysis of the 6'-C-spiro-thymidine monomer revealed that its torsion angle γ was in the +synclinal range (approx. 60°), which is similar to that in a natural RNA duplex, as expected. On the other hand, the sugar conformation of the RNA duplex is known to be predominantly an N-type, whereas that of the synthesized monomer was an S-type. The results of the UV melting analysis demonstrated that the duplex-forming ability of 6'-C-spiro-thymidine was inferior to that of natural DNA. Contrarily, 6'-C-spiro-thymidine could enhance the stability of oligonucleotides toward nucleases. Particularly, the incorporation of 6'-C-spiro-thymidine on the 3'-ends of the oligonucleotides significantly increased the nuclease resistance of the oligonucleotides.
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Affiliation(s)
- Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Natsumi Yano
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University
- National Institutes of Biomedical Innovation, Health and Nutrition
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8
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Yamaguchi T, Yamamoto C, Horiba M, Aoyama H, Obika S. Synthesis and duplex-forming ability of oligonucleotides modified with 4'-C,5'-C-methylene-bridged nucleic acid (4',5'-BNA). Bioorg Med Chem 2021; 46:116359. [PMID: 34391942 DOI: 10.1016/j.bmc.2021.116359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 01/16/2023]
Abstract
We describe herein the design and synthesis of 4'-C,5'-C-methylene-bridged nucleic acid (4',5'-BNA), a novel artificial nucleic acid with the torsion angle γ in a non-canonical +ac range. The 4',5'-BNA phosphoramidite bearing a thymine nucleobase was synthesized from a commercially available thymidine analog in 11 steps and successfully incorporated into oligonucleotides. The resulting oligonucleotides were evaluated for their duplex-forming ability toward single-stranded DNA and RNA.
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Affiliation(s)
- Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Chika Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masahiko Horiba
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.
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9
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Vasquez G, Freestone GC, Wan WB, Low A, De Hoyos CL, Yu J, Prakash TP, Ǿstergaard ME, Liang XH, Crooke ST, Swayze EE, Migawa MT, Seth PP. Site-specific incorporation of 5'-methyl DNA enhances the therapeutic profile of gapmer ASOs. Nucleic Acids Res 2021; 49:1828-1839. [PMID: 33544849 PMCID: PMC7913697 DOI: 10.1093/nar/gkab047] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/07/2021] [Accepted: 02/02/2021] [Indexed: 01/01/2023] Open
Abstract
We recently showed that site-specific incorporation of 2′-modifications or neutral linkages in the oligo-deoxynucleotide gap region of toxic phosphorothioate (PS) gapmer ASOs can enhance therapeutic index and safety. In this manuscript, we determined if introducing substitution at the 5′-position of deoxynucleotide monomers in the gap can also enhance therapeutic index. Introducing R- or S-configured 5′-Me DNA at positions 3 and 4 in the oligodeoxynucleotide gap enhanced the therapeutic profile of the modified ASOs suggesting a different positional preference as compared to the 2′-OMe gap modification strategy. The generality of these observations was demonstrated by evaluating R-5′-Me and R-5′-Ethyl DNA modifications in multiple ASOs targeting HDAC2, FXI and Dynamin2 mRNA in the liver. The current work adds to a growing body of evidence that small structural changes can modulate the therapeutic properties of PS ASOs and ushers a new era of chemical optimization with a focus on enhancing the therapeutic profile as opposed to nuclease stability, RNA-affinity and pharmacokinetic properties. The 5′-methyl DNA modified ASOs exhibited excellent safety and antisense activity in mice highlighting the therapeutic potential of this class of nucleic acid analogs for next generation ASO designs.
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Affiliation(s)
- Guillermo Vasquez
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - W Brad Wan
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Audrey Low
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - Jinghua Yu
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - Xue-Hai Liang
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Michael T Migawa
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
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10
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Osawa T, Kawaguchi M, Jang YJ, Ito Y, Hari Y. Synthesis and properties of oligonucleotides bearing thymidine derivatives with 1,6-dioxaspiro[4.5]decane skeleton. Bioorg Med Chem 2021; 31:115966. [DOI: 10.1016/j.bmc.2020.115966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 11/29/2022]
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12
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Salinas JC, Seth PP, Hanessian S. Design And Synthesis Of An Azabicyclic Nucleoside Phosphoramidite For Oligonucleotide Antisense Constructs. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:384-406. [PMID: 31380707 DOI: 10.1080/15257770.2019.1646916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We report the synthesis and biophysical evaluation of an azabicycle dinucleotide with restricted γ, β, and ε torsion angles, featuring the introduction of a piperidine ring that locks the conformation of the nucleoside into an RNA-type nucleic acid. The conceptual basis of the design is predicated upon the notion that the conformation of the phosphate group linking two RNA nucleotides can be approximated with an azabicyclic phosphoramidite which may also benefit from a unique stereoelectronic effect.
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Affiliation(s)
- Juan C Salinas
- Department of Chemistry, Université de Montréal, Downtown Station, Montréal, P.O. Box 6128, Canada QC H3C 3J7
| | - Punit P Seth
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, Downtown Station, Montréal, P.O. Box 6128, Canada QC H3C 3J7
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13
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Gerland B, Addamiano C, Renard BL, Payrastre C, Gopaul D, Escudier JM. Thio- and Seleno-Dioxaphosphorinane-Constrained Dinucleotides (D-CNA): Synthesis and Conformational Study. European J Org Chem 2017. [DOI: 10.1002/ejoc.201601568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Béatrice Gerland
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068; Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Claudia Addamiano
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068; Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Brice-Loïc Renard
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068; Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Corinne Payrastre
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068; Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Deshmukh Gopaul
- Laboratoire de Génomes et Génétique; UMR 3525 Institut Pasteur; 25 rue du Docteur Roux 75015 Paris France
| | - Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068; Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
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14
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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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