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Brzezinska J, Trzciński S, Strzelec J, Chmielewski MK. From CPG to hybrid support: Review on the approaches in nucleic acids synthesis in various media. Bioorg Chem 2023; 140:106806. [PMID: 37660625 DOI: 10.1016/j.bioorg.2023.106806] [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: 06/07/2023] [Revised: 07/26/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023]
Abstract
Solid-phase synthesis is, to date, the preferred method for the manufacture of oligonucleotides, in quantities ranging from a few micrograms for research purposes to several kilograms for therapeutic or commercial use. But for large-scale oligonucleotide manufacture, scaling up and hazardous waste production pose challenges that necessitate the investigation of alternate synthetic techniques. Despite the disadvantages of glass supports, using soluble supports as a substitute presents difficulties because of their high overall yield and complex purification steps. To address these challenges, various independent approaches have been developed; however, other problems such as insufficient cycle efficiency and synthesis of oligonucleotide chains of desired length continue to exist. In this study, we present a review of the current developments, advantages, and difficulties of recently reported alternatives to supports based on controlled pore glass, and discuss the importance of a support choice to resolve issues arising during oligonucleotide synthesis.
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Affiliation(s)
- Jolanta Brzezinska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Stanisław Trzciński
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Joanna Strzelec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marcin K Chmielewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; FutureSynthesis sp. z o.o., ul. Rubież 46B, 61-612 Poznan, Poland.
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Osawa T, Ren Q, Obika S. Development of Phosphoramidite Reagents for the Synthesis of Base-Labile Oligonucleotides Modified with a Linear Aminoalkyl and Amino-PEG Linker at the 3'-End. Molecules 2022; 27:molecules27238501. [PMID: 36500594 PMCID: PMC9736658 DOI: 10.3390/molecules27238501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
Oligonucleotides with an amino linker at the 3'-end are useful for the preparation of conjugated oligonucleotides. However, chemically modified nucleosides, which are unstable under basic conditions, cannot be incorporated into oligonucleotides using the conventional method entailing the preparation of oligonucleotides bearing a 3'-amino linker. Therefore, we designed Fmoc-protected phosphoramidites for the synthesis of base-labile oligonucleotides modified with a 3'-amino linker. The resultant phosphoramidites were then successfully incorporated into oligonucleotides bearing a 3'-amino linker. Various basic solutions were investigated for protecting group removal. All the protecting groups were removed by treating the oligonucleotides with 40% aqueous methylamine at room temperature for 2 h. Thus, the deprotection time and temperature were significantly reduced compared to the conventional conditions (28% NH3 aq., 55 °C, 17 h). In addition, the oligonucleotide protecting groups could be removed using a mild base (e.g., 50 mM potassium carbonate methanol solution). Furthermore, base-labile oligonucleotides bearing an amino linker at the 3'-end were successfully synthesized using the developed phosphoramidite reagents, highlighting the utility of our strategy.
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Affiliation(s)
- Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Osaka 565-0871, Japan
| | - Qin Ren
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 1-3, Osaka 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 1-3, Osaka 565-0871, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Osaka 567-0085, Japan
- Correspondence: ; Tel.: +81-6-6879-8200
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Datta D, Mori S, Madaoui M, Wassarman K, Zlatev I, Manoharan M. Aminooxy Click Chemistry as a Tool for Bis-homo and Bis-hetero Ligand Conjugation to Nucleic Acids. Org Lett 2022; 24:4496-4501. [PMID: 35715221 PMCID: PMC9251770 DOI: 10.1021/acs.orglett.2c00988] [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] [Indexed: 11/30/2022]
Abstract
![]()
An aminooxy click
chemistry (AOCC) strategy was used to synthesize
nucleoside building blocks for incorporation during solid-support
synthesis of oligonucleotides to enable bis-homo and bis-hetero conjugation
of various biologically relevant ligands. The bis-homo aminooxy conjugation
leads to bivalent ligand presentation, whereas the bis-hetero conjugation
allows the placement of different ligands with either the same or
different chemical linkages. This facile synthetic methodology allows
introduction of two different ligands with different biological functions
simultaneously.
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Affiliation(s)
- Dhrubajyoti Datta
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Shohei Mori
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Mimouna Madaoui
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Kelly Wassarman
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Ivan Zlatev
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
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Oligonucleotide conjugation by tyrosine‐click reaction. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Chardet C, Payrastre C, Gerland B, Escudier JM. Convertible and Constrained Nucleotides: The 2'-Deoxyribose 5'-C-Functionalization Approach, a French Touch. Molecules 2021; 26:5925. [PMID: 34641475 PMCID: PMC8512084 DOI: 10.3390/molecules26195925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5'-C-position of the nucleoside sugar. This allows the introduction of an additional chemical handle at any position on the nucleotide chain without disturbing the Watson-Crick base-pairing. We show that 5'-C bromo or propargyl convertible nucleotides (CvN) are accessible in pure diastereoisomeric form, either for nucleophilic displacement or for CuAAC conjugation. Alternatively, the 5'-carbon can be connected in a stereo-controlled manner to the phosphate moiety of the nucleotide chain to generate conformationally constrained nucleotides (CNA). These allow the precise control of the sugar/phosphate backbone torsional angles. The consequent modulation of the nucleic acid shape induces outstanding stabilization properties of duplex or hairpin structures in accordance with the preorganization concept. Some biological applications of these distorted oligonucleotides are also described. Effectively, the convertible and the constrained approaches have been merged to create constrained and convertible nucleotides (C2NA) providing unique tools to functionalize and stabilize nucleic acids.
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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, CEDEX 9, 31062 Toulouse, France; (C.C.); (C.P.)
| | - Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d′Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (C.C.); (C.P.)
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Qiu N, Du X, Ji J, Zhai G. A review of stimuli-responsive polymeric micelles for tumor-targeted delivery of curcumin. Drug Dev Ind Pharm 2021; 47:839-856. [PMID: 34033496 DOI: 10.1080/03639045.2021.1934869] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Despite a potential drug with multiple pharmacological activities, curcumin has disadvantages of the poor water solubility, rapid metabolism, low bioavailability, which considerably limit its clinical application. Currently, polymeric micelles (PMs) have gained widespread concern due to their advantageous physical and chemical properties, easy preparation, and biocompatibility. They can be used to improve drug solubility, prolong blood circulation time, and allow passive targeted drug delivery to tumor through enhanced penetration and retention effect. Moreover, studies focused on tumor microenvironment offer alternatives to design stimulus-responsive smart PMs based on low pH, high levels of glutathione, altered enzyme expression, increased reactive oxygen species production, and hypoxia. There are various external stimuli, such as light, ultrasound, and temperature. These endogenous/exogenous stimuli can be used for the research of intelligent micelles. Intelligent PMs can effectively load curcumin with improved solubility, and intelligently respond to release the drug at a controlled rate at targeted sites such as tumors to avoid early release, which markedly improves the bioavailability of curcumin. The present review is aimed to discuss and summarize recent developments in research of curcumin-loaded intelligent PMs based on endogenous and exogenous stimuli, and facilitates the development of novel delivery systems for future research.
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Affiliation(s)
- Na Qiu
- Department of Pharmaceutics, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, P. R. China
| | - Xiyou Du
- Department of Pharmaceutics, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, P. R. China
| | - Jianbo Ji
- Department of Pharmaceutics, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, P. R. China
| | - Guangxi Zhai
- Department of Pharmaceutics, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, P. R. China
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Design, Synthesis and Characterization of Cyclic NU172 Analogues: A Biophysical and Biological Insight. Int J Mol Sci 2020; 21:ijms21113860. [PMID: 32485818 PMCID: PMC7312020 DOI: 10.3390/ijms21113860] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/20/2020] [Accepted: 05/28/2020] [Indexed: 11/16/2022] Open
Abstract
NU172—a 26-mer oligonucleotide able to bind exosite I of human thrombin and inhibit its activity—was the first aptamer to reach Phase II clinical studies as an anticoagulant in heart disease treatments. With the aim of favoring its functional duplex-quadruplex conformation and thus improving its enzymatic stability, as well as its thrombin inhibitory activity, herein a focused set of cyclic NU172 analogues—obtained by connecting its 5′- and 3′-extremities with flexible linkers—was synthesized. Two different chemical approaches were exploited in the cyclization procedure, one based on the oxime ligation method and the other on Cu(I)-assisted azide-alkyne cycloaddition (CuAAC), affording NU172 analogues including circularizing linkers with different length and chemical nature. The resulting cyclic NU172 derivatives were characterized using several biophysical techniques (ultraviolet (UV) and circular dichroism (CD) spectroscopies, gel electrophoresis) and then investigated for their serum resistance and anticoagulant activity in vitro. All the cyclic NU172 analogues showed higher thermal stability and nuclease resistance compared to unmodified NU172. These favorable properties were, however, associated with reduced—even though still significant—anticoagulant activity, suggesting that the conformational constraints introduced upon cyclization were somehow detrimental for protein recognition. These results provide useful information for the design of improved analogues of NU172 and related duplex-quadruplex structures.
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Riccardi C, Meyer A, Vasseur JJ, Russo Krauss I, Paduano L, Morvan F, Montesarchio D. Fine-tuning the properties of the thrombin binding aptamer through cyclization: Effect of the 5'-3' connecting linker on the aptamer stability and anticoagulant activity. Bioorg Chem 2019; 94:103379. [PMID: 31699393 DOI: 10.1016/j.bioorg.2019.103379] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/21/2019] [Accepted: 10/21/2019] [Indexed: 12/14/2022]
Abstract
A small library of cyclic TBA analogues (named cycTBA I-IV), obtained by covalently connecting its 5'- and 3'-ends with flexible linkers, has been synthesized with the aim of improving its chemical and enzymatic stability, as well as its anticoagulant properties. Two chemical procedures have been exploited to achieve the desired cyclization, based on the oxime ligation method (providing cycTBA I and II) or on Cu(I)-assisted azide-alkyne cycloaddition (CuAAC) protocols (for cycTBA III and IV), leading to analogues containing circularizing linkers with different chemical nature and length, overall spanning from 22 to 48 atoms. The resulting cyclic TBAs have been characterized using a variety of biophysical methods (UV, CD, gel electrophoresis, SE-HPLC analyses) and then tested for their serum resistance and anticoagulant activity under in vitro experiments. A fine-tuning of the length and flexibility of the linker allowed identifying a cyclic analogue, cycTBA II, with improved anticoagulant activity, associated with a dramatically stabilized G-quadruplex structure (ΔTm = +17 °C) and a 6.6-fold higher enzymatic resistance in serum compared to unmodified TBA.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy
| | - Albert Meyer
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, I-50019 Sesto Fiorentino (Fi), Italy
| | - Luigi Paduano
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, I-50019 Sesto Fiorentino (Fi), Italy
| | - François Morvan
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, Montpellier, France.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy.
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